bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early 21st Century cyclone climatology: a 3D perspective.Basic Characterization
Authors: Lakkis Susan G. , Canziani Pablo O. , Rodriguez Joaquín O. , Yuchechen Adrián E. , O'Neill Alan , Albers Kim H. , Hodges Kevin 
Published: February 2021

AbstractExtra‐tropical cyclones are a relevant feature in the climate at middle and high latitudes. Despite their importance, most studies typically focus only on cyclones identified at a single atmospheric level and on events close to the surface. This paper provides a new perspective on the Southern Hemisphere (SH) cyclone events based on the multilevel cyclone tracking algorithm STACKER. The algorithm, using relative vorticity, detects the raw tracks at single levels and objectively combines them to provide the 3D events and their evolutionary timeline. As a result, a 3D cyclone climatology, based on ECMWF Reanalysis ERA‐I data from 12 pressure levels in the troposphere and lowermost stratosphere is presented. To the best of our knowledge, this is the first analysis carried out throughout the troposphere and the lowermost extratropical/subpolar stratosphere in order to give a comprehensive picture of the cyclone events as physical entities throughout their lifetime. Cyclone properties analysed are track densities, translational velocity, vorticity and lifetimes. For the subtropical and extra‐tropical SH, results support many previous ideas about cyclone characteristics, but new insights are also obtained. A total of 58,231 multilevel cyclone events lasting at least 2 days were detected, with vertical structures spanning two or more levels. This means an average of 303 cyclone events of all types per month, between 2001 and 2017, disregarding seasonality. Results show that cyclones are most frequently detected at the lowest levels of 925 and 700 hPa. By considering that cyclonic systems can be grouped into families according to their vertical extent, results per month on average show that shallow systems are the most frequent events with approximately 248 systems detected, followed by 43 intermediary and 11 deep events. Shallow and deep systems have a large percentage of events with genesis at 925 and 700 hPa. Density statistics show that shallow events are present at all latitude ranges mostly poleward of 30°S with high‐ and medium‐intensities, while intermediate ones are mostly restricted to mid‐latitudes and deep events are mostly confined to sub‐polar and polar latitudes. Cyclones over Antarctica seem to be mostly intermediary and deep cyclones, with longer lifetimes and lower velocities.
Multi‐chemical analysis combined with chemometrics to characterize PDO and PGI Italian apples
Authors: Aguzzoni Agnese , Bassi Michele , Pignotti Emanuela , Robatscher Peter , Scandellari Francesca , Tirler Werner , Tagliavini Massimo 
Published: February 2021

AbstractBACKGROUNDThe use of PDO (protected designation of origin) and PGI (protected geographical indication) labels allows to protect and promote agricultural products characterized by unique features related to the place of origin and traditional know‐how. However, the presence of non‐authentic products in the market represents a fraud that can be tackled applying analytical techniques combined with chemometric analysis. In this study, we applied multi‐element and multi‐isotope analysis to characterize PDO and PGI apples cultivated in northern Italy, comparing them with Italian apples without labels of geographical indications.RESULTSThe multi‐element and multi‐isotope approach allowed to characterize the apples cultivated in northern Italy. Despite a significant effect of the sampling sites on the apple composition, the comparison of the multi‐chemical fingerprint of the apples significantly varied among cultivation areas. Results of this characterization were used to classify samples according to their cultivation area applying a linear discriminant analysis (LDA). Outputs of the LDA showed that correct sample classification can be successfully achieved (balanced accuracy > 96%). Moreover, using a selection of variables, it was possible to correctly classify samples also at regional level.CONCLUSIONThe presented evidences indicate that the multi‐element and multi‐isotope fingerprint can be successfully applied to traceability studies. The combination of this characterization with chemometric tools allows the classification of Italian apples based on their origin both on a national and regional scale. This approach represents an interesting tool to enhance and protect PDO and PGI Italian products.© 2021 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Comprehensive two‐dimensional gas chromatography as a boosting technology in food‐omic investigations
Authors: Stilo Federico , Bicchi Carlo , Reichenbach Stephen E. , Cordero Chiara 
Published: February 2021

AbstractThis review focuses on the role that comprehensive two‐dimensional gas chromatography can play within the investigation workflows of food‐omics and related disciplines and subdisciplines, including food metabolomics, nutrimetabolomics, sensomics, and food safety. After a short introductory survey, discussing the intriguing context of system biology and integrationist approaches of investigation, the concepts of analytical dimensions and the key characteristics of comprehensive two‐dimensional gas chromatography are introduced. Through a selection of relevant examples, the boosting role of comprehensive two‐dimensional gas chromatography within food‐omics is described, providing to the reader evidence of how comprehensive multidimensional separations based platforms have introduced new concepts and tools in the analytical measurement of complex biological samples.
PolyBoost: An enhanced genomic variant classifier using extreme gradient boosting
Authors: Parente Daniel J. 
Published: February 2021

AbstractPurposeHuman exome sequences contain 15,000–20,000 variants but many variants have unknown clinical impact. In silico predictive classifiers are recognized by the American College of Medical Genetics as a resource for interpreting these “variants of uncertain significance.” Many in silico classifiers have been developed, of which PolyPhen‐2 is highly successful and widely used. PolyPhen‐2 uses a naïve Bayes model to synthesize sequence, structural and genomic information. I investigated whether predictive performance could be improved by replacing PolyPhen‐2′s naïve Bayes model with alternative machine learning methods.Experimental designClassifiers using the PolyPhen‐2 feature set were retrained using extreme gradient boosting (XGBoost), random forests, artificial neural networks, and support vector machines. Classifiers were externally validated on “pathogenic” and “benign” ClinVar variants absent from the training datasets. Software is implemented in Python and is freely available athttps://github.com/djparente/polyboostand the Python Package Index (PyPI) under the BSD license.ResultsAn XGBoost‐based classifier—designated PolyBoost (PolyPhen‐2 Booster)—improves discriminative performance and calibration relative to PolyPhen‐2 in external validation on ClinVar.Conclusions and clinical relevancePolyBoost analyzes PolyPhen‐2 output and can be incorporated into existing bioinformatics workflows as a post‐analysis method to improve interpretation of clinical exome sequences obtained to identify monogenic disease.
Neutralizing antibodies targeting the SARS‐CoV‐2 receptor binding domain isolated from a naïve human antibody library
Authors: Bell Benjamin N. , Powell Abigail E. , Rodriguez Carlos , Cochran Jennifer R. , Kim Peter S. 
Published: February 2021

AbstractInfection with SARS‐CoV‐2 elicits robust antibody responses in some patients, with a majority of the response directed at the receptor binding domain (RBD) of the spike surface glycoprotein. Remarkably, many patient‐derived antibodies that potently inhibit viral infection harbor few to no mutations from the germline, suggesting that naïve antibody libraries are a viable means for discovery of novel SARS‐CoV‐2 neutralizing antibodies. Here, we used a yeast surface‐display library of human naïve antibodies to isolate and characterize three novel neutralizing antibodies that target the RBD: one that blocks interaction with angiotensin‐converting enzyme 2 (ACE2), the human receptor for SARS‐CoV‐2, and two that target other epitopes on the RBD. These three antibodies neutralized SARS‐CoV‐2 spike‐pseudotyped lentivirus with IC50 values as low as 60 ng/ml in vitro. Using a biolayer interferometry‐based binding competition assay, we determined that these antibodies have distinct but overlapping epitopes with antibodies elicited during natural COVID‐19 infection. Taken together, these analyses highlight how in vitro selection of naïve antibodies can mimic the humoral response in vivo, yielding neutralizing antibodies and various epitopes that can be effectively targeted on the SARS‐CoV‐2 RBD.
Estimating specific surface area: Incorporating the effect of surface roughness and probing molecule size
Authors: Ghanbarian Behzad , Hunt Allen G. , Bittelli Marco , Tuller Markus , Arthur Emmanuel 
Published: February 2021

AbstractThe pore–solid interface and its characteristics play a key role in chemical interactions between minerals in the solid soil matrix and the liquid in pore space and, consequently, solute transport in soils. Specific surface area (SSA), typically measured to characterize the pore–solid interface, depends not only on the particle size distribution (PSD) but also on particle shapes and surface roughness. In this note, we investigate the effects of surface roughness and probing molecule size on SSA estimation, use concepts from fractals, and theoretically estimate SSA from PSD and the water retention curve (WRC). The former is used to characterize the particle sizes and the latter to approximately quantify the pore–solid interface roughness by determining the surface fractal dimension. To evaluate our approach, we use five Washington and 21 Arizona soils for which both PSDs and WRCs were accurately measured over a wide range of particle sizes and matric potentials. Comparison with the experiments show that the proposed method estimates the SSA reasonably well, with RMSE = 16.8 and 30.1 m2 g–1 and average relative error = –56 and –35% for the Washington and Arizona datasets, respectively.
Do soil health tests match farmer experience? Assessing biological, physical, and chemical indicators in the Upper Midwest United States
Authors: O'Neill Brendan , Sprunger Christine D. , Robertson G. Philip 
Published: February 2021

AbstractSoil health testing provides an integrated assessment of biological, physical, and chemical attributes to inform the sustainable management of farm fields. However, it is unclear how tests reflect farmers’ own assessments of soil quality and agronomic performance, which may disproportionately influence farm management practices. We asked farmers in three regions of Michigan to identify three fields to compare their own assessments against soil health tests: a “best,” a “worst,” and a “non‐row crop” reference field. Each field was tested for soil aggregate stability, available water capacity, soil organic matter (SOM), mineralizable carbon (MinC), permanganate oxidizable carbon (POXC), pH, P, and K. We evaluated soil health scores using paired t tests to compare results from contrasting fields with farmers’ assessments of each field. Across all farms, the overall soil health test score for cropped fields was significantly higher on fields farmers rated as “Best.” This result was driven solely by physical and biological (including C) parameters; inorganic chemical tests did not distinguish among field types. On reference fields in all regions, biological parameters were consistently higher, but inorganic chemical and physical measures were not. The performance of soil C measures was inconsistent: SOM and MinC consistently detected significant differences between “Best” and “Worst” cropped fields, but POXC did not. Our results suggest that common soil health assays for physical and biological attributes generally align well with farmers’ assessments of their fields. That soil health tests match farmer experience reinforces the value of these tests as a meaningful guide for soil management decisions.
Synthesis, Crystal Structures and Properties of Polymorphic and Isomeric Nickel(II)thiocyanate Coordination Compounds with 3‐Bromopyridine as Coligand
Authors: Krebs Christoph , Ceglarska Magdalena , Näther Christian 
Published: February 2021

AbstractReaction of different molar ratios of Ni(NCS)2 and 3‐bromopyridine in water, methanol or acetonitrile leads to the formation of two polymorphs of composition Ni(NCS)2(3‐bromopyridine)4 (1‐I and 1‐II), as well as Ni(NCS)2(3‐bromopyridine)2(H2O)2 (2), Ni(NCS)2(3‐Bromopyridine)2(CH3OH)2 (3), Ni(NCS)2(3‐bromopyridine)2 ⋅ CH3CN (4) and Ni(NCS)2(3‐bromopyridine)2 (5). Compounds 1‐I, 1‐II, 2 and 3 consist of discrete octahedral complexes with terminal N‐bonded anionic ligands. In compound 4 the Ni cations are cis‐cis‐trans coordinated and linked into corrugated chains by pairs of μ‐1,3‐bridging thiocyanate anions. Solvent mediated conversion experiments prove that form 1‐I represents the thermodynamically stable polymorph at room temperature. TG‐DTA measurements reveal that upon heating compounds 1‐I, 1‐II, 2 and 3 lose their coligands stepwise and transform into the new crystalline phase 5 that can also be obtained from solution if the reaction is performed in n‐butanol. If the acetonitrile solvate molecules are removed from compound 4, it also transforms into 5. DC magnetic measurements for compound 4 show a maximum, which is indicative for antiferromagnetic ordering, whereas for compound 5 no magnetic ordering is observed. For both compounds, the ferromagnetic exchange constants were determined.
Mechanismen und Funktionen von bakteriellen AAA+­Entfaltungsmaschinen
Authors: Mogk Axel 
Published: February 2021

AbstractBacterial AAA+ proteins play crucial roles in proteostasis networks and ensure protein homeostasis during stress conditions. They function as ATP-dependent components of proteolytic complexes degrading misfolded proteins or as disaggregases reactivating aggregated proteins. AAA+ proteins generate an ATP-fueled threading force driving substrate unfolding and translocation. Their central functions in protein quality control qualify them as antibacterial drug target.
3D-Printed Flexible Penile Model Simulator for Plaque Incision and Graft for Peyronie's Disease
Authors: Miranda Alexandre 
Published: February 2021

Abstract

Introduction
Plaque incision and graft (PIG) is suggested for the treatment of significant Peyronie's disease (PD), but most surgeons perform very few PIG surgeries annually, and the number of PD cases requiring PIG is inadequate to maintain the necessary skills and completely master the procedure.

Aim
To develop and validate a new 3D-printed model of a curved penis and graft to simulate PIG surgery. This is the first PIG surgical training simulator described in the medical literature.

Methods
A 3D-printed model of the corpora cavernosa with a 60-degree curvature and an associated urethra was created using a flexible filament of thermoplastic polyurethane. Twenty-two urologists from Brazil were recruited to perform simulated surgery on the 3D model. The participants included 12 senior-level and 10 trainee-level urologists.

Main outcome measures
Evaluation of the device was based on a 15-item questionnaire using a 5-point Likert-type scale for each item.

Results
Each participant performed one simulated surgery with the 3D-printed model. All participants agreed that the simulation should be implemented into training programs. Participants ranked all content validity components ≥4.41 and all face validity components ≥3.83. The mean usability score was 4.25, and the overall experience scores were 4.75 (senior) and 5.0 (trainee).

Conclusion
Senior and trainee urologists evaluated this first reported simulated PIG training model for penile curvature correction as an acceptable tool for training and maintaining necessary PIG skills. This model may improve PIG training and surgeon skill, thereby improving patient safety and outcomes.
Female Sexual Dysfunction After Pelvic Fracture: A Comprehensive Review of the Literature
Authors: Walton Alice B. , Leinwand Gabriel Z. , Raheem Omer , Hellstrom Wayne J.G. , Brandes Steven B. , Benson Cooper R. 
Published: February 2021

ABSTRACTBackgroundFemale sexual dysfunction (FSD) after pelvic fracture (PFx) has garnered little attention in the urology literature.AimTo review and summarize the current evidence regarding female PFx-related sexual function.MethodsWe performed a systematic review in accordance with PRISMA guidelines, including PubMed, EMBASE, and MEDLINE. We included only English-language manuscripts and abstracts with sufficient data for inclusion. We used the search terms “female sexual dysfunction AND pelvic fracture,” “sexual dysfunction AND pelvic fracture,” and “female pelvic fracture AND sexual dysfunction.” A total of 177 articles were identified; 41 abstracts were reviewed; of which, 19 manuscripts were reviewed. Fifteen met inclusion criteria for analysis.OutcomesThe main outcome measures of this study are rates and types of female sexual dysfunction after pelvic fracture.RESULTSFSD is prevalent after PFx, with reported rates between 25% and 62%. Three studies used the validated Female Sexual Function Index. The other 12 used non-validated questionnaires or adapted quality-of-life questionnaires with specific questions regarding FSD. The most common complaints include difficulty with intercourse, dyspareunia, orgasmic dysfunction, genitourinary pain, decreased interest in intercourse, decreased satisfaction with intercourse, and pelvic floor dysfunction. Only 1 study addressed resolution of dysfunction (30 of 98 patients [30.4%]).Clinical ImplicationsFSD is prevalent and an under-recognized sequela of pelvic fracture. This requires future prospective study to better characterize sexual dysfunction and identify effective treatments in trauma survivors.Strength and LimitationsTo Increase awareness of FSD after pelvic trauma and the impact on the quality of life in trauma survivors. The current literature is limited by a lack of standardized assessment of FSD, limited follow-up, and minimal discussion of treatment options, in addition to the inherent bias of retrospective studies.CONCLUSIONSFSD after traumatic PFx is not uncommon, occurs mostly in young women, and can be morbid. FSD after PFx is underreported in the urology literature. Thus, all female PFx patients should be screened for FSD by validated questionnaires. The published literature offers little knowledge as to the epidemiology, evaluation, definition, and potential treatments of FSD after PFx. Prospective studies are needed to better understand female sexual function in trauma survivors and the potential methods for prevention and rehabilitation, all within the context of a multidisciplinary approach.
Objective screening for olfactory and gustatory dysfunction during the COVID‐19 pandemic: A prospective study in healthcare workers using self‐administered testing
Authors: Cao Austin C. , Nimmo Zachary M. , Mirza Natasha , Cohen Noam A. , Brody Robert M. , Doty Richard L. 
Published: February 2021

AbstractBackgroundSmell and taste loss are highly prevalent symptoms in coronavirus disease 2019 (COVID‐19), although few studies have employed objective measures to quantify these symptoms, especially dysgeusia. Reports of unrecognized anosmia in COVID‐19 patients suggests that self‐reported measures are insufficient for capturing patients with chemosensory dysfunction.ObjectivesThe purpose of this study was to quantify the impact of recent COVID‐19 infection on chemosensory function and demonstrate the use of at‐home objective smell and taste testing in an at‐risk population of healthcare workers.MethodsTwo hundred and fifty healthcare workers were screened for possible loss of smell and taste using online surveys. Self‐administered smell and taste tests were mailed to respondents meeting criteria for elevated risk of infection, and one‐month follow‐up surveys were completed.ResultsAmong subjects with prior SARS‐CoV‐2 infection, 73% reported symptoms of olfactory and/or gustatory dysfunction. Self‐reported smell and taste loss were both strong predictors of COVID‐19 positivity. Subjects with evidence of recent SARS‐CoV‐2 infection (<45 days) had significantly lower olfactory scores but equivalent gustatory scores compared to other subjects. There was a time‐dependent increase in smell scores but not in taste scores among subjects with prior infection and chemosensory symptoms. The overall infection rate was 4.4%, with 2.5% reported by PCR swab.ConclusionHealthcare workers with recent SARS‐CoV‐2 infection had reduced olfaction and normal gustation on self‐administered objective testing compared to those without infection. Rates of infection and chemosensory symptoms in our cohort of healthcare workers reflect those of the general public.
Evaluation of Interaction Between Emergency Medical System and Hospital Network During a Train Derailment in Milano
Authors: Faccincani Roberto , Stucchi Riccardo , Carlucci Michele , Sannicandro Riccardo , Formenti-Ujlaki George , Pascucci Federico , Montan Carl , Zoli Alberto , Picco Carlo , Fumagalli Roberto 
Published: February 2021

AbstractOn January 25, 2018 a 5-car train derailed in Pioltello, 10 kilometers North-East of Milano City. A standardized post-hoc form was distributed to the hospitals involved in the management of the victims and allowed for an evaluation of the response to the incident.The management of the incident by EMS (Emergency Medical System) was effective in terms of organization of the scene and distribution of the patients, although the time for the first severe patient to reach the closest appropriate hospital was very long (2 hours). This can be partially explained by the extrication time.None of the alerted hospitals exceeded their capacity, as patients were distributed carefully among the hospitals. The overall outcome was quite satisfactory; no deaths were reported except for those on scene. Some responding hospitals reported that there was an over-activation based on the services ultimately needed. However this is common in MCIs, as an over-activation is preferable to an under-estimation. To address this concern, as more data are available, activation should be scaled down based on a plan established prior to it; this mechanism of scaling down seems to have failed in this event.It is of note that the highest performing hospitals underwent recently to an educational program on MCI management.
RAMSEY’S COHEIRS
Authors: COLLA EUGENIO , ZAMBELLA DOMENICO 
Published: February 2021

AbstractWe use the model theoretic notion of coheir to give short proofs of old and new theorems in Ramsey Theory. As an illustration we start from Ramsey’s theorem itself. Then we prove Hindman’s theorem and the Hales–Jewett theorem. Finally, we prove two Ramsey theoretic principles that have among their consequences partition theorems due to Carlson and to Gowers.