bluuebunny/crossref_metadata_2025_split huggingface dataset:
ampir: an R package for fast genome-wide prediction of antimicrobial peptides
Authors: Fingerhut Legana C H W , Miller David J , Strugnell Jan M , Daly Norelle L , Cooke Ira R 
Published: July 2020

Abstract

Summary
Antimicrobial peptides (AMPs) are the key components of the innate immune system that protect against pathogens, regulate the microbiome and are promising targets for pharmaceutical research. Computational tools based on machine learning have the potential to aid discovery of genes encoding novel AMPs but existing approaches are not designed for genome-wide scans. To facilitate such genome-wide discovery of AMPs we developed a fast and accurate AMP classification framework, ampir. ampir is designed for high throughput, integrates well with existing bioinformatics pipelines, and has much higher classification accuracy than existing methods when applied to whole genome data.

Availability and implementation
ampir is implemented primarily in R with core feature calculation methods written in C++. Release versions are available via CRAN and work on all major operating systems. The development version is maintained at https://github.com/legana/ampir.

Supplementary information
Supplementary data are available at Bioinformatics online.
Characterization of parameters with a mixed bias property
Authors: Rotnitzky A , Smucler E , Robins J M 
Published: July 2020

Summary
We study a class of parameters with the so-called mixed bias property. For parameters with this property, the bias of the semiparametric efficient one-step estimator is equal to the mean of the product of the estimation errors of two nuisance functions. In nonparametric models, parameters with the mixed bias property admit so-called rate doubly robust estimators, i.e., estimators that are consistent and asymptotically normal when one succeeds in estimating both nuisance functions at sufficiently fast rates, with the possibility of trading off slower rates of convergence for the estimator of one of the nuisance functions against faster rates for the estimator of the other nuisance function. We show that the class of parameters with the mixed bias property strictly includes two recently studied classes of parameters which, in turn, include many parameters of interest in causal inference. We characterize the form of parameters with the mixed bias property and of their influence functions. Furthermore, we derive two functional loss functions, each being minimized at one of the two nuisance functions. These loss functions can be used to derive loss-based penalized estimators of the nuisance functions.
Phylogeographical and cytogeographical history ofArtemisia herba-alba(Asteraceae) in the Iberian Peninsula and North Africa: mirrored intricate patterns on both sides of the Mediterranean Sea
Authors: Bougoutaia Youcef , Garnatje Teresa , Vallès Joan , Kaid-Harche Meriem , Ouhammou Ahmed , Dahia Mostefa , Tlili Abderrazak , Vitales Daniel 
Published: July 2020

AbstractArtemisia herba-alba is an important component of Mediterranean dry steppe floras, being widely distributed in arid areas of the Iberian Peninsula and North-West Africa. In this study, we use genetic, cytogenetic and niche modelling tools to investigate the natural history of the species, focusing particularly on the role played by polyploidization to explain current diversity patterns throughout the main distribution range of the plant. Our sequencing data indicate a complex phylogeographical structure showing similar haplotype diversity patterns on both sides of the Strait of Gibraltar and no clear signals of genetic refugia. According to our cytogeographical results, we inferred multiple polyploidization events, which probably took place on the Iberian Peninsula and in North Africa independently. Environmental niche modelling suggested stable potential distributions of A. herba-alba on both sides of the Mediterranean Sea under present and past Last Glacial Maximum conditions, which could be related to the intricate spatial genetic and cytogenetic patterns shown by the species. Finally, environmental modelling comparison among cytotypes revealed that the niche of tetraploids is narrower and nested in that of diploids, a result that could indicate environmental specialization and could potentially explain recurrent establishment success of tetraploids.
Autoimmune encephalitis mediated by B-cell response against N-methyl-d-aspartate receptor
Authors: Wagnon Isabelle , Hélie Pauline , Bardou Isabelle , Regnauld Caroline , Lesec Léonie , Leprince Jerôme , Naveau Mikaël , Delaunay Barbara , Toutirais Olivier , Lemauff Brigitte , Etard Olivier , Vivien Denis , Agin Véronique , Macrez Richard , Maubert Eric , Docagne Fabian 
Published: July 2020

Abstract
Anti-N-methyl-d-aspartate receptor (NMDAR) encephalitis is a neuropsychiatric disease characterized by an antibody-mediated autoimmune response against NMDAR. Recent studies have shown that anti-NMDAR antibodies are involved in the pathophysiology of the disease. However, the upstream immune and inflammatory processes responsible for this pathogenic response are still poorly understood. Here, we immunized mice against the region of NMDA receptor containing the N368/G369 amino acids, previously implicated in a pathogenic response. This paradigm induced encephalopathy characterized by blood–brain barrier opening, periventricular T2-MRI hyperintensities and IgG deposits into the brain parenchyma. Two weeks after immunization, mice developed clinical symptoms reminiscent of encephalitis: anxiety- and depressive-like behaviours, spatial memory impairment (without motor disorders) and increased sensitivity to seizures. This response occurred independently of overt T-cell recruitment. However, it was associated with B220+ (B cell) infiltration towards the ventricles, where they differentiated into CD138+ cells (plasmocytes). Interestingly, these B cells originated from peripheral lymphoid organs (spleen and cervical lymphoid nodes). Finally, blocking the B-cell response using a depleting cocktail of antibodies reduced the severity of symptoms in encephalitis mice. This study demonstrates that the B-cell response can lead to an autoimmune reaction against NMDAR that drives encephalitis-like behavioural impairments. It also provides a relevant platform for dissecting encephalitogenic mechanisms in an animal model, and enables the testing of therapeutic strategies targeting the immune system in anti-NMDAR encephalitis.
Risk Factors for Intensive Care Unit Admission and In-hospital Mortality Among Hospitalized Adults Identified through the US Coronavirus Disease 2019 (COVID-19)-Associated Hospitalization Surveillance Network (COVID-NET)
Authors: Kim Lindsay , Garg Shikha , O’Halloran Alissa , Whitaker Michael , Pham Huong , Anderson Evan J , Armistead Isaac , Bennett Nancy M , Billing Laurie , Como-Sabetti Kathryn , Hill Mary , Kim Sue , Monroe Maya L , Muse Alison , Reingold Arthur L , Schaffner William , Sutton Melissa , Talbot H Keipp , Torres Salina M , Yousey-Hindes Kimberly , Holstein Rachel , Cummings Charisse , Brammer Lynnette , Hall Aron J , Fry Alicia M , Langley Gayle E 
Published: July 2020

AbstractBackgroundCurrently, the United States has the largest number of reported coronavirus disease 2019 (COVID-19) cases and deaths globally. Using a geographically diverse surveillance network, we describe risk factors for severe outcomes among adults hospitalized with COVID-19.MethodsWe analyzed data from 2491 adults hospitalized with laboratory-confirmed COVID-19 between 1 March–2 May 2020, as identified through the Coronavirus Disease 2019–Associated Hospitalization Surveillance Network, which comprises 154 acute-care hospitals in 74 counties in 13 states. We used multivariable analyses to assess associations between age, sex, race and ethnicity, and underlying conditions with intensive care unit (ICU) admission and in-hospital mortality.ResultsThe data show that 92% of patients had ≥1 underlying condition; 32% required ICU admission; 19% required invasive mechanical ventilation; and 17% died. Independent factors associated with ICU admission included ages 50–64, 65–74, 75–84, and ≥85 years versus 18–39 years (adjusted risk ratios [aRRs], 1.53, 1.65, 1.84, and 1.43, respectively); male sex (aRR, 1.34); obesity (aRR, 1.31); immunosuppression (aRR, 1.29); and diabetes (aRR, 1.13). Independent factors associated with in-hospital mortality included ages 50–64, 65–74, 75–84, and ≥ 85 years versus 18–39 years (aRRs, 3.11, 5.77, 7.67, and 10.98, respectively); male sex (aRR, 1.30); immunosuppression (aRR, 1.39); renal disease (aRR, 1.33); chronic lung disease (aRR 1.31); cardiovascular disease (aRR, 1.28); neurologic disorders (aRR, 1.25); and diabetes (aRR, 1.19).ConclusionsIn-hospital mortality increased markedly with increasing age. Aggressive implementation of prevention strategies, including social distancing and rigorous hand hygiene, may benefit the population as a whole, as well as those at highest risk for COVID-19–related complications.
Efficacy and Safety of a Naphthoquine-Azithromycin Coformulation for Malaria Prophylaxis in Southeast Asia: A Phase 3, Double-blind, Randomized, Placebo-controlled Trial
Authors: Yang Henglin , Wang Jingyan , Liu Hui , Zhao Yan , Lakshmi Seetha , Li Xingliang , Nie Renhua , Li Chunfu , Wang Hengye , Cao Yaming , Menezes Lynette , Cui Liwang 
Published: July 2020

Abstract

Background
A prophylactic antimalarial drug that is both effective for protection and improves compliance is in high demand.

Methods
We conducted a randomized, placebo-controlled, double-blinded phase 3 trial to evaluate the 1:1 fixed-dose combination of naphthoquine-azithromycin (NQAZ) for safety and protection against Plasmodium infections in villages along the China-Myanmar border. A total of 631 residents, 5–65 years of age, were randomized into the drug group (n = 319) and the placebo group (n = 312) to receive NZAQ and placebo, respectively, as a single-dose monthly treatment. Follow-ups were conducted weekly to monitor for adverse events and malaria infections.

Results
Of the 531 subjects completing the trial, there were 46 and 3 blood smear–positive Plasmodium infections in the placebo and treatment groups, respectively. For the intent-to-treat analysis, the single-dose monthly NQAZ treatment had 93.62% protective efficacy (95% confidence interval [CI]: 91.72%–95.52%). For the per-protocol analysis, NQAZ treatment provided a 93.04% protective efficacy (95% CI: 90.98%–95.1%). Three smear-positive cases in the NQAZ group were all due to acute falciparum malaria. In comparison, NQAZ treatment provided 100% protection against the relapsing malaria Plasmodium vivax and Plasmodium ovale. The treatment group had 5.6% of participants experiencing transient elevation of liver aminotransferases compared with 2.2% in the placebo group (P &gt; .05).

Conclusions
Monthly prophylaxis with NQAZ tablets was well tolerated and highly effective for preventing Plasmodium infections. It may prove useful for eliminating P. vivax in areas with a high prevalence of glucose-6-phosphate dehydrogenase deficiency in the population.

Clinical Trials Registration
ChiCTR1800020140.
Recommendations for advance care planning in adults with congenital heart disease: a position paper from the ESC Working Group of Adult Congenital Heart Disease, the Association of Cardiovascular Nursing and Allied Professions (ACNAP), the European Association for Palliative Care (EAPC), and the International Society for Adult Congenital Heart Disease (ISACHD)
Authors: Schwerzmann Markus , Goossens Eva , Gallego Pastora , Kovacs Adrienne H , Moons Philip , Swan Lorna , Tobler Daniel , de Stoutz Noémi , Gabriel Harald , Greutmann Matthias , Roos-Hesselink Jolien W , Sobanski Piotr Z , Thomet Corina 
Published: July 2020

Abstract
Survival prospects in adults with congenital heart disease (CHD), although improved in recent decades, still remain below expectations for the general population. Patients and their loved ones benefit from preparation for both unexpected and predictable deaths, sometimes preceded by a prolonged period of declining health. Hence, advance care planning (ACP) is an integral part of comprehensive care for adults with CHD. This position paper summarizes evidence regarding benefits of and patients’ preferences for ACP and provides practical advice regarding the implementation of ACP processes within clinical adult CHD practice. We suggest that ACP be delivered as a structured process across different stages, with content dependent upon the anticipated disease progression. We acknowledge potential barriers to initiate ACP discussions and emphasize the importance of a sensitive and situation-specific communication style. Conclusions presented in this article reflect agreed expert opinions and include both patient and provider perspectives.
Ubiquilin-2 differentially regulates polyglutamine disease proteins
Authors: Gerson Julia E , Safren Nathaniel , Fischer Svetlana , Patel Ronak , Crowley Emily V , Welday Jacqueline P , Windle Alexandra K , Barmada Sami , Paulson Henry L , Sharkey Lisa M 
Published: July 2020

Abstract
Divergent protein context helps explain why polyglutamine expansion diseases differ clinically and pathologically. This heterogeneity may also extend to how polyglutamine disease proteins are handled by cellular pathways of proteostasis. Studies suggest, for example, that the ubiquitin-proteasome shuttle protein Ubiquilin-2 (UBQLN2) selectively interacts with specific polyglutamine disease proteins. Here we employ cellular models, primary neurons and mouse models to investigate the potential differential regulation by UBQLN2 of two polyglutamine disease proteins, huntingtin (HTT) and ataxin-3 (ATXN3). In cells, overexpressed UBQLN2 selectively lowered levels of full-length pathogenic HTT but not of HTT exon 1 fragment or full-length ATXN3. Consistent with these results, UBQLN2 specifically reduced accumulation of aggregated mutant HTT but not mutant ATXN3 in mouse models of Huntington’s disease (HD) and spinocerebellar ataxia type 3 (SCA3), respectively. Normally a cytoplasmic protein, UBQLN2 translocated to the nuclei of neurons in HD mice but not in SCA3 mice. Remarkably, instead of reducing the accumulation of nuclear mutant ATXN3, UBQLN2 induced an accumulation of cytoplasmic ATXN3 aggregates in neurons of SCA3 mice. Together these results reveal a selective action of UBQLN2 toward polyglutamine disease proteins, indicating that polyglutamine expansion alone is insufficient to promote UBQLN2-mediated clearance of this class of disease proteins. Additional factors, including nuclear translocation of UBQLN2, may facilitate its action to clear intranuclear, aggregated disease proteins like HTT.
A systematic literature review of automatic Alzheimer’s disease detection from speech and language
Authors: Petti Ulla , Baker Simon , Korhonen Anna 
Published: July 2020

AbstractObjectiveIn recent years numerous studies have achieved promising results in Alzheimer’s Disease (AD) detection using automatic language processing. We systematically review these articles to understand the effectiveness of this approach, identify any issues and report the main findings that can guide further research.Materials and MethodsWe searched PubMed, Ovid, and Web of Science for articles published in English between 2013 and 2019. We performed a systematic literature review to answer 5 key questions: (1) What were the characteristics of participant groups? (2) What language data were collected? (3) What features of speech and language were the most informative? (4) What methods were used to classify between groups? (5) What classification performance was achieved?Results and DiscussionWe identified 33 eligible studies and 5 main findings: participants’ demographic variables (especially age ) were often unbalanced between AD and control group; spontaneous speech data were collected most often; informative language features were related to word retrieval and semantic, syntactic, and acoustic impairment; neural nets, support vector machines, and decision trees performed well in AD detection, and support vector machines and decision trees performed well in decline detection; and average classification accuracy was 89% in AD and 82% in mild cognitive impairment detection versus healthy control groups.ConclusionThe systematic literature review supported the argument that language and speech could successfully be used to detect dementia automatically. Future studies should aim for larger and more balanced datasets, combine data collection methods and the type of information analyzed, focus on the early stages of the disease, and report performance using standardized metrics.
Single-Laboratory Validation of a Multi-residue Method for Simultaneous Analysis of Multi-class Pesticides in Turmeric by Liquid Chromatography Tandem Mass Spectrometry
Authors: Ghosh Bappa , Bhattacharyya Arijita , Hingmire Sandip , Aher Pushpa , Zende Pradnya , Banerjee Kaushik 
Published: July 2020

Abstract

Background
For years, turmeric has been used in several cuisines worldwide because of its proven health benefits. However, as its cultivation often involves applications of polar and semi-polar pesticides, their residues might cause health hazards to consumers. The dearth of a validated LC-MS/MS method for the residue analysis of these pesticides in turmeric has warranted the present study.

Objective
The aim was to develop and validate a multi-residue method for simultaneous determination of multi-class pesticides in turmeric (both rhizome and powder) by LC-MS/MS.

Method
Both the rhizome and powder samples (1 kg) were soaked in water for 30 min, followed by homogenization. Each homogenate (2 g) was mixed with 10 mL water, and extracted with acetonitrile (10 mL) in the presence of acetic acid and NaCl. The extract was cleaned by using dispersive solid phase extraction (dSPE) with graphitized carbon (5 mg/mL) sorbent. The cleaned extract was measured by LC-MS/MS with a runtime of 20 min. The method was validated on 211 multi-class pesticides.

Results
The method performance was satisfactory at 10 ng/g and higher levels, in compliance with the SANTE/12682/2019 guidelines. The dSPE cleanup was effective in minimizing the matrix effects. The use of matrix-matched calibrations specific for turmeric powder and rhizome corrected all recoveries within the satisfactory range of 70–120%. The precision -RSDs were &lt;20% for all test pesticides. The Horwitz ratio and measurement uncertainty results were satisfactory as well.

Conclusions
As the method was convenient, selective, accurate, and repeatable, it is recommended for regulatory and commercial testing purposes.

Highlights
For the first time, this study reports a validated LC-MS/MS method for the multi-residue analysis of pesticides in turmeric. The method provided a high throughput analysis of multi-class pesticides in turmeric rhizome and powder matrices with satisfactory selectivity, sensitivity, accuracy, and precision. The method performance satisfied the requirements of the SANTE/12682/2019 guidelines, and the method sensitivity complied with the EU-MRL requirements.
Nuclear accumulation of ZFP36L1 is cell cycle-dependent and determined by a C-terminal serine-rich cluster
Authors: Matsuura Yuki , Noguchi Aya , Sakai Shunsuke , Yokota Naoto , Kawahara Hiroyuki 
Published: July 2020

Abstract
ZFP36L1 is an RNA-binding protein responsible for mRNA decay in the cytoplasm. ZFP36L1 has also been suggested as a nuclear-cytoplasmic shuttling protein because it contains a potential nuclear localization signal and a nuclear export signal. However, it remains unclear how the nuclear localization of ZFP36L1 is controlled. In this study, we provide evidence that the nuclear accumulation of ZFP36L1 protein is modulated in a cell cycle-dependent manner. ZFP36L1 protein accumulation in fractionated nuclei was particularly prominent in cells arrested at G1-/S-phase boundary, while it was downregulated in S-phase cells, and eventually disappeared in G2-phase nuclei. Moreover, forced nuclear targeting of ZFP36L1 revealed marked downregulation of this protein in S- and G2-phase cells, suggesting that ZFP36L1 can be eliminated in the nucleus. The C-terminal serine-rich cluster of ZFP36L1 is critical for the regulation of its nuclear accumulation because truncation of this probable disordered region enhanced the nuclear localization of ZFP36L1, increased its stability and abolished its cell cycle-dependent fluctuations. These findings provide the first hints to the question of how ZFP36L1 nuclear accumulation is controlled during the course of the cell cycle.
Filtering of a Ricker wavelet induced by anelastic seismic wave propagation and reflection
Authors: Ker Stephan , Le Gonidec Yves 
Published: July 2020

AbstractA varying Q factor with depth induces modifications of seismic wave features due to anelastic propagation but also reflections at the discontinuities. Standard signal analysis methods often neglect the reflection contribution when assessing Q values from seismic data. We have developed an analytical quantification of the cumulative effects of both the propagation and reflection contributions by considering Kjartansson's model and a seismic plane wave at normal incidence on a step-like discontinuity. We show that the cumulative effects are equivalent to a frequency filter characterised by a bandform and phase that both depend on the ratio between the elastic and anelastic contrasts. When considering this filter applied to a Ricker wavelet, we establish an analytical expression of the peak-frequency attribute as a function of propagation and reflection properties. We demonstrate that this seismic attribute depends on the anelastic contrast, which cannot be neglected when assessing Q factors: the error in Q estimate is not linearly dependent on the anelastic contrast and we establish an analytical expression for the case where this contrast is weak. An unexpected phenomenon for a step-like interface is an increase in the peak frequency that is observed when the anelastic and elastic contrasts have opposite signs, with a constraint on the anelastic propagation properties. This behaviour allows for assessment of the elastic and anelastic parameters.
The value of asymmetry: how polarity proteins determine plant growth and morphology
Authors: Wallner Eva-Sophie 
Published: July 2020

AbstractCell polarity is indispensable for forming complex multicellular organisms. Proteins that polarize at specific plasma membrane domains can either serve as scaffolds for effectors or coordinate intercellular communication and transport. Here, I give an overview of polarity protein complexes and their fundamental importance for plant development, and summarize novel mechanistic insights into their molecular networks. Examples are presented for proteins that polarize at specific plasma membrane domains to orient cell division planes, alter cell fate progression, control transport, direct cell growth, read global polarity axes, or integrate external stimuli into plant growth. The recent advances in characterizing protein polarity during plant development enable a better understanding of coordinated plant growth and open up intriguing paths that could provide a means to modulate plant morphology and adaptability in the future.