bluuebunny/crossref_metadata_2025_split huggingface dataset:
HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal to noise fluorescence
Authors: Chiang Hsiao , Koo Daniel , Kitano Masahiro , Unruh Jay , Trinh Le , Fraser Scott , Cutrale Francesco 
Published: January 2022

Abstract
The expanded application of fluorescence imaging in biomedical and biological research towards more complex systems and geometries requires tools that can analyze a multitude of components at widely varying time- and length-scales. The major challenge in such complex imaging experiments is to cleanly separate multiple fluorescent labels with overlapping spectra from one another and background autofluorescence, without perturbing the sample with high levels of light. Thus, there is a requirement for efficient and robust analysis tools capable of quantitatively separating these signals.
In response, we have combined multispectral fluorescence microscopy with hyperspectral phasors and linear unmixing to create Hybrid Unmixing (HyU). Here we demonstrate its capabilities in the dynamic imaging of multiple fluorescent labels in live, developing zebrafish embryos. HyU is more sensitive to low light levels of fluorescence compared to conventional linear unmixing approaches, permitting better multiplexed volumetric imaging over time, with less bleaching. HyU can also simultaneously image both bright exogenous and dim endogenous labels because of its high dynamic range. This allows studies of cellular behaviors, tagged components, and cell metabolism within the same specimen, offering a powerful window into the orchestrated complexity of biological systems.
Forces that control self-organization of chemically-propelled Janus tori
Authors: Aronson Igor , Wang Jiyuan , Huang Mu-Jie , Baker-Sediako Remmi , Kapral Raymond 
Published: January 2022

Abstract
Control of the individual and collective behavior of self-propelled synthetic micro-objects has immediate application for nanotechnology, robotics, and precision medicine. Despite significant progress in the synthesis and characterization of self-propelled Janus (two-faced) particles, predictive understanding of their behavior remains challenging, especially if the particles have anisotropic forms. Here, by using molecular simulation, we describe the interactions of chemically-propelled microtori near a wall. The results show that a torus hovers at a certain distance from the wall due to a combination of gravity and hydrodynamic flows generated by the chemical activity. Moreover, electrostatic dipolar interactions between the torus and the wall result in a spontaneous tilt and horizontal translation, in a qualitative agreement with the experiment. Simulations of the dynamics of two tori near a wall provide evidence for the formation of stable self-propelled bound states. Our results illustrate that self-organization at the microscale occurs due to a combination of multiple factors, including hydrodynamic, chemical, and electrostatic interactions.
Clinical Predictors of Survival for Patients with Atypical Teratoid/Rhabdoid Tumors
Authors: Bachu Vismaya S , Shah Pavan , Jimenez Adrian E , Khalafallah Adham M , Tailor Jignesh , Mukherjee Debraj , Cohen Alan R 
Published: January 2022

Abstract
Purpose: Atypical teratoid/rhabdoid tumors (AT/RT) are malignant central nervous system (CNS) neoplasms of the young. Our study analyzed a large AT/RT cohort from the National Cancer Database (NCDB) to elucidate predictors of short-term mortality and overall survival (OS). Methods: Information was collected on patients with histologically-confirmed AT/RT using the NCDB (2004-2016). Kaplan-Meier analysis indicated OS. Prognostic factors for 30-day mortality, 90-day mortality, and OS were determined via multivariate Cox proportional-hazards (CPH) and logistic regression models. Results: Our cohort of 189 patients had a median age of 1 year (IQR [1, 4]) and tumor size of 4.7±2.0 cm at diagnosis. Seventy-two percent were under 3 years old; 55.6% were male and 71.0% were Caucasian. Fifty (27.2%) patients received only surgery (S) (OS=5.91 months), 51 (27.7%) received surgery and chemotherapy (S+CT) (OS=11.2 months), and 9 (4.89%) received surgery and radiotherapy (S+RT) (OS=10.3 months). Forty-five (24.5%) received S+CT+RT combination therapy (OS=45.4 months), 13 (17.1%) received S+CT+BMT/SCT (bone marrow or stem cell transplant) (OS=55.5 months), and 16 (8.70%) received S+CT+RT+BMT/SCT (OS=68.4 months). Bivariate analysis of dichotomized age (HR=0.550, 95% CI[0.357, 0.847], p=0.0067) demonstrated significantly increased patient survival if diagnosed at or above 1 year old. On multivariate analysis, administration of S+CT+RT, S+CT+BMT/SCT, or S+CT+RT+BMT/SCT combination therapy predicted significantly (p<0.05) increased OS compared to surgery alone. Conclusion: AT/RTs are CNS tumors where those diagnosed under 1 year old have a significantly worse prognosis. Our study demonstrates that while traditional CT, RT, and BMT/SCT combination regimens prolong life, overall survival in this population is still low.
Preoperative anaemia and red blood cell transfusion in patients with aneurysmal subarachnoid and intracerebral haemorrhage – A multicentre subanalysis of the German PBM Network Registry
Authors: Schmitt Elke , Meybohm Patrick , Neef Vanessa , Baumgarten Peter , Bayer Alexandra , Choorapoikayil Suma , Friederich Patrick , Friedrich Jens , Geisen Christof , Güresir Erdem , Grünewald Matthias , Gutjahr Martin , Helmer Philipp , Herrmann Eva , Müller Markus , Narita Diana , Raadts Ansgar , Schwendner Klaus , Seifried Erhard , Stark Patrick , Steinbicker Andrea U. , Thoma Josef , Velten Markus , Weigt Henry , Wiesenack Christoph , Wittmann Maria , Zacharowski Kai , Piekarski Florian 
Published: January 2022

Abstract
Purpose
Anaemia is common in patients presenting with aneurysmal subarachnoid (aSAH) and intracerebral haemorrhage (ICH). In surgical patients, anaemia was identified as an idenpendent risk factor for postoperative mortality, prolonged hospital length of stay (LOS) and increased risk of red blood cell (RBC) transfusion. This multicentre cohort observation study describes the incidence and effects of preoperative anaemia in this critical patient collective for a 10-year period.
Methods
This multicentre observational study included adult in-hospital surgical patients diagnosed with aSAH or ICH of 21 German hospitals (discharged from 1 January 2010 until 30 September 2020). Descriptive, univariate and multivariate analyses were performed to investigate the incidence and association of preoperative anaemia with RBC transfusion, in-hospital mortality and postoperative complications in patients with aSAH and ICH.
Results
A total of n = 9,081 patients were analysed (aSAH n = 5,008; ICH n = 4,073). Preoperative anaemia was present at 28.3% in aSAH and 40.9% in ICH. RBC transfusion rates were 29.9% in aSAH and 29.3% in ICH. Multivariate analysis revealed that preoperative anaemia is associated with a higher risk for RBC transfusion (OR= 3.25 in aSAH, OR = 4.16 in ICH, p < 0.001), for in-hospital mortality (OR= 1.48 in aSAH, OR= 1.53 in ICH, p < 0.001) and for several postoperative complications.
Conclusions
Preoperative anaemia is associated with increased RBC transfusion rates, in-hospital mortality and postoperative complications in patients with aSAH and ICH.
Trial registration:
ClinicalTrials.gov, NCT02147795, https://clinicaltrials.gov/ct2/show/NCT02147795
Based on Serum Raman and Fluorescence Spectra to Diagnose Liver Cancer
Authors: Ou Quanhong , Yang Xien , Yang Weiye , Jiang Liqin , Qian Kai , Shi Youming , Liu Gang 
Published: January 2022

Abstract
Background: Raman and fluorescence spectra techniques are potential tools for disease diagnosis. In recent years, the application of Raman and fluorescence spectra techniques in biological studies has increased a great deal, and clinical investigations relevant to cancer detection by spectroscopic means have attracted particularly attention from both clinical and non-clinical researchers. Methods: In this article, Raman and fluorescence spectra were employed for the detection of liver cancer and healthy individuals using their serum samples. These serum samples were compared with their spectral features acquired by Raman and fluorescence spectroscopy to initially establish spectral features that can be considered spectral markers of liver cancer diagnosis. Resuits: The intensity differences from characteristic peaks of carotene, protein and lipid associated Raman spectra were clearly observed in liver cancer patient serum samples versus normal human serum. The changes in the serum fluorescence profiles of liver cancer patients were also analyzed. To probe the capacity and contrast of Raman spectroscopy as an analytical implement for the early diagnosis of liver cancer, principal component analysis (PCA) was used to analyze the Raman spectra of controls , liver cancer patients and healthy individuals. Furthermore, the Partial Least Squares-Discriminant Analysis (PLS-DA) was performed to compare the diagnostic performance of Raman spectroscopy for the classification of disease samples and healthy samples.Conclusion: Compare with the existing diagnostic techniques, the Raman spectroscopy technique has an excellent advantage in extremely low sample requirements, ease of use and ideal screening procedures. Thus, Raman spectroscopy has great potential to be developed as a powerful tool for distinguishing between healthy and liver cancer serum samples.
Role of gut microbiota in post-operative atrial fibrillation: a randomized trial of berberine
Authors: Wang Huishan , Zhang Jian , wang yang , Jiang hui , Tao Dengshun , Zhao Keyan , Yin Zongtao , Han Jinsong , Ran Fang , Jin Yan 
Published: January 2022

Abstract
Post-operative atrial fibrillation (POAF) is one of the most common complications. However, the underlying factors governing POAF are not well understood. The aim of this study was to investigate the relationship between gut microbiota and POAF. Then, we conducted a randomized, double-blind, placebo-controlled trial with patients underwent isolated coronary artery bypass grafting (CABG) in China to measure gut microbiota altering and impact on the incidence of POAF by oral berberine. Compared with no-POAF patients, gut microbiota composition was significantly altered, including Veillonella increasing. The POAF incidence was reduced from 35–20% under the treatment of berberine. Oral berberine significantly decreased Veillonella abundances, and lipopolysaccharide (LPS), C-reactive protein (CRP) and Interleukin- 6 (IL-6) level. Elevated LPS after surgery is associated with POAF. Our results showed that POAF patients show significantly gut microbiota shift. Altering gut microbiota like oral berberine reduced the POAF.
DFT Based Modeling of Asymmetric Non-Fullerene Acceptors for High-Performance Organic Solar Cell
Authors: Kanwal Noureen , Hussain Riaz , Satar Abdul , Assiri Mohammed A. , Imran Muhammad , Hussain Ajaz , Yawer Mirza Arfan , Hussain Riaz , Mehboob Muhammad Yasir , Khalid Muhammad , Ayub Khurshid 
Published: January 2022

Abstract
AbstractFive new asymmetric NFA-based polymer solar cells i.e., N1-N5 are designed by doing modification in terminal groups of the acceptor part of experimentally synthesized reference molecule with (4,4,9,9-tetramethyl-4,9 dihydroselenopheno [2’,3’:5,6]-s-indaceno [1,2-b] thiophene) core. Frontier molecular orbital analysis is used to study their photovoltaic and optoelectronic properties. It confirmed the electrons' transportation from the donor to the acceptor part. It stated that all molecules have a lower bandgap than R and N2 has the lowest bandgap of 2.01 eV. The molecular orbital potential analysis confirmed the electron-withdrawing properties of the terminal groups. Optical properties studies evaluated maximum absorption with transition energies. All newly designed molecules N1-N5 show higher λmax values than R i.e., in the range of 680-740 nm with N2 having the highest λmax of 735 nm and lowest transition energy of 1.69 eV. Dipole moment studies showed that N3 has a maximum dipole moment of 7-40 D with all others having comparable values. TDM plots confirmed the electron shifting from donor to acceptor region. Reorganization energy analysis showed that N1 and N3 have the lowest reorganization energy values thus giving the highest electron mobilities. Voc calculated results of all molecules N1-N5 have lower values than R when coupled with PTB7-Th donor polymer. Charge transport analysis of N2 and PTB7-Th coupled molecule confirmed the acceptor type nature of our designed molecules.
Continuous Rotation of Three Large Biomass Crops With High Bioconcentration Factor of Cadmium Can Effectively Repair Contaminated Farmlands
Authors: Chen Linhan , Yang Wenjun , Yang Yang , Tu Pengfei , Hu Shengnan , Zeng Qingru 
Published: January 2022

Abstract
Traditional phytoremediation is one means for remediation of heavy metal pollution. For developing countries, the key factor in promoting the practical application of phytoremediation in polluted soils is selecting suitable plants tolerant to heavy metals and using these to produce products with economic value. A chicory-tobacco-peanut, three-season, rotation field experiment was carried on the utilization and remediation of cadmium (Cd) in contaminated farmlands. The results showed that all three crops had a strong capacity to accumulate Cd, with bioconcentration factors of chicory, tobacco, and peanut 6.61 to 11.97, 3.85 to 21.61, and 1.36 to 7, respectively. The yield of total dry biomass and phytoextraction efficiency for Cd reached 32.4 t ha-1 and 10.3% per year, respectively. The aboveground tissues of the three crops accounted for 83.9–91.2% of the total biomass in this rotation experiment. The content of peanut grain and oil met the National Food Safety Standard of China (0.5 mg kg-1, GB 2762-2017) and the Food Contaminant Limit of the European Union (0.1 mg kg-1, 18812006). Therefore, in addition to being used for phytoremediation in contaminated soils, this crop rotation system can also lead to economic benefits for local farmers.
Economic Analysis of Smallholder Dairy Cattle Enterprises In Senegal
Authors: Malenje Evaristo Mukunda , Missohou Ayao , Tebug Stanly Fon , König Emelie Zonabend , Jung’a Joseph Owino , Bett Rawlynce Cheruiyot , Marshall Karen 
Published: January 2022

Abstract
Smallholder dairy production in Senegal is important to both livelihoods and food and nutrition security. Here we examine the economic performance of smallholder dairy cattle enterprises in Senegal, using data from longitudinal monitoring of 113 households. The mean (and standard deviation) of the net returns (NR) per cow per annum (pcpa) was 21.7 (202.9) USD, whilst the NR per household herd per annum (phpa) was 106.1 (1740.3) USD. Only about half (52.2 %) of the dairy cattle enterprise had a positive NR. The most significant income components were milk sale followed by animal sale, whilst the most significant cost components were animal feed followed by animal purchase. When households were grouped by ranking on NRpcpa an interesting trend was observed: whilst the mean NRpcpa showed a fairly linear increase from the lowest to highest NR groups, income and cost did not. Income and costs were both higher for the lowest and highest NR groups, in comparison to the intermediate NR groups. The mean NRs of households grouped by the main breed-type they kept were not significantly different from each other, due to large variances within the breed groups. However, the mean total income and costs were significantly higher for households mainly keeping improved dairy breeds (Bos taurus or Zebu x Bos taurus crosses) in comparison to those keeping indigenous Zebu or Zebu by Guzerat crosses. This study highlights the highly variable (and often low) profitability of smallholder dairy cattle enterprise in Senegal. Further actions to address this are strongly recommended.
Analysis of Adoption and Intensity Adoption of Soil and Water Conservation Practices: The Case of Goromti Watershed West Shewa Zone, Oromia National Regional State, Ethiopia
Authors: Gessese Hawi Hailu , Dassa Aman Rikitu 
Published: January 2022

Abstract
In Ethiopia, soil erosion is a severe problem and a major cause of the decline of agricultural productivity. Interventions were taken by introducing SWC practices. However, the adoption rates of these practices remain below the expected levels in Ethiopia and particularly in the study area. Therefore, this study aims to identify factors affecting adoption and intensity adoption of physical SWC practices in the study areas. A three-stage sampling technique was employed to select 150 sample HHs. Both quantitative and qualitative data were collected from primary and secondary sources. Descriptive statistics and a Double hurdle model were used to analyze data. The first stage of the Double hurdle model results showed that sex of HHs, education level, frequency of extension contact, perception on soil erosion problems, family size, and training affect the probability of adoption of physical SWC practices positively and significantly while age affects it negatively and significantly. Age, plot size, steep slope, training, and frequency of extension contact affect the intensity adoption of physical SWC practices positively and significantly. The finding depicts that the identified demographic, physical, socio-economic, and institutional factors influence the adoption and intensity adoption of physical SWC practices so, the Agricultural and Natural resource Office and other concerned bodies should consider these influential factors to enhance HHs’ adoption of introduced physical SWC practices and to promote agricultural productivity and environmental quality.
The first deep-learning search for radio technosignatures from 820 nearby stars
Authors: Ma Peter , Ng Cherry , Rizk Leandro , Croft Steve , Siemion Andrew , Brzycki Bryan , Czech Daniel , Drew Jamie , Gajjar Vishal , Hoang John , Isaacson Howard , Lebofsky Matt , MacMahon David , Price Danny , Sheikh Sofia , Worden S. 
Published: January 2022

Abstract
The goal of the Search for Extraterrestrial Intelligence (SETI) is to quantify the prevalence of technological life beyond Earth via their “technosignatures". One theorized technosignature are narrowband Doppler drifting radio signals. The principal challenge in conducting SETI in the radio domain is developing a generalized technique to reject human radio frequency interference (RFI) that dominate the features across the band in searches for technosignatures. Here, we present the first comprehensive deep-learning based technosignature search to date, returning 8 promising ETI signals-of-interest for re-observation as part of the Breakthrough Listen initiative. The search comprises 820 unique targets observed with the Robert C. Byrd Green Bank Telescope, totaling over 480 hr of on-sky data. We implement a novel β−Convolutional Variational Autoencoder with an embedded discriminator combined with Random Forest Decision Trees to classify technosignature candidates in a semiunsupervised manner. We compare our results with prior classical techniques on the same dataset and conclude that our algorithm returns more convincing and novel signals-of-interest with a manageable false positive rate. This new approach presents itself as a leading solution in accelerating SETI and other transient research into the age of data-driven astronomy.
Comparative Transcriptome and WGCNA RevealKey Genes Involved in Lignocellulose Degradation in Sarcomyxa Edulis
Authors: Duan Chao , Tian Feng-Hua , Yao Lan , Lv Jian-Hua , Jia Chuan-Wen , Li Chang-Tian 
Published: January 2022

Abstract
In order to explore the molecular mechanism of Sarcomyxa edulis response to lignocelluloses degradation, the developmental transcriptomes was analyzed for six stages covering the whole developmental process, including mycelium growing to half bag (B1), mycelium in cold stimulation after full bag (B2), mycelium in primordia appearing (B3), primordia (B4), mycelium at the harvest stage (B5) and mature fruiting body (B6). A total of 6 samples were used for transcriptome sequencing, with three biological replicates. Based on the above transcriptome data, we constructed a co-expression network of weighted genes associated with extracellular enzyme physiological traits by WGCNA, and obtained 19 gene co-expression modules closely related to lignocelluloses degradation. In addition, a number of key genes involved in lignocelluloses degradation pathways were discovered from the four modules with the highest correlation with target traits. These results provide clues for further study on the molecular genetic mechanisms of Sarcomyxa edulis lignocelluloses degradation.
Quality Improvement in Juvenile Idiopathic Arthritis: a Mixed-methods Implementation Pilot of the CAPTURE-JIA Dataset
Authors: Mcerlane Flora , Anderson Chris , Lawson-Tovey Saskia , Lee Barbara , Lee Chris , Lunt Laura , McDonagh Janet E , Smith Andrew D , Smith Nicola , Cleary Gavin 
Published: January 2022

Abstract
BackgroundA significant proportion of children and young people with juvenile idiopathic arthritis (JIA) do not achieve inactive disease during the first two years following diagnosis. Refinements to clinical care pathways have the potential to improve clinical outcomes but a lack of consistent and contemporaneous clinical data presently precludes standard setting and implementation of meaningful quality improvement programmes. This study was the first to pilot clinical data collection and analysis using the CAPTURE-JIA dataset, and to explore patient and clinician-reported feasibility and acceptability data.MethodsA multiphase mixed-methods approach enabled prospective collection of quantitative data to examine the feasibility and efficacy of dataset collection and of qualitative data informing the context and processes of implementation. An initial paper pilot informed the design of a bespoke electronic data collection system (the Agileware system), with a subsequent electronic pilot informing the final CAPTURE-JIA data collection tool. ResultsPaper collection of patient data was feasible but time-consuming in the clinical setting. Phase 1 paper pilot data (121 patients) identified three themes: problematic data items (14/62 data items received >40% missing data), formatting of data collection forms and a clinician-highlighted need for digital data collection, informing Phase 2 electronic data collection tool development. Patients and families were universally supportive of the collection and analysis of anonymised patient data to inform clinical care. No apparent preference for paper / electronic data collection was reported by families. Phase 3 electronic pilot data (38 patients) appeared complete and the system reported to be easy to use. Analysis of the study dataset and a dummy longitudinal dataset confirmed that all eleven JIA national audit questions can be answered using the electronic system. ConclusionsMulticentre CAPTURE-JIA data collection is feasible and acceptable, with a bespoke data collection system highlighted as the most satisfactory solution. The study is informing ongoing work towards a streamlined and flexible national paediatric data collection system to drive quality improvement in clinical care.