bluuebunny/crossref_metadata_2025_split huggingface dataset:
Results of an early second PCR test performed on SARS-CoV-2 positive patients may support risk assessment for severe COVID-19
Authors: Mizrahi Barak , Bivas-Benita Maytal , Kalkstein Nir , Akiva Pinchas , Yanover Chen , Yehezkelli Yoav , Kessler Yoav , Alon Sharon Hermoni , Rubin Eitan , Chodick Gabriel 
Published: October 2021

AbstractIdentifying patients at increased risk for severe COVID-19 is of high priority during the pandemic as it could affect clinical management and shape public health guidelines. In this study we assessed whether a second PCR test conducted 2–7 days after a SARS-CoV-2 positive test could identify patients at risk for severe illness. Analysis of a nationwide electronic health records data of 1683 SARS-CoV-2 positive individuals indicated that a second negative PCR test result was associated with lower risk for severe illness compared to a positive result. This association was seen across different age groups and clinical settings. More importantly, it was not limited to recovering patients but also observed in patients who still had evidence of COVID-19 as determined by a subsequent positive PCR test. Our study suggests that an early second PCR test may be used as a supportive risk-assessment tool to improve disease management and patient care.
Clinical validation of automated and rapid mariPOC SARS-CoV-2 antigen test
Authors: Koskinen Juha M. , Antikainen Petri , Hotakainen Kristina , Haveri Anu , Ikonen Niina , Savolainen-Kopra Carita , Sundström Kati , Koskinen Janne O. 
Published: October 2021

AbstractCOVID-19 diagnostics was quickly ramped up worldwide early 2020 based on the detection of viral RNA. However, based on the scientific knowledge for pre-existing coronaviruses, it was expected that the SARS-CoV-2 RNA will be detected from symptomatic and at significant rates also from asymptomatic individuals due to persistence of non-infectious RNA. To increase the efficacy of diagnostics, surveillance, screening and pandemic control, rapid methods, such as antigen tests, are needed for decentralized testing and to assess infectiousness. A novel automated mariPOC SARS-CoV-2 test was developed for the detection of conserved structural viral nucleocapsid proteins. The test utilizes sophisticated optical laser technology for two-photon excitation and individual detection of immunoassay solid-phase particles. We validated the new method against qRT-PCR. Sensitivity of the test was 100.0% (13/13) directly from nasopharyngeal swab specimens and 84.4% (38/45) from swab specimens in undefined transport mediums. Specificity of the test was 100.0% (201/201). The test's limit of detection was 2.7 TCID50/test. It showed no cross-reactions. Our study shows that the new test can detect infectious individuals already in 20 min with clinical sensitivity close to qRT-PCR. The mariPOC is a versatile platform for syndromic testing and for high capacity infection control screening of infectious individuals.
Mucoviscidose: Quand les bactéries coopèrent pour mieux régner
Authors: Dorado Doncel Romane , Larcher Philéas , Schmitter Céline , Zouaghi Sarah 
Published: October 2021

Le dossier que nous présentons a été rédigé par les étudiantes et étudiants de Master 1 de Biologie de l’École Normale Supérieure de Lyon à l’issue de l’UE Microbiologie Moléculaire et Structurale (2020-2021).
Le Master de Biologie de l’ENS de Lyon accueille chaque année environ 40 étudiants en M1 et en M2 et propose une formation de haut niveau à la recherche en biosciences. Chaque étudiant y construit son parcours à la carte, en choisissant ses options parmi un large panel de modules, favorisant ainsi une approche pluridisciplinaire des sciences du vivant, et cela en relation étroite avec les laboratoires de recherche du tissu local, national et international.
En participant à diverses activités scientifiques liées aux UE de leur formation, les étudiants préparent également l’obtention du Diplôme de l’ENS de Lyon, qui valide leur scolarité à l’ENS. La rédaction du présent dossier, qui vise à transmettre de façon claire les messages issus d’une sélection d’articles scientifiques publiés récemment dans le domaine de la microbiologie, constitue l’une de ces activités connexes proposées aux étudiants.
The human olfactory bulb processes odor valence representation and cues motor avoidance behavior
Authors: Iravani Behzad , Schaefer Martin , Wilson Donald A. , Arshamian Artin , Lundström Johan N. 
Published: October 2021

SignificanceWhether an odor's perceived valence induces an approach response or triggers avoidance is critical for survival, and yet little is known about the neural mechanisms supporting this decision. Using electrophysiological measures from the human olfactory bulb (OB), the first processing stage of the olfactory system, and measures of full-body movement, we provide evidence that this process is initiated in the human OB. We demonstrate that odor valence is associated with both gamma and beta activity in the OB. Furthermore, we show that unpleasant odors have privileged temporal OB access, as indicated by early beta activity that is linked to a preparatory neural motor response in the motor cortex, which, in turn, is associated behaviorally with a fast full-body avoidance response.
Twisted distorted wave Born approximation as a new tool to investigate collisional processes
Authors: Singh Prithvi , Champion Christophe , Sharma Ram K 
Published: October 2021

Abstract
In this work, we report on triply differential ionization cross sections (e,2e) for atomic and molecular targets, namely, Ar(3p), Kr(4p), Xe(5p) and H2 impacted by twisted electron beams. The calculations were performed within the distorted wave Born approximation by using twisted and distorted waves for describing the incident and outgoing electrons, respectively. We found that the triply differential cross sections were strongly influenced by both the opening angle θ

p
and the orbital angular momentum OAM number m. Comparisons with experiments as well as existing results were reported.
Predicted stable high-pressure phases of copper-nitrogen compounds
Authors: Zhou Yuting , Jiang Xingxing , Zheng Yueshao , Xie Sheng-Yi , Feng Yexin , Chen Keqiu 
Published: October 2021

Abstract
The nitrogen-rich compounds are promising candidates for high-energy-density applications, owing to the large difference in the bonding energy between triple and single/double nitrogen bonds. The exploration of stable copper–nitrogen (Cu–N) compounds with high-energy-density has been challenging for a long time. Recently, through a combination of high temperatures and pressures, a new copper diazenide compound (P63/mmc-CuN2) has been synthesized (Binns et al 2019 J. Phys. Chem. Lett.
10 1109–1114). But the pressure-composition phase diagram of Cu–N compounds at different temperatures is still highly unclear. Here, by combining first-principles calculations with crystal structure prediction method, the Cu–N compounds with different stoichiometric ratios were searched within the pressure range of 0–150 GPa. Four Cu–N compounds are predicted to be thermodynamically stable at high pressures, Pnnm-CuN2, two CuN3 compounds with the P-1 space group (named as I-CuN3 and II-CuN3) and P21/m-CuN5 containing cyclo-N5
−. Finite temperature effects (vibrational energies) play a key role in stabilizing experimentally synthesized P63/mmc-CuN2 at ∼55 GPa, compared to our predicted Pnnm-CuN2. These new Cu–N compounds show great promise for potential applications as high-energy-density materials with the energy densities of 1.57–2.74 kJ g−1.
Magnetic field driven phase transitions in EuTiO3
Authors: Pappas P , Calamiotou M , Polentarutti M , Bais G , Bussmann-Holder A , Liarokapis E 
Published: October 2021

Abstract
The influence of an external static magnetic field (up to 480 mT) on the structural properties of EuTiO3 (ETO) polycrystalline samples was examined by powder XRD at the Elettra synchrotron facilities in the temperature range 100–300 K. While the cubic to tetragonal structural phase transition temperature in this magnetic field range remains almost unaffected, significant lattice effects appear at two characteristic temperatures (∼200 K and ∼250 K), which become more pronounced at a critical threshold field. At ∼200 K a change in the sign of magnetostriction is detected attributed to a modification of the local magnetic properties from intrinsic ferromagnetism to intrinsic antiferromagnetism. These data are a clear indication that strong spin–lattice interactions govern also the high temperature phase of ETO and trigger the appearance of magnetic domain formation and phase transitions.
Lattice dynamics of zircon-type NdVO4 and scheelite-type PrVO4 under high-pressure
Authors: Marqueño T , Pellicer-Porres J , Errandonea D , Santamaria-Perez D , Martinez-Garcia D , Rodríguez-Hernández P , Muñoz A , Nieves-Pérez I , Achary S N , Bettinelli M 
Published: October 2021

Abstract
Zircon-type NdVO4 and scheelite-type PrVO4 have been studied by means of Raman spectroscopy up to approximately 20 GPa. In the first compound, zircon-scheelite and scheelite-fergusonite phase transitions are reported at 6.4(3) and 19.6(4) GPa, respectively. In the case of scheelite-type PrVO4, a reversible phase transition to a PbWO4-III structure is observed at 16.8(5) GPa. In both cases, a scheelite-type structure is recovered in a metastable state at low pressures. The pressure evolution of the Raman modes is also reported. Our experimental findings are supported by ab initio calculations, which allowed us to discuss the role of mechanic and dynamical instabilities in the phase transition mechanisms.
Design of high-quality reflectors for vertical III–V nanowire lasers on Si
Authors: Zhang Xin , Yang Hui , Zhang Yunyan , Liu Huiyun 
Published: October 2021

Abstract
Nanowires (NWs) with a unique one-dimensional structure can monolithically integrate high-quality III–V semiconductors onto Si platform, which is highly promising to build lasers for Si photonics. However, the lasing from vertically-standing NWs on silicon is much more difficult to achieve compared with NWs broken off from substrates, causing significant challenges in the integration. Here, the challenge of achieving vertically-standing NW lasers is systematically analysed with III–V materials, e.g. GaAs(P) and InAs(P). The poor optical reflectivity at the NW/Si interface results severe optical field leakage to the substrate, and the commonly used SiO2 or Si2N3 dielectric mask at the interface can only improve it to ∼10%, which is the major obstacle for achieving low-threshold lasing. A NW super lattice distributed Bragg reflector is therefore proposed, which is able to greatly improve the reflectivity to >97%. This study provides a highly-feasible method to greatly improve the performance of vertically-standing NW lasers, which can boost the rapid development of Si photonics.
Enhancement of heavy ion track-etching in polyimide membranes with organic solvents
Authors: Froehlich Kristina , Scheuerlein Martin Christoph , Ali Mubarak , Nasir Saima , Ensinger Wolfgang 
Published: October 2021

Abstract
The effect of organic solvents on the ion track-etching of polyimide (PI) membranes is studied to enhance the nanopore fabrication process and the control over pore diameter growth. To this end, two approaches are employed to investigate the influence of organic solvents on the nanopore fabrication in PI membranes. In the first approach, the heavy ion irradiated PI samples are pretreated with organic solvents and then chemically etched with sodium hypochlorite (NaOCl) solution, resulting up to ∼4.4 times larger pore size compared to untreated ones. The second approach is based on a single-step track-etching process where the etchant (NaOCl) solution contains varying amounts of organic solvent (by vol%). The experimental data shows that a significant increase in both the bulk-etch and track-etch rates is observed by using the etchant mixture, which leads to ∼47% decrease in the nanopore fabrication time. This enhancement of nanopore fabrication process in PI membranes would open up new opportunities for their implementation in various potential applications.
Simulations of positive streamers in air in different electric fields: steady motion of solitary streamer heads and the stability field
Authors: Francisco Hani , Teunissen Jannis , Bagheri Behnaz , Ebert Ute 
Published: October 2021

Abstract
We simulate and characterize positive streamers in ambient air in homogeneous background electric fields from 4.5 to 26 kV cm−1 in a 4 cm gap. They can accelerate or decelerate depending on the background electric field. Many experiments have shown that a streamer keeps propagating in a stable manner in the so-called stability field of 4.5 to 5 kV cm−1. Our fluid streamer simulations in STP air show that: (1) in a homogeneous field larger than 4.675 kV cm−1, a single streamer accelerates, and in a lower field, it decelerates and eventually stagnates with a small radius and very high field enhancement. (2) In a field of 4.675 kV cm−1, the streamer head propagates with an approximately constant velocity of 6.7 × 104 m s−1 and an optical radius of 55 μm over distances of several centimeters as a stable coherent structure. These values for the radius and velocity agree well with measurements of so-called minimal streamers. (3) Behind the uniformly translating streamer head, the channel conductivity decreases due to electron attachment and recombination, and the electric field returns to its background value about 1 cm behind the head. The propagation behavior of the solitary streamer agrees with the original definition of the stability field, which is the homogeneous field in which a streamer can propagate with a constant speed and shape.
Distorted mirror images organised by cuspoid and umbilic caustics
Authors: Berry M V 
Published: October 2021

Abstract
The anatomy of the distorted and topologically disrupted images of an extended object after reflection by curved mirrors, and of their refraction analogues, e.g. in gravitational lensing, is determined by the caustic surfaces enveloping the ray family issuing from each point of the object. Simulations are presented of reflections of the same object when organised by each of the five caustics (elementary catastrophes) that are stable in three-dimensional space: the fold, cusp, swallowtail, elliptic and hyperbolic umbilic catastrophes. The object is a picture of a face, whose familiar features make the image distortions and disruptions easier to understand. An important distinction is between mirrors curved in one direction and those curved in two.
Autophagy deficiency boosts the production of kojic acid in the filamentous fungus Aspergillus oryzae
Authors: Chen Junlin , Arioka Manabu 
Published: October 2021

ABSTRACT
We found that the expression of genes involved in kojic acid (KA) biosynthesis, kojA, kojR, and kojT, was highly elevated in the Aspergillus oryzae autophagy-deficient mutants. In agreement, KA production was much increased in these mutants. Nuclear translocation of KojR, a transcription factor, was observed in the autophagy mutants before they were starved, explaining why KA production was boosted.
Rediscover: an R package to identify mutually exclusive mutations
Authors: Ferrer-Bonsoms Juan A , Jareno Laura , Rubio Angel 
Published: October 2021

Abstract

Motivation
Discover is an algorithm developed to identify mutually exclusive genomic events. Its main contribution is a statistical analysis based on the Poisson–Binomial (PB) distribution to take into account the mutation rate of genes and samples. Discover is very effective for identifying mutually exclusive mutations at the expense of speed in large datasets: the PB is computationally costly to estimate, and checking all the potential mutually exclusive alterations requires millions of tests.

Results
We have implemented a new version of the package called Rediscover that implements exact and approximate computations of the PB. Rediscover exact implementation is slightly faster than Discover for large and medium-sized datasets. The approximation is 100–1000 times faster for them making it possible to get results in less than a minute with a standard desktop. The memory footprint is also smaller in Rediscover. The new package is available at CRAN and provides some functions to integrate its usage with other R packages such as maftools and TCGAbiolinks.

Availability and implementation
Rediscover is available at CRAN (https://cran.r-project.org/web/packages/Rediscover/index.html).

Supplementary information
Supplementary data are available at Bioinformatics online.
Inequality in Exposure to Crime, Social Disorganization and Collective Efficacy: Evidence from Greater Manchester, United Kingdom
Authors: Lymperopoulou Kitty , Bannister Jon , Krzemieniewska-Nandwani Karolina 
Published: October 2021

Abstract
This paper assesses the relevance of social disorganization and collective efficacy in accounting for neighbourhood inequalities in the exposure to crime. Specifically, it questions the potential of community and voluntary organizations to enhance informal social control and reduce exposure to crime. It utilizes calls-for-service (incident) data for Greater Manchester (UK) and a Bayesian spatio-temporal modelling approach. Contrary to expectations, the research finds that measures of social disorganization (concentrated disadvantage aside) and collective efficacy hold a limited effect on neighbourhood exposure to crime. We discuss the implications of these findings for criminological inquiry and theoretical development, highlighting the necessity of such endeavour to account for the national political-economy and welfare regime of research settings
1023 An Audit of The Prevalence of Frailty and The Impact on Surgical Management and Resource Use, For Vascular Inpatients Using the National Vascular Registry (NVR) Frailty Classifications
Authors: Hitchman L , Palmer J , Sethi S , Chetter I 
Published: October 2021

Abstract

Aim
To determine if the NVR frailty score was being routinely collected on all relevant vascular patients on admission, identify the prevalence of frailty in vascular inpatients and determine if frailty was associated with a higher mortality and morbidity.

Method
A prospective audit of consecutive patients admitted onto the vascular ward who were eligible for inclusion on the NVR. Data was collected from electronic patient records and paper case notes between November 2019 and February 2020. The primary outcome was completeness of frailty assessment. Secondary outcomes were prevalence of frailty and mortality and morbidity associated with frailty score.

Results
Frailty status was documented in 65% of patients. 43% (28/65) were assessed to be frail. The 30-day mortality rate was 1.53% (1/65). 26.15% (17/65) had one or more complication. The commonest complications were graft occlusions, acute kidney injury, hospital acquired pneumonia and groin infections. 93.84% (61/65) were discharged home. There was no correlation between frailty and number of post-operative complications (p = 0.394), length of stay (p = 0.171) or mortality (p = 0.371).

Conclusions
This audit found frailty assessment is poorly assessed and the current NVR frailty classification did not correlate to increase mortality or morbidity in this patient cohort.
1087 Establishing Guidelines for VTE Prophylaxis for Acute ENT Admissions
Authors: Wallace J , Hepburn K , O'Hanlon J , Davis S 
Published: October 2021

Abstract

Aim
VTE prophylaxis is a vital aspect of patient safety. The decision whether to offer pharmacological thromboprophylaxis is a balance of risk versus benefit. There is a low incidence of VTE in ENT patients, admissions are often short and active bleeding on admission is not uncommon (epistaxis patients, already on anticoagulation are particularly difficult to manage}. There are no clear, specialty specific guidelines to assist in these frequently encountered endeavours.

Method
The number of emergency ENT admissions who had a documented VTE during admission or in the 28 days following was used to calculate the incidence of VTE in acute admissions. An audit of VTE prophylaxis and documentation was also conducted using 20 admissions over 24 hours.

Results
Incidence was 0.12%. 75% had a documented VTE risk assessment. Only 50% patients were prescribed chemical and mechanical thromboprophylaxis. 0% had appropriately documented that the patient did not require thromboprophylaxis on the drug chart (as per trust guidelines).

Conclusions
The results showed that both documentation and prescribing related to VTE prevention were poor. By highlighting the low incidence amongst this patient group, we were able to establish clearer guidance for VTE prophylaxis in acute ENT admissions and a protocol to standardise the management of anticoagulation in actively bleeding epistaxis patients.
1229 Standardising Consent for General Surgical Patients
Authors: Mamun M , Charles E 
Published: October 2021

Abstract

Aim
Informed consent requires all material risks to be discussed, as per Montgomery vs Lanarkshire 2015. This audit was based on the latest RCS England guidelines on consenting patients. We aimed to assess our adherence and to introduce standardised procedure-specific consent stickers to ensure the highest standards of care, which were reproducible.

Method
We undertook two retrospective case note reviews of patients undergoing emergency and elective general surgery procedures from 01/01-15/06 and 01/10-30/11 in 2020. RCS Good Surgical Practice 3.5.1 “Consent” details the standards for this audit. We included patients undergoing appendicectomy, cholecystectomy, incision and drainage and hernia repair (inguinal, umbilical, and incisional). We did not audit laparotomy due to variability in procedural risks precluding a specific sticker and we excluded patients unable to give consent.

Results
Our initial audit of 82 patients highlighted the variability between practitioners in the material risk discussion. Different patients undergoing the same procedures were being consented differently with significant omissions. We designed procedure specific-consent stickers to be used when consenting to address this imbalance and made these stickers available on surgical wards. A re-audit of 50 patients showed increase from 41% to 88% in documentation of material risks. While only 34% of the audited consent forms featured the stickers, those forms that did have the stickers on had 100% material risk documentation.

Conclusions
We saw an improvement in material risk discussion by implementing procedure-specific consent stickers. This supports the growing need for standardising consent across General Surgery to reduce variability. We will next aim to design laparotomy stickers.