bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene Set Knowledge Discovery with Enrichr
Authors: Xie Zhuorui , Bailey Allison , Kuleshov Maxim V. , Clarke Daniel J. B. , Evangelista John E. , Jenkins Sherry L. , Lachmann Alexander , Wojciechowicz Megan L. , Kropiwnicki Eryk , Jagodnik Kathleen M. , Jeon Minji , Ma'ayan Avi 
Published: March 2021

AbstractProfiling samples from patients, tissues, and cells with genomics, transcriptomics, epigenomics, proteomics, and metabolomics ultimately produces lists of genes and proteins that need to be further analyzed and integrated in the context of known biology. Enrichr (Chen et al., 2013; Kuleshov et al., 2016) is a gene set search engine that enables the querying of hundreds of thousands of annotated gene sets. Enrichr uniquely integrates knowledge from many high‐profile projects to provide synthesized information about mammalian genes and gene sets. The platform provides various methods to compute gene set enrichment, and the results are visualized in several interactive ways. This protocol provides a summary of the key features of Enrichr, which include using Enrichr programmatically and embedding an Enrichr button on any website. © 2021 Wiley Periodicals LLC.Basic Protocol 1: Analyzing lists of differentially expressed genes from transcriptomics, proteomics and phosphoproteomics, GWAS studies, or other experimental studiesBasic Protocol 2: Searching Enrichr by a single gene or key search termBasic Protocol 3: Preparing raw or processed RNA‐seq data through BioJupies in preparation for Enrichr analysisBasic Protocol 4: Analyzing gene sets for model organisms using modEnrichrBasic Protocol 5: Using Enrichr in GeneshotBasic Protocol 6: Using Enrichr in ARCHS4Basic Protocol 7: Using the enrichment analysis visualization Appyter to visualize Enrichr resultsBasic Protocol 8: Using the Enrichr APIBasic Protocol 9: Adding an Enrichr button to a website
A linear group delay filter with tunable positive slope for analog signal processing
Authors: Avignon‐Meseldzija Emilie , Anastasov Jelena , Milic Dejan 
Published: March 2021

SummaryThis article describes the design of a tunable positive slope linear group delay filter dedicated to analog signal processing applications. The designed filter is composed of eight second‐order all‐pass cells which have been optimized to obtain a highly linear global group delay characteristic over a specified bandwidth for a specified dispersion. Each of these second‐order cells is designed with a dedicated Gm‐C topology to fit the ideal group delay characteristic with a high efficiency. Based on the sensitivity analysis of the topology, the possibility of tuning the group delay slope is highlighted. The design has been achieved with the ST CMOS 55 nm technology and has a maximum bandwidth of 2.5 GHz, a maximum reachable delay of 5.12 ns, and a group delay maximum variation of 2.5 ns. The positive slope of the group delay can be tuned in the range from 1.48 ns/GHz up to 2.03 ns/GHz. The concept of slope tunability is validated through post‐layout statistical analysis.
Identifying biotic drivers of population dynamics in a benthic–pelagic community
Authors: Forsblom Louise , Lindén Andreas , Engström‐Öst Jonna , Lehtiniemi Maiju , Bonsdorff Erik 
Published: March 2021

AbstractBenthic species and communities are linked to pelagic zooplankton through life‐stages encompassing both benthic and pelagic habitats and through a mutual dependency on primary producers as a food source. Many zooplankton taxa contribute to the sedimentary system as benthic eggs. Our main aim was to investigate the nature of the population level biotic interactions between and within these two seemingly independent communities, both dependent on the pelagic primary production, while simultaneously accounting for environmental drivers (salinity, temperature, and oxygen conditions). To this end, we applied multivariate autoregressive state‐space models to long (1966–2007) time series of annual abundance data, comparing models with and without interspecific interactions, and models with and without environmental variables included. We were not able to detect any direct coupling between sediment‐dwelling benthic taxa and pelagic copepods and cladocerans on the annual scale, but the most parsimonious model indicated that interactions within the benthic community are important. There were also positive residual correlations between the copepods and cladocerans potentially reflecting the availability of a shared resource or similar seasonal dependence, whereas both groups tended to correlate negatively with the zoobenthic taxa. The most notable single interaction within the benthic community was a tendency for a negative effect of Limecola balthica on the amphipods Monoporeia affinis and Pontoporeia femorata which can help explain the observed decrease in amphipods due to increased competitive interference.
Development and testing of an environmental DNA (eDNA) assay for endangered Atlantic sturgeon to assess its potential as a monitoring and management tool
Authors: Plough Louis V. , Bunch Aaron J. , Lee Benjamin B. , Fitzgerald Catherine L. , Stence Chuck P. , Richardson Brian 
Published: March 2021

AbstractSignificant declines in Atlantic sturgeon (Acipenser oxyrhynchus oxyrhynchus) abundances along the US east coast have spurred major research efforts and management actions over the last 50 years, yet information on spawning stock abundances and habitat use is still lacking for many river systems, including in the Chesapeake Bay, USA. Here, we developed and tested a new quantitative PCR (qPCR) assay to detect Atlantic sturgeon environmental DNA (eDNA) in water samples with the goal of providing an alternative method to monitor presence and relative abundance. We also examined Atlantic sturgeon eDNA shedding rates in laboratory experiments. A qPCR‐probe assay targeting Cytochrome B was developed and showed no amplification of other related and co‐occurring fishes. Pond trials at a density of ~0.2 g/L sturgeon produced relatively strong eDNA detections (~1,000–25,000 copies/L) in all seven water samples assayed. Water samples taken from two river systems in the Chesapeake Bay produced zero eDNA detections in the summer, while fall sampling during sturgeon spawning produced positive eDNA detections in 26% of samples, though at much lower concentrations (400–1,800 copies/L) compared with the pond (mesocosm) detections. Acoustic detections of sturgeon near river sampling sites were positively associated with eDNA detections. However, the eDNA assay failed to detect the presence of sturgeon in some samples when abundances were very low or when fish were in deep water. Finally, Atlantic sturgeon eDNA shedding rates were estimated to be on the order of estimates for other fish species, which suggests that relatively weak detections in the field are not necessarily driven by low rates of eDNA shedding. Overall, eDNA analysis represents a promising new monitoring tool for Atlantic sturgeon. Applying these methods in other rivers along the US east coast is an important next step in documenting Atlantic sturgeon distribution for management and conservation purposes.
Multiplexed measurement of candidate blood protein biomarkers of heart failure
Authors: Tonry Claire , McDonald Ken , Ledwidge Mark , Hernandez Belinda , Glezeva Nadezhda , Rooney Cathy , Morrissey Brian , Pennington Stephen R. , Baugh John A. , Watson Chris J. 
Published: March 2021

AbstractAimsThere is a critical need for better biomarkers so that heart failure can be diagnosed at an earlier stage and with greater accuracy. The purpose of this study was to design a robust mass spectrometry (MS)‐based assay for the simultaneous measurement of a panel of 35 candidate protein biomarkers of heart failure, in blood. The overall aim was to evaluate the potential clinical utility of this biomarker panel for prediction of heart failure in a cohort of 500 patients.Methods and resultsMultiple reaction monitoring (MRM) MS assays were designed with Skyline and Spectrum Mill PeptideSelector software and developed using nanoflow reverse phase C18 chromatographic Chip Cube‐based separation, coupled to a 6460 triple quadrupole mass spectrometer. Optimized MRM assays were applied, in a sample‐blinded manner, to serum samples from a cohort of 500 patients with heart failure and non‐heart failure (non‐HF) controls who had cardiovascular risk factors. Both heart failure with reduced ejection fraction (HFrEF) patients and heart failure with preserved ejection fraction (HFpEF) patients were included in the study. Peptides for the Apolipoprotein AI (APOA1) protein were the most significantly differentially expressed between non‐HF and heart failure patients (P = 0.013 and P = 0.046). Four proteins were significantly differentially expressed between non‐HF and the specific subtypes of HF (HFrEF and HFpEF); Leucine‐rich‐alpha‐2‐glycoprotein (LRG1, P < 0.001), zinc‐alpha‐2‐glycoprotein (P = 0.005), serum paraoxanse/arylesterase (P = 0.013), and APOA1 (P = 0.038). A statistical model found that combined measurements of the candidate biomarkers in addition to BNP were capable of correctly predicting heart failure with 83.17% accuracy and an area under the curve (AUC) of 0.90. This was a notable improvement on predictive capacity of BNP measurements alone, which achieved 77.1% accuracy and an AUC of 0.86 (P = 0.005). The protein peptides for LRG1, which contributed most significantly to model performance, were significantly associated with future new onset HF in the non‐HF cohort [Peptide 1: odds ratio (OR) 2.345 95% confidence interval (CI) (1.456–3.775) P = 0.000; peptide 2: OR 2.264 95% CI (1.422–3.605), P = 0.001].ConclusionsThis study has highlighted a number of promising candidate biomarkers for (i) diagnosis of heart failure and subtypes of heart failure and (ii) prediction of future new onset heart failure in patients with cardiovascular risk factors. Furthermore, this study demonstrates that multiplexed measurement of a combined biomarker signature that includes BNP is a more accurate predictor of heart failure than BNP alone.
Dipyrromethane‐Based PGeP Pincer Methylgermyl and Methoxidogermyl Nickel and Palladium Complexes
Authors: Cabeza Javier A. , García‐Álvarez Pablo , Laglera‐Gándara Carlos J. , Pérez‐Carreño Enrique 
Published: March 2021

AbstractThe dipyrromethane‐based chloridogermyl complexes [MCl{κ3P,Ge,P‐GeCl(pyrmPiPr2)2CMe2}] (1M; M=Ni, Pd; (pyrmPiPr2)2CMe2=5,5’‐dimethyl‐2,2’‐bis(di‐isopropylphosphanylmethyl)dipyrromethane‐1,1’‐diyl) reacted with one or more equivalents of LiOMe to give the monosubstituted complexes [MCl{κ3P,Ge,P‐Ge(OMe)(pyrmPiPr2)2CMe2}] (2M−OMe; M=Ni, Pd). However, analogous treatments of complexes 1M with LiMe afforded the dimethyl complexes [MMe{κ3P,Ge,P‐GeMe(pyrmPiPr2)2CMe2}] (3M−Me; M=Ni, Pd). The monomethyl complexes [MCl{κ3P,Ge,P‐GeMe(pyrmPiPr2)2CMe2}] (2M−Me; M=Ni, Pd), which were identified as intermediates in the syntheses of 3M−Me, were satisfactorily prepared by treating 3M−Me with HCl. The regioselectivities of these reactions have been rationalized with DFT calculations.
Leith, a Transnational Tribute
Authors: Furani Khaled 
Published: March 2021

AbstractIn memoriam of Professor Leith Mullings, my teacher, I raise questions she can no longer answer, although her deeds can speak still. She provides a model of scholarship, mentoring, and activism infused with courage, humility, and nurturance. In her final years and days, she worked with Palestinian anthropologists to form an independent association and forge ties with Black anthropologists. May they remain enduring testaments to a life striving for Truth and Justice.
A generating‐absorbing boundary condition for dispersive waves
Authors: Borsboom Mart , Jacobsen Niels G. 
Published: March 2021

AbstractThe detailed modeling of free‐surface waves and their interaction with bottom‐mounted or floating structures requires large computational resources, which is why efficient boundary conditions with low spurious reflection are desirable. The present work presents a review of existing generating‐absorbing boundary conditions (GABCs) for dispersive waves and their reflection characteristics. Hereafter, an adaptation of the classical Sommerfeld condition is proposed by using a depth‐varying coefficient to improve absorption efficiency over a range of wave numbers. An analytical model is proposed to analyse the reflection characteristics for both propagating and evanescent modes, and a considerable improvement in comparison to the Sommerfeld condition is documented over a broad frequency range (reflection coefficients below 5% for nondimensional wave numbers in the range [0, 10]). The new boundary condition is implemented in OpenFoam (waves2Foam) and the functioning for regular, irregular, solitary, and phase‐focused waves is presented.
Phytochemical profiles of lemon verbena (Lippia citriodora H.B.K.) and its potential application to cookie enrichment
Authors: Hematian Sourki Abdollah , Ghani Askar , Kiani Farzaneh , Alipour Azar 
Published: March 2021

AbstractIn this research, phytochemical properties of lemon verbena and oxidative stability of the fat component in cookies (contain lemon verbena powder and EO) were investigated. The essential oil (EO) profile and polyphenol compounds were identified by GC/MS and HPLC, respectively. Different concentrations of lemon verbena powder and EO were added to the cookies in comparison with TBHQ. The oxidative stability of fat component in cookies (peroxide value, p‐Anisidine, TOTOX value), along with the physicochemical (pH, acidity, weight loss, and moisture content) and sensory properties of the cookies were evaluated over a period of 6 months during storage at room temperature. The main constituents of EO are geranial (27.21%), neral (20.01%), spathulenol (7.28%), and limonene, while trans‐Ferulic acid (6.71 mg/g), Hesperidin (1.87 mg/g), and ρ‐Coumaric acid (0.04 mg/g) were measured as main phenolic compounds. The peroxide value increased in all samples for the first 2 months of storage and then decreased as hydroperoxide was converted to secondary oxidation products. The p‐Anisidine value increased in all samples during storage. This parameter was lower in cookies containing lemon verbena EO and TBHQ treatments. Sensory evaluations of cookies showed that lemon verbena EO had positive effects on the aroma and taste of cookies during storage, whereas lemon verbena powder had adverse effects on mouthfeel and consumer acceptance. The results showed that lemon verbena can increase the eating quality, prolong the shelf life, and maintain the integrity of bakery products with high‐fat content.
Survival outcomes for head and neck patients with Medicaid: A health insurance paradox
Authors: Pannu Jaibir S. , Simpson Matthew C. , Adjei Boakye Eric , Massa Sean T. , Cass Lauren M. , Challapalli Sai D. , Rohde Rebecca L. , Osazuwa‐Peters Nosayaba 
Published: March 2021

AbstractPurposePrivately insured patients with head and neck cancer (HNC) typically have better outcomes; however, differential outcome among Medicaid versus the uninsured is unclear. We aimed to describe outcome disparities among HNC patients uninsured versus on Medicaid.MethodsA cohort of 18–64‐year‐old adults (n = 57 920) with index HNC from the Surveillance, Epidemiology, and End Results 18 database (2007–2015) was analyzed using Fine and Gray multivariable competing risks proportional hazards models for HNC‐specific mortality.ResultsMedicaid (sdHR = 1.65, 95% CI 1.58, 1.72) and uninsured patients (sdHR = 1.55, 95% CI 1.46, 1.65) had significantly greater mortality hazard than non‐Medicaid patients. Medicaid patients had increased HNC mortality hazard than those uninsured.ConclusionCompared with those uninsured, HNC patients on Medicaid did not have superior survival, suggesting that there may be underlying mechanisms/factors inherent in this patient population that could undermine access to care benefits from being on Medicaid.
Risk of HCC With Hepatitis B Viremia Among HIV/HBV‐Coinfected Persons in North America
Authors: Kim H. Nina , Newcomb Craig W. , Carbonari Dena M. , Roy Jason A. , Torgersen Jessie , Althoff Keri N. , Kitahata Mari M. , Reddy K. Rajender , Lim Joseph K. , Silverberg Michael J. , Mayor Angel M. , Horberg Michael A. , Cachay Edward R. , Kirk Gregory D. , Sun Jing , Hull Mark , Gill M. John , Sterling Timothy R. , Kostman Jay R. , Peters Marion G. , Moore Richard D. , Klein Marina B. , Lo Re Vincent ,   for the North American AIDS Cohort Collaboration on Research, Design of IeDEA
Published: March 2021

Background and Aims
Chronic HBV is the predominant cause of HCC worldwide. Although HBV coinfection is common in HIV, the determinants of HCC in HIV/HBV coinfection are poorly characterized. We examined the predictors of HCC in a multicohort study of individuals coinfected with HIV/HBV.

Approach and Results
We included persons coinfected with HIV/HBV within 22 cohorts of the North American AIDS Cohort Collaboration on Research and Design (1995‐2016). First occurrence of HCC was verified by medical record review and/or cancer registry. We used multivariable Cox regression to determine adjusted HRs (aHRs [95% CIs]) of factors assessed at cohort entry (age, sex, race, body mass index), ever during observation (heavy alcohol use, HCV), or time‐updated (HIV RNA, CD4+ percentage, diabetes mellitus, HBV DNA). Among 8,354 individuals coinfected with HIV/HBV (median age, 43 years; 93% male; 52.4% non‐White), 115 HCC cases were diagnosed over 65,392 person‐years (incidence rate, 1.8 [95% CI, 1.5‐2.1] events/1,000 person‐years). Risk factors for HCC included age 40‐49 years (aHR, 1.97 [1.22‐3.17]), age ≥50 years (aHR, 2.55 [1.49‐4.35]), HCV coinfection (aHR, 1.61 [1.07‐2.40]), and heavy alcohol use (aHR, 1.52 [1.04‐2.23]), while time‐updated HIV RNA >500 copies/mL (aHR, 0.90 [0.56‐1.43]) and time‐updated CD4+ percentage <14% (aHR, 1.03 [0.56‐1.90]) were not. The risk of HCC was increased with time‐updated HBV DNA >200 IU/mL (aHR, 2.22 [1.42‐3.47]) and was higher with each 1.0 log10 IU/mL increase in time‐updated HBV DNA (aHR, 1.18 [1.05‐1.34]). HBV suppression with HBV‐active antiretroviral therapy (ART) for ≥1 year significantly reduced HCC risk (aHR, 0.42 [0.24‐0.73]).

Conclusion
Individuals coinfected with HIV/HBV on ART with detectable HBV viremia remain at risk for HCC. To gain maximal benefit from ART for HCC prevention, sustained HBV suppression is necessary.
Incidence, diagnosis, and outcome of immune‐mediated thrombotic thrombocytopenic purpura: A nationwide survey by the Spanish registry of thrombotic thrombocytopenic purpura
Authors: Pascual‐Izquierdo Cristina , del Rio‐Garma Julio , de la Rubia Javier , Viejo Aurora , Mingot Eva , Cid Joan , Solanich Xavier , Fernández‐Sojo Jesús , Martín‐Sánchez Jesús , Hernández Luis , García‐Gala José María , Alonso Nieves , González Victoria , Oliva Ana , Gómez‐Seguí Inés , Goterris Rosa , Guerra Luisa , García‐Candel Faustino , Fernández‐Docampo Marta , Antelo María Luisa , Salgado‐Barreira Ángel , Salinas Ramón ,   Spanish Apheresis Group (GEA) and Spanish Thrombotic Thrombocytopenic Purpura Registry (REPTT)
Published: March 2021

AbstractBackgroundImmune‐mediated thrombotic thrombocytopenic purpura (iTTP) is a rare disease characterized by the presence of anti‐ADAMTS13 autoantibodies. Achieving accurate information on incidence and customary disease management is important to provide appropriate diagnostic and therapeutic resources. The aim of this study was to determine the incidence and outcomes of iTTP in Spain.Study design and methodsA cross‐sectional survey was carried out among Spanish hospitals, focused on iTTP patients ≥16 years old attended between 2015 and 2017, and those at follow‐up before that interval. Incidence, prevalence, mortality, refractoriness, exacerbations, treatment complications, relapses, and sequelae were estimated.ResultsForty‐two hospitals covering roughly 20 million inhabitants answered the survey and reported 203 episodes (138 newly‐diagnosed and 65 relapses), of which 193 (95.1%) were treated. Incidence was 2.67 (95% CI 1.90‐3.45) patients per million inhabitants per year and prevalence 21.44 (95% CI% 19.10‐23.73) patients per million inhabitants. At diagnosis, ADAMTS13 activity and anti‐ADAMTS13 autoantibody were measured in 97% and 84.3% of reported episodes, respectively. Fifteen patients (7.4%) died as a direct consequence of iTTP, 6 of them before receiving any iTTP‐specific treatment. Thirty‐one (16.1%) of the 193 treated episodes were refractory to plasma exchange and corticosteroids, and 51 (26.4%) suffered at least one exacerbation.ConclusioniTTP incidence and prevalence were somewhat higher than those documented in neighboring countries. Together with data on treatments and outcomes, this information will allow us to better estimate what is needed to improve diagnosis and prognosis of iTTP patients in Spain.
Ethnic group and social support contribution to posttraumatic growth after sudden spousal loss among Jewish, Muslim, and Druze widows in Israel
Authors: Khatib Anwar , Ben‐David Vered , Gelkopf Marc , Levine Stephen Z. 
Published: March 2021

AbstractThis study aimed to examine the contribution of ethnic group status and social support to posttraumatic growth (PTG) among widows after sudden spousal loss. Participants included 184 widows from three ethnic groups: 59 (32.3%) Jewish, 58 (31.7%) Muslim, and 66 (36%) Druze. Information was gathered via a demographic questionnaire, PTG Inventory, and Multidimensional Scale of Perceived Social Support. Analysis of covariance was used to test ethnic group status differences in social support, controlling for demographic variables. Hierarchical linear models were used to assess groups differences in the study outcome variables. The results showed that the PTG total score was higher for Jewish widows than for Muslim and Druze widows, with a null difference between the latter two, and social support contributed to increased PTG among Jewish widows more than among Muslim and Druze widows, with no significant association between social support and PTG among Druze widows. The highest PTG levels were observed among widows from modern individualistic cultural backgrounds, compared with traditional collectivist, cultural backgrounds after sudden spousal death. The social support system may be a pathway to enhance PTG among widows in traditional collectivist societies.
Fast‐adaptive weighted constellation designs based on hybrid constellation shaping for long‐haul optical fiber communication systems
Authors: Zhou Wenmao , Zhang Qi , Gao Ran , Xin Xiangjun , Liu Bingchun , Wang Xishuo , Tian Feng , Tian Qinghua , Sheng Xia , Wang Yongjun , Chang Huan , Yang Leijing 
Published: March 2021

AbstractA novel fast‐adaptive weighted hybrid‐shaped M‐ary quadrature amplitude modulation (HS‐MQAM) format is proposed in this paper. By introducing a fast‐adaptive weighting factor array related to geometric shaping and probabilistic shaping, the non‐linear impairment is mitigated and the bit error rate (BER) and mutual information (MI) performances are further improved. The simulation results show that the proposed HS‐61QAM outperforms both geometric‐shaped 61 quadrature amplitude modulation (GS‐61QAM) and regular 64QAM, and has more obvious advantages in the long‐haul optical transmission system. For a 120‐Gb/s optical communication system over 10 × 75 km fiber transmission link, compared with GS‐61QAM and regular 64QAM, the proposed approach can achieve about 4.2 and 8 dB OSNR gain at the BER of 10−2, and 0.21 and 0.55 bits/symbol MI gain at the OSNR of 22 dB.