bluuebunny/crossref_metadata_2025 huggingface dataset:
Advanced spectroscopic investigation of colour centres in LiF crystals irradiated with monochromatic hard x-rays
Authors: Vincenti M A , Montereali R M , Bonfigli F , Nichelatti E , Nigro V , Piccinini M , Koenig M , Mabey P , Rigon G , Dabrowski H J , Benkadoum Y , Mercere P , Da Silva P , Pikuz T , Ozaki N , Makarov S , Pikuz S , Albertazzi B
Published: February 2024

Nominally-pure lithium fluoride (LiF) crystals were irradiated with monochromatic hard x-rays of energy 5, 7, 9 and 12 keV at the METROLOGIE beamline of the SOLEIL synchrotron facility, in order to understand the role of the selected x-ray energy on their visible photoluminescence (PL) response, which is used for high spatial resolution 2D x-ray imaging detectors characterized by a wide dynamic range. At the energies of 7 and 12 keV the irradiations were performed at five different doses corresponding to five uniformly irradiated areas, while at 5 and 9 keV only two irradiations at two different doses were carried out. The doses were planned in a range between 4 and 1.4 × 103 Gy (10.5 mJ cm−3 to 3.7 J cm−3), depending on the x-ray energy. After irradiation at the energies of 7 and 12 keV, the spectrally-integrated visible PL intensity of the F2 and F3
+ colour centres (CCs) generated in the LiF crystals, carefully measured by fluorescence microscopy under blue excitation, exhibits a linear dependence on the irradiation dose in the investigated dose range. This linear behaviour was confirmed by the optical absorption spectra of the irradiated spots, which shows a similar linear behaviour for both the F2 and F3
+ CCs, as derived from their overlapping absorption band at around 450 nm. At the highest x-ray energy, the average concentrations of the radiation-induced F, F2 and F3
+ CCs were also estimated. The volume distributions of F2 defects in the crystals irradiated with 5 and 9 keV x-rays were reconstructed in 3D by measuring their PL signal using a confocal laser scanning microscope operating in fluorescence mode. On-going investigations are focusing on the results obtained through this z-scanning technique to explore the potential impact of absorption effects at the excitation laser wavelength.
Twist angle, strain, corrugation and moire unit cell in twisted bi-layer graphene
Authors: Pal Veer , Ajay
Published: February 2024

Knowledge of the internal configuration of carbon atoms inside a moire unit cell of twisted bi-layer graphene (TBG) would enhance the accuracy of many-body quantum mechanical calculations related to TBG. This work put forward a comprehensive theoretical study of moire pattern in TBG, supported with computational analysis; which seek a mechanism to determine the internal configuration of carbon atoms inside a moire unit cell of TBG. This study first time establishes that all twist angles are commensurate twist angles which produce perfectly periodic commensurate moire patterns of TBG. It is also first time established that strain appearing in moire patterns of TBG can occur purely due to intrinsic reasons. Taking some insight from available experimental data related to TBG systems and conventional bi-layer graphene systems, a mathematical model is also presented for corrugation in TBG. Finally we present an universal algorithm to determine the internal configuration of carbon atoms inside a moire unit cell of TBG, which is first of its kind.
Simulation and non-linear optimization of kinetic models for solid-state processes
Authors: Luciano Giorgio , Svoboda Roman
Published: February 2024

Numerical simulations and optimizations methods are increasingly used in the field of kinetic analysis of solid-state processes, such as the crystallization of glassy materials. The influence of the simulations accuracy (with the two main factors being the initial value of conversion rate and the density of points) on the kinetic distortions was tested for the major solid-state kinetic models: nucleation-growth Johnson–Mehl–Avrami model, nth order reaction model, autocatalyzed nth order reaction model, diffusion models, contracting cylinder and contracting sphere models. The simulations were performed using a self-developed software based on the LSODA initial-value-problem-solver; the evaluation of the changes in the shape of the kinetic peaks was done using a commercial software that utilizes a standardized multivariate kinetic analysis approach. The accuracy was found to be influenced mainly by initial value of conversion rate. For majority of the tested kinetic models, the simulation accuracy had negligible effect on the consequently determined values activation energy, pre-exponential factor, integrated area of the kinetic peaks, or the asymmetry-determining values of the models kinetic exponents. Significant influence of the simulation accuracy was observed for the models with active autocatalytic features, which were identified to be the main source of the deviations introduced and propagated through the simulation algorithm. Contrary to the previous research, the deviations of the simulated peaks shape cannot be associated solely with the positive asymmetry of the kinetic peaks.
An ultra-sensitive SARS-CoV-2 antigen optical biosensor based on angiotensin converting enzyme 2 (ACE-2) functionalized magnetic-fluorescent silica nanoparticles
Authors: Maulana Muhammad Yovinanda , Raissa Raissa , Nurrudin Ahmad , Andreani Agustina Sus , Angelina Marissa , Septiani Ni Luh Wulan , Yuliarto Brian , Jenie S N Aisyiyah
Published: February 2024

This work reports on the design and synthesis of an angiotensin-converting enzyme 2 (ACE-2) functionalized magnetic fluorescent silica nanoparticles (Fe-FSNP) as a biosensing platform to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigen. Iron oxide (Fe3O4) nanoparticles were synthesized via ultrasonic-assisted coprecipitation and then coated with fluorescent silica nanoparticles (FSNP) through the sol–gel method forming the Fe-FSNP samples. Silica obtained from local geothermal powerplant was used in this work and Rhodamine B was chosen as the incorporated fluorescent dye, hence this reports for the first time ACE-2 was immobilized on the natural silica surface. The Fe-FSNP nanoparticle consists of a 18–25 nm magnetic core and a silica shell with a thickness of 30 nm as confirmed from the transmission electron microscopy image. Successful surface functionalization of the Fe-FSNP with ACE-2 as bioreceptor was conducted through hydrosylilation reaction and confirmed through the Fourier transform infrared spectroscopy. The detection of SARS-Cov-2 antigen by Fe-FSNP/ACE2 was measured through the change in its maximum fluorescence intensity at 588 nm where fluorescence- quenching had occurred. The biosensing platform showed a rapid response at 30 min with a linear range of 10–6 to 10−2
μg ml–1. The magnetic-fluorescent properties of the nanoparticle enables an ultra-sensitive detection of SARS-Cov-2 antigen with the limit of detection as low as 2 fg ml–1.
Porous rod-shaped Fe2O3/Ag/BP: a novel substrate for highly sensitive SERS detection of persistent organic pollutants
Authors: Chen Hang , Han Caiqin , Zhang Le , Wu Ying
Published: February 2024

A surface enhanced Raman scattering (SERS) substrate of porous rod-shaped ferric oxide (Fe2O3) combined with silver nanoparticles (Ag NPs) and black phosphorus (Fe2O3/Ag/BP) was fabricated to detect the persistent organic pollutants (POPs) at low concentration. The organic pollutant Rhodamine 6G (R6G) was used as the probe molecule to study the performances of Fe2O3/Ag/BP, and 4-chlorobiphenyl (PCB-3) was the target of detection. The limit of detection (LOD) of R6G based on this novel SERS substrate Fe2O3/Ag/BP was as low as 1.0 × 10−15 M, which was five orders of magnitude lower than that of Fe2O3/Ag (10−10 M). The enhancement factor (EF) of Fe2O3/Ag/BP was 6.44 × 108, which was 3.1 times higher than that of porous rod-shaped Fe2O3/Ag (2.08 × 108). The Raman signal of R6G based on Fe2O3/Ag/BP had a good homogeneity, and the relative standard deviation (RSD) of Raman signal intensities of R6G at 1643 cm−1 was only 5.97%. Furthermore, the Fe2O3/Ag/BP substrate exhibited a recyclability through the photocatalytic degradation of R6G. The LOD of PCB-3 based on Fe2O3/Ag/BP was 10−9 M. Besides, Fe2O3/Ag/BP had a high SERS activity even it was kept in a centrifuge tube without requiring complicated treatment. These results highlight the potential application of Fe2O3/Ag/BP for ultra-trace detection of POPs in the environment.
Core–shell engineered g-C3N4 @ NaNbO3 for enhancing photocatalytic reduction of CO2
Authors: Wang Shuo , Yin Haotian , Wang Lei , Ding Jing , Zhang Jinfeng , Wan Hui , Guan Guofeng
Published: February 2024

Photocatalytic reduction of carbon dioxide is a technology that effectively utilizes CO2 and solar energy. Sodium niobate (NaNbO3) has received much attention in the field of photocatalysis due to its excellent photocatalytic properties. However, the application of NaNbO3 in the field of photocatalysis is still limited by poor reaction to visible light and easy recombination of photo-generated carriers. Heterojunction with g-C3N4 to construct core–shell structure can effectively improve the above problems. Combining the two can design a core–shell composite material that is beneficial for photocatalytic reduction of CO2. Herein, we prepared a core–shell heterojunction g-C3N4/NaNbO3 by uniformly impregnating urea on the surface of NaNbO3 chromium nanofibers with NaNbO3 nanofibers prepared by electrospinning as a catalyst carrier, and urea as a precursor of g-C3N4. The core–shell structure of g-C3N4/NaNbO3 was verified by a series of characterization methods such as XPS, XRD, and TEM. It was found that under the same conditions, the methanol yield of core–shell g-C3N4/NaNbO3 was 12.86 μmol·g−1·h−1, which is twice that of pure NaNbO3 (6.67 μmol·g−1·h−1). This article highlights an impregnation method to build core–shell structures for improved photocatalytic reduction of CO2.
Recovery of the spatially-variant deformations in dual-panel PET reconstructions using deep-learning
Authors: Raj Juhi , Millardet Maël , Krishnamoorthy Srilalan , Karp Joel S , Surti Suleman , Matej Samuel
Published: February 2024

Dual panel PET systems, such as Breast-PET (B-PET) scanner, exhibit strong asymmetric and anisotropic spatially-variant deformations in the reconstructed images due to the limited-angle data and strong depth of interaction effects for the oblique LORs inherent in such systems. In our previous work, we studied time-of-flight (TOF) effects and image-based spatially-variant PSF resolution models within dual-panel PET reconstruction to reduce these deformations. The application of PSF based models led to better and more uniform quantification of small lesions across the field of view (FOV). However, the ability of such a model to correct for PSF deformation is limited to small objects. On the other hand, large object deformations caused by the limited-angle reconstruction cannot be corrected with the PSF modeling alone. In this work, we investigate the ability of deep-learning (DL) networks to recover such strong spatially-variant image deformations using first simulated PSF deformations in image space of a generic dual panel PET system and then using simulated and acquired phantom reconstructions from dual panel B-PET system developed in our lab at University of Pennsylvania. For the studies using real B-PET data, the network was trained on the simulated synthetic data sets providing ground truth for objects resembling experimentally acquired phantoms on which the network deformation corrections were then tested. The synthetic and acquired limited-angle B-PET data were reconstructed using DIRECT-RAMLA reconstructions, which were then used as the network inputs. Our results demonstrate that DL approaches can significantly eliminate deformations of limited angle systems and improve their quantitative performance.
Validation of complex radiotherapy techniques using polymer gel dosimetry
Authors: Karger Christian P , Elter Alina , Dorsch Stefan , Mann Philipp , Pappas Evangelos , Oldham Mark
Published: February 2024

Modern radiotherapy delivers highly conformal dose distributions to irregularly shaped target volumes while sparing the surrounding normal tissue. Due to the complex planning and delivery techniques, dose verification and validation of the whole treatment workflow by end-to-end tests became much more important and polymer gel dosimeters are one of the few possibilities to capture the delivered dose distribution in 3D. The basic principles and formulations of gel dosimetry and its evaluation methods are described and the available studies validating device-specific geometrical parameters as well as the dose delivery by advanced radiotherapy techniques, such as 3D-CRT/IMRT and stereotactic radiosurgery treatments, the treatment of moving targets, online-adaptive magnetic resonance-guided radiotherapy as well as proton and ion beam treatments, are reviewed. The present status and limitations as well as future challenges of polymer gel dosimetry for the validation of complex radiotherapy techniques are discussed.
Time scales in the dynamics of political opinions and the voter model
Authors: Meyer Philipp G , Metzler Ralf
Published: February 2024

Opinions in human societies are measured by political polls on time scales of months to years. Such opinion polls do not resolve the effects of individual interactions but constitute a stochastic process. Voter models with zealots (individuals who do not change their opinions) can describe the mean-field dynamics in systems where no consensus is reached. We show that for large populations, the voter model with zealots is equivalent to the noisy voter model and it has a single characteristic time scale associated with the number of zealots in the population. We discuss which parameters are observable in real data by analysing time series of approval ratings of several political leaders that match the statistical behaviour of the voter model using the technique of the time-averaged mean squared displacement. The characteristic time scale of political opinions in societies is around 12 months, so it cannot be resolved by analysing election data, for which the resolution is several years. The effective population size in all fitted data sets is much smaller than the real population size, which indicates positive correlations of successive voter model steps. We also discuss the heterogeneity of voters as a cause of subdiffusion on long time scales, i.e. slow changes in the society.
Prospecting for rare earth element (hyper)accumulators in the Paris Herbarium using X-ray fluorescence spectroscopy reveals new distributional and taxon discoveries
Authors: Goudard Léo , Blaudez Damien , Sirguey Catherine , Purwadi Imam , Invernon Vanessa , Rouhan Germinal , van der Ent Antony
Published: February 2024

Background

Rare earth elements (REEs) are increasingly crucial for modern technologies. Plants could be used as a biogeochemical pathfinder and a tool to extract REEs from deposits. However, a paucity of information on suitable plants for these tasks exists.

Methods

We aimed to discover new REE-(hyper)accumulating plant species by performing an X-ray fluorescence (XRF) survey at the Herbarium of the Muséum national d’Histoire naturelle (MNHN, Paris, France). We selected specific families based on the likelihood of containing REE-hyperaccumulating species, using known taxa that accumulate REEs. A total of 4425 specimens, taken in the two main evolutionary lineages of extant vascular plants, were analysed, including the two fern families Blechnaceae (n = 561) and Gleicheniaceae (n = 1310), and the two flowering plant families Phytolaccaceae (n = 1137) and Juglandaceae (n = 1417).

Key Results

Yttrium (Y) was used as a proxy for REEs for methodological reasons, and a total of 268 specimens belonging to the genera Blechnopsis (n = 149), Dicranopteris (n = 75), Gleichenella (n = 32), Phytolacca (n = 6), Carya (n = 4), Juglans (n = 1) and Sticherus (n = 1) were identified with Y concentrations ranging from the limit of detection (LOD) >49 µg g−1 up to 1424 µg g−1. Subsequently, analysis of fragments of selected specimens by inductively coupled plasma atomic emission spectroscopy (ICP-AES) revealed that this translated to up to 6423 µg total REEs g−1 in Dicranopteris linearis and up to 4278 µg total REEs g−1 in Blechnopsis orientalis which are among the highest values ever recorded for REE hyperaccumulation in plants. It also proved the validity of Y as an indicator for REEs in XRF analysis of herbarium specimens. The presence of manganese (Mn) and zinc (Zn) was also studied by XRF in the selected specimens. Mn was detected in 1440 specimens ranging from the detection limit at 116 µg g−1 up to 3807 µg g−1 whilst Zn was detected in 345 specimens ranging from the detection limit at 77 µg g−1 up to 938 µg g−1.

Conclusions and Implications

This study led to the discovery of REE accumulation in a range of plant species, substantially higher concentrations in species known to be REE hyperaccumulators, and records of REE hyperaccumulators outside of the well-studied populations in China.
Uncertainty directed factorial clinical trials
Authors: Kotecha Gopal , Ventz Steffen , Fortini Sandra , Trippa Lorenzo
Published: February 2024

The development and evaluation of novel treatment combinations is a key component of modern clinical research. The primary goals of factorial clinical trials of treatment combinations range from the estimation of intervention-specific effects, or the discovery of potential synergies, to the identification of combinations with the highest response probabilities. Most factorial studies use balanced or block randomization, with an equal number of patients assigned to each treatment combination, irrespective of the specific goals of the trial. Here, we introduce a class of Bayesian response-adaptive designs for factorial clinical trials with binary outcomes. The study design was developed using Bayesian decision-theoretic arguments and adapts the randomization probabilities to treatment combinations during the enrollment period based on the available data. Our approach enables the investigator to specify a utility function representative of the aims of the trial, and the Bayesian response-adaptive randomization algorithm aims to maximize this utility function. We considered several utility functions and factorial designs tailored to them. Then, we conducted a comparative simulation study to illustrate relevant differences of key operating characteristics across the resulting designs. We also investigated the asymptotic behavior of the proposed adaptive designs. We also used data summaries from three recent factorial trials in perioperative care, smoking cessation, and infectious disease prevention to define realistic simulation scenarios and illustrate advantages of the introduced trial designs compared to other study designs.
For Better or Worse? Improving the Response to Domestic Abuse Offenders on Probation
Authors: Renehan Nicole , Gadd David
Published: February 2024

As the Ministry of Justice looks to develop a ‘new generation’ of programmes to reduce reoffending, we reflect on what can be learnt from the only accredited domestic abuse programme in England and Wales, Building Better Relationships (BBR). Findings from an ethnographic study of BBR are situated within the Probation Inspectorate’s recent inspection of domestic abuse work within the newly unified Probation Service which revealed a fractured and overstretched workforce. Our central argument is that if we are to avoid making matters worse, practitioners must be equipped with the time, supervision and skill needed to maintain something akin to a ‘therapeutic alliance’, that will endure in moments of crisis in their own lives as well as those of their clients.
Lusting out loud: racialized aurality, podcast intimacy, and the uses of thirst
Authors: Johnson Jacqueline E
Published: February 2024

This article examines how the podcast Thirst Aid Kit makes Black women’s desires—often erased or distorted in media—audible. Using Critical Technocultural Discourse Analysis (CTDA) and feminist close reading, I make three interrelated arguments: (1) The hosts’ use of regional, Black vernaculars and cultural touchstones disrupts podcasting’s Whiteness and builds intimacy with Black women listeners; (2) The podcast’s aural expressions of thirst articulate Black women’s desires rather than shield them from broader publics; (3) The show’s expression of thirst is connected to the romance genre; however, Thirst Aid Kit, ruptures the genre’s investment in Whiteness and the happy ending. This article builds from and intervenes in podcasting research, studies of Black women and media, and popular romance studies.
Allogeneic NK cells induce the in vitro activation of monocyte-derived and conventional type-2 dendritic cells and trigger an inflammatory response under cancer-associated conditions
Authors: Toffoli E C , van Vliet A A , Forbes C , Arns A J , Verheul H W M , Tuynman J , van der Vliet H J , Spanholtz J , de Gruijl T D
Published: February 2024

Natural killer (NK) cells are innate lymphocytes capable to recognize and kill virus-infected and cancer cells. In the past years, the use of allogeneic NK cells as anti-cancer therapy gained interest due to their ability to induce graft-versus-cancer responses without causing graft-versus-host disease and multiple protocols have been developed to produce high numbers of activated NK cells. While the ability of these cells to mediate tumor kill has been extensively studied, less is known about their capacity to influence the activity of other immune cells that may contribute to a concerted anti-tumor response in the tumor microenvironment (TME). In this study, we analyzed how an allogeneic off-the-shelf cord blood stem cell-derived NK-cell product influenced the activation of dendritic cells (DC). Crosstalk between NK cells and healthy donor monocyte-derived DC (MoDC) resulted in the release of IFNγ and TNF, MoDC activation, and the release of the T-cell-recruiting chemokines CXCL9 and CXCL10. Moreover, in the presence of prostaglandin-E2, NK cell/MoDC crosstalk antagonized the detrimental effect of IL-10 on MoDC maturation leading to higher expression of multiple (co-)stimulatory markers. The NK cells also induced activation of conventional DC2 (cDC2) and CD8+ T cells, and the release of TNF, GM-CSF, and CXCL9/10 in peripheral blood mononuclear cells of patients with metastatic colorectal cancer. The activated phenotype of MoDC/cDC2 and the increased release of pro-inflammatory cytokines and T-cell-recruiting chemokines resulting from NK cell/DC crosstalk should contribute to a more inflamed TME and may thus enhance the efficacy of T-cell-based therapies.
External Validation of the 2023 Duke–International Society for Cardiovascular Infectious Diseases Diagnostic Criteria for Infective Endocarditis
Authors: van der Vaart Thomas W , Bossuyt Patrick M M , Durack David T , Baddour Larry M , Bayer Arnold S , Durante-Mangoni Emanuele , Holland Thomas L , Karchmer Adolf W , Miro Jose M , Moreillon Philippe , Rasmussen Magnus , Selton-Suty Christine , Fowler Vance G , van der Meer Jan T M
Published: February 2024

Background

The 2023 Duke–International Society of Cardiovascular Infectious Diseases (ISCVID) criteria for infective endocarditis (IE) were introduced to improve classification of IE for research and clinical purposes. External validation studies are required.

Methods

We studied consecutive patients with suspected IE referred to the IE team of Amsterdam University Medical Center (from October 2016 to March 2021). An international expert panel independently reviewed case summaries and assigned a final diagnosis of “IE” or “not IE,” which served as the reference standard, to which the “definite” Duke-ISCVID classifications were compared. We also evaluated accuracy when excluding cardiac surgical and pathologic data (“clinical” criteria). Finally, we compared the 2023 Duke-ISCVID with the 2000 modified Duke criteria and the 2015 and 2023 European Society of Cardiology (ESC) criteria.

Results

A total of 595 consecutive patients with suspected IE were included: 399 (67%) were adjudicated as having IE; 111 (19%) had prosthetic valve IE, and 48 (8%) had a cardiac implantable electronic device IE. The 2023 Duke-ISCVID criteria were more sensitive than either the modified Duke or 2015 ESC criteria (84.2% vs 74.9% and 80%, respectively; P < .001) without significant loss of specificity. The 2023 Duke-ISCVID criteria were similarly sensitive but more specific than the 2023 ESC criteria (94% vs 82%; P < .001). The same pattern was seen for the clinical criteria (excluding surgical/pathologic results). New modifications in the 2023 Duke-ISCVID criteria related to “major microbiological” and “imaging” criteria had the most impact.

Conclusions

The 2023 Duke-ISCVID criteria represent a significant advance in the diagnostic classification of patients with suspected IE.
Evaluation of the 2023 Duke-International Society of Cardiovascular Infectious Diseases Criteria in a Multicenter Cohort of Patients With Suspected Infective Endocarditis
Authors: Papadimitriou-Olivgeris Matthaios , Monney Pierre , Frank Michelle , Tzimas Georgios , Tozzi Piergiorgio , Kirsch Matthias , Van Hemelrijck Mathias , Bauernschmitt Robert , Epprecht Jana , Guery Benoit , Hasse Barbara
Published: February 2024

Background

Since publication of Duke criteria for infective endocarditis (IE) diagnosis, several modifications have been proposed. We aimed to evaluate the diagnostic performance of the Duke-ISCVID (International Society of Cardiovascular Infectious Diseases) 2023 criteria compared to prior versions from 2000 (Duke-Li 2000) and 2015 (Duke-ESC [European Society for Cardiology] 2015).

Methods

This study was conducted at 2 university hospitals between 2014 and 2022 among patients with suspected IE. A case was classified as IE (final IE diagnosis) by the Endocarditis Team. Sensitivity for each version of the Duke criteria was calculated among patients with confirmed IE based on pathological, surgical, and microbiological data. Specificity for each version of the Duke criteria was calculated among patients with suspected IE for whom IE diagnosis was ruled out.

Results

In total, 2132 episodes with suspected IE were included, of which 1101 (52%) had final IE diagnosis. Definite IE by pathologic criteria was found in 285 (13%), 285 (13%), and 345 (16%) patients using the Duke-Li 2000, Duke-ESC 2015, or the Duke-ISCVID 2023 criteria, respectively. IE was excluded by histopathology in 25 (1%) patients. The Duke-ISCVID 2023 clinical criteria showed a higher sensitivity (84%) compared to previous versions (70%). However, specificity of the new clinical criteria was lower (60%) compared to previous versions (74%).

Conclusions

The Duke-ISCVID 2023 criteria led to an increase in sensitivity compared to previous versions. Further studies are needed to evaluate items that could increase sensitivity by reducing the number of IE patients misclassified as possible, but without having detrimental effect on specificity of Duke criteria.
Performance of the 2023 Duke-International Society of Cardiovascular Infectious Diseases Diagnostic Criteria for Infective Endocarditis in Relation to the Modified Duke Criteria and to Clinical Management—Reanalysis of Retrospective Bacteremia Cohorts
Authors: Lindberg Helena , Berge Andreas , Jovanovic-Stjernqvist Martin , Hagstrand Aldman Malin , Krus David , Öberg Jonas , Kahn Fredrik , Bläckberg Anna , Sunnerhagen Torgny , Rasmussen Magnus
Published: February 2024

Background

Revised diagnostic criteria for infective endocarditis (IE), the 2023 Duke-ISCVID criteria, were recently presented and need validation. Here, we compare the 2000 modified Duke criteria for IE with Duke-ISCVID among patients with bacteremia and relate the diagnostic classification to IE treatment.

Methods

We reanalyzed patient cohorts with Staphylococcus aureus, Staphylococcus lugdunensis, non–β-hemolytic streptococci, Streptococcus-like bacteria, Streptococcus dysgalactiae, Enterococcus faecalis, and HACEK (Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella) bacteremia. Episodes were classified as definite, possible, or rejected IE with the modified Duke and Duke-ISCVID criteria. Reclassification included the microbiology criteria, positron emission tomography–computed tomography, and cardiac implanted electronic devices. To calculate sensitivity, patients treated for IE were considered as having IE.

Results

In 4050 episodes of bacteremia, the modified Duke criteria assigned 307 episodes (7.6%) as definite IE, 1190 (29%) as possible IE, and 2553 (63%) as rejected IE. Using the Duke-ISCVID criteria, 13 episodes (0.3%) were reclassified from possible to definite IE, and 475 episodes (12%) were reclassified from rejected to possible IE. With the modified Duke criteria, 79 episodes that were treated as IE were classified as possible IE, and 11 of these episodes were reclassified to definite IE with Duke-ISCVID. Applying the decision to treat for IE as a reference standard, the sensitivity of the Duke-ISCVID criteria was 80%. None of the 475 episodes reclassified to possible IE were treated as IE.

Conclusions

The Duke-ISCVID criteria reclassified a small proportion of episodes to definite IE at the expense of more episodes of possible IE. Future criteria should minimize the possible IE group while keeping or improving sensitivity.
First-break prediction in 3-D land seismic data using the dynamic time warping algorithm
Authors: Souza W E , Cerqueira A G , Porsani M J
Published: February 2024

This paper presents a new methodology to assist geophysicists in determining the first-break event in a 3-D seismic data set using the well-known technique called dynamic time warping algorithm (DTW), which is usually used to find the optimal alignment between two time-series. We used the optimal path from the cost matrix to identify the first break in the seismogram using a few picks (seeds) made by an interpreter as a reference to perform this task. Furthermore, the data were pre-conditioned by the topographic and linear moveout to improve the method’s accuracy. To demonstrate the technique’s robustness, first, we applied the methodology in a synthetic seismic data. After demonstrating the efficiency of the algorithm, we applied the aforementioned methodology in the Polo-Miranga 3-D seismic cube located in the Recôncavo sedimentary basin, Bahia-Brazil, and in the seismic data acquired from the Blackfoot field in Alberta, Canada. The high-quality results showed consistency in determining the first break in all ranges of offsets, demonstrating an alternative way to accelerate this seismic processing step. Furthermore, we compared the results obtained by the proposed methodology with an algorithm based on comparing the short-time averages with long-time averages. Finally, we performed the static correction calculation to ensure that the time distortion resulting from the terrain and the low-velocity layer was mitigated in shoot gathers and in the stacked section.
Analysis of the Infectious Diseases Fellowship Program Directors Postmatch 2023 Survey
Authors: Andrews Hayden S , Chirch Lisa M , Luther Vera P , Shnekendorf Rachel , Nolan Nathanial S , Paras Molly L
Published: February 2024

The 2023 United States infectious diseases (ID) fellowship match resulted in a large percentage of programs with unfilled positions. A survey was sent to ID program directors nationwide to better understand their perceptions on the match. Program directors perceived geography, a small applicant pool, and low specialty pay as contributing factors to the match results. Developing specialized fellowship tracks, increasing funding for the ID trainee pipeline, and national advocacy for higher compensation were identified as areas to focus on to increase the applicant pool. Areas of controversy, such as decreasing the number or size of fellowship programs, require further discussion.
Impact of Micafungin on Candida auris β-glucan Masking and Neutrophil Interactions
Authors: Horton Mark V , Eix Emily F , Johnson Chad J , Dean Megan E B , Andes Brody D , Wartman Kayla M , Nett Jeniel E
Published: February 2024

Invasive fungal pathogen Candida auris has become a public health threat causing outbreaks of high mortality infections. Drug resistance often limits treatment options. For Candida albicans, subinhibitory concentrations of echinocandins unmask immunostimulatory β-glucan, augmenting immunity. Here we analyze the impact of echinocandin treatment of C. auris on β-glucan exposure and human neutrophil interactions. We show subinhibitory concentrations lead to minimal glucan unmasking and only subtle influences on neutrophil functions for the isolates belonging to circulating clades. The data suggest that echinocandin treatment will not largely alter phagocytic responses. Glucan masking pathways appear to differ between C. auris and C. albicans.
Uropathogenic Escherichia coli Subverts Host Autophagic Defenses by Stalling Preautophagosomal Structures to Escape Lysosome Exocytosis
Authors: Li Xueping , Jiang Lingyan , Zhang Si , Zhou Jiarui , Liu Le , Jin Chen , Sun Hongmin , Wang Qian , Liu Yutao , Pang Yu
Published: February 2024

Urinary tract infections are primarily caused by uropathogenic Escherichia coli (UPEC). UPEC infects bladder epithelial cells (BECs) via fusiform vesicles and escapes into the cytosol by disrupting fusiform vesicle membrane using outer membrane phospholipase PldA, and establishes biofilm-like intracellular bacterial communities (IBCs) for protection from host immune clearance. Cytosolic UPEC is captured by autophagy to form autophagosomes, then transported to lysosomes, triggering the spontaneous exocytosis of lysosomes. The mechanism by which UPEC evades autophagy to recognize and form IBCs remains unclear. Here, we demonstrate that by inhibiting autophagic flux, UPEC PldA reduces the lysosome exocytosis of BECs. By reducing intracellular phosphatidylinositol 3-phosphate levels, UPEC PldA increases the accumulation of NDP52 granules and decreases the targeting of NDP52 to autophagy, hence stalling preautophagosome structures. Thus, our results uncover a critical role for PldA to inhibit autophagic flux, favoring UPEC escapes from lysosome exocytosis, thereby contributing to acute urinary tract infection.
Risk of Cardiovascular Events After Influenza: A Population-Based Self-Controlled Case Series Study, Spain, 2011–2018
Authors: Muñoz-Quiles Cintia , López-Lacort Mónica , Urchueguía Arantxa , Díez-Domingo Javier , Orrico-Sánchez Alejandro
Published: February 2024

This study explores the relationship between influenza infection, both clinically diagnosed in primary care and laboratory confirmed in hospital, and atherothrombotic events (acute myocardial infarction and ischemic stroke) in Spain. A population-based self-controlled case series design was used with individual-level data from electronic registries (n = 2 230 015). The risk of atherothrombotic events in subjects ≥50 years old increased more than 2-fold during the 14 days after the mildest influenza cases in patients with fewer risk factors and more than 4-fold after severe cases in the most vulnerable patients, remaining in them more than 2-fold for 2 months. The transient increase of the association, its gradient after influenza infection, and the demonstration by 4 different sensitivity analyses provide further evidence supporting causality. This work reinforces the official recommendations for influenza prevention in at-risk groups and should also increase the awareness of even milder influenza infection and its possible complications in the general population.
Mortality Rates of the Spanish Flu and Coronavirus Disease 2019 in the Netherlands: A Historical Comparison
Authors: Harteloh Peter , van Mechelen Rob
Published: February 2024

The coronavirus disease 2019 (COVID-19) pandemic has been called the deadliest disease event in history. In this study, we compared the cause-specific mortality rate of the Spanish flu (1918–1920) with that of COVID-19 (2020–2022) in the Netherlands. During the periods of exposure, about 50 000 people died of COVID-19 and 32 000 people of the Spanish flu. In absolute numbers, COVID-19 seems to be deadlier than Spanish flu. However, the crude mortality rates for COVID-19 and Spanish flu were 287 and 486 per 100 000 inhabitants, respectively. Comparing age-standardized mortality rates, there would have been 28 COVID-19– and 194 Spanish flu–related deaths in 1918–1920, or 214 Spanish flu– and 98 COVID-19–related deaths in 2020–2022 per 100 000 inhabitants per year. Thus, taking the population differences into account, the Spanish flu would have been deadlier than COVID-19.
Molecular Interactions Leading to Advancements in the Techniques for COVID-19 Detection: A Review
Authors: Kashif Mohammad , Acharya Swati , Khalil Adila
Published: February 2024

Since 2019 the world has been in a combat with the highly contagious disease COVID-19 which is caused by the rapid transmission of the SARS-CoV-2 virus (severe acute respiratory syndrome coronavirus 2). Detection of this disease in an early stage helps to control its spread and management. To combat this epidemic with one-time effective medication, improved quick analytical procedures must be developed and validated. The requirement for accurate and precise analytical methods for the diagnosis of the virus and antibodies in infected patients has been a matter of concern. The global impact of this virus has motivated scientists and researchers to investigate and develop various analytical diagnostic techniques. This review includes the study of standard methods which are reliable and accredited for the analytical recognition of the said virus. For early detection of SARS-CoV-2 RNA, RT-PCR (Real-time reverse transcriptase-polymerase chain reaction) is an accurate method among other methods and, thus, considered as the “gold standard” technique. Here, we outline the most extensively used analytical methods for diagnosing COVID-19, along with a brief description of each technique and its analytical aspects/perspective.
Genetic mapping reveals new loci and alleles for flowering time and plant height using the double round-robin population of barley
Authors: Cosenza Francesco , Shrestha Asis , Van Inghelandt Delphine , Casale Federico A , Wu Po-Ya , Weisweiler Marius , Li Jinquan , Wespel Franziska , Stich Benjamin
Published: February 2024

Flowering time and plant height are two critical determinants of yield potential in barley (Hordeum vulgare). Despite their role in plant physiological regulation, a complete overview of the genetic complexity of flowering time and plant height regulation in barley is still lacking. Using a double round-robin population originated from the crossings of 23 diverse parental inbred lines, we aimed to determine the variance components in the regulation of flowering time and plant height in barley as well as to identify new genetic variants by single and multi-population QTL analyses and allele mining. Despite similar genotypic variance, we observed higher environmental variance components for plant height than flowering time. Furthermore, we detected new QTLs for flowering time and plant height. Finally, we identified a new functional allelic variant of the main regulatory gene Ppd-H1. Our results show that the genetic architecture of flowering time and plant height might be more complex than reported earlier and that a number of undetected, small effect, or low-frequency genetic variants underlie the control of these two traits.
The role of the co-chaperone HOP in plant homeostasis during development and stress
Authors: Castellano M Mar , Muñoz Alfonso , Okeke Isabel C , Novo-Uzal Esther , Toribio René , Mangano Silvina
Published: February 2024

Proteins need to acquire their native structure in order to become fully functional. In specific cases, the active conformation is obtained spontaneously; nevertheless, many proteins need the assistance of chaperones and co-chaperones to be properly folded. These proteins help to maintain protein homeostasis under control conditions and under different stresses. HOP (HSP70–HSP90 organizing protein) is a highly conserved family of co-chaperones that assist HSP70 and HSP90 in the folding of specific proteins. In the last few years, findings in mammals and yeast have revealed novel functions of HOP and re-defined the role of HOP in protein folding. Here, we provide an overview of the most important aspects of HOP regulation and function in other eukaryotes and analyse whether these aspects are conserved in plants. In addition, we highlight the HOP clients described in plants and the role of HOP in plant development and stress response.
Quasar outflow deceleration or acceleration: predictions and a search
Authors: Hall P B , Weiss E , Brandt W N , Mulholland C J
Published: February 2024

Quasar winds can shock and sweep up ambient interstellar medium (ISM) gas, contributing to galactic quenching. We combine and extend past models of energy-conserving shock bubbles around quasars, investigate model implications from an observational standpoint, and test model predictions using new high-resolution spectroscopic observations of the broad absorption-line quasar SDSS J030000.56+004828.0 (J0300). Even with constant energy input from the wind, a bubble’s expansion decelerates over time as more ISM gas is swept up. Our new observations enable a direct search for this deceleration. We obtain the tightest reported 3σ limit on the average rest-frame deceleration (or acceleration) of a quasar outflow: |a| < 0.1 km s−1 yr−1 (<3 × 10−4 cm s−2) in the relatively low-velocity Ca ii outflow of J0300 over 9.65 rest-frame years. We can satisfy these limits with certain parameter choices in our model, but the large velocity range of the Ca ii absorption in J0300 rules out the hypothesis that such gas shares the velocity of the swept-up ISM gas in a self-similar shock bubble. We investigate the possibility of ram-pressure acceleration of preexisting ISM clouds and conclude that the velocity range seen in Ca ii in J0300 is potentially consistent with such an explanation. The Ca ii-absorbing gas clouds in J0300 have been inferred to have high densities by Choi et al., in which case they can only have been accelerated to their current speeds if they were originally at least an order of magnitude less dense than they are today.
Observations of interstellar scattering of six pulsars using Polish LOFAR station PL611
Authors: Filothodoros Alexandros , Lewandowski Wojciech , Kijak Jarosław , Śmierciak Bartosz , Chyży Krzysztof , Błaszkiewicz Leszek , Krankowski Andrzej
Published: February 2024

We present the preliminary results of 4 yr of observations of the scattering of pulsar radiation in the interstellar medium using the Low Frequency Array (LOFAR) PL611 station located in Lazy near Krakow. In this work we show the initial results for six pulsars from our observing campaign. We used the HBA antennas of the station, with a central frequency of 154 MHz and a 72 MHz bandwidth and we were able to detect the frequency-dependent change in the pulse profiles. Splitting the bandwidth into a number of separate sub-bands we obtained independent scatter time estimates, which allowed for the estimation of the scattering frequency scaling slope for each individual observation. Our project has been accumulating data for more than 4 yr and as a result we are in a position to study the time variability of the scattering parameters over this period. We detected significant changes in the scatter time and its frequency scaling for at least two of pulsars. The average values of the frequency scaling index for the six pulsars selected for this work are below the range of values predicted by the simple thin screen model of interstellar scattering. This is in accordance with previous results shown for both higher dispersion measure pulsars observed in the past, as well as the more recent LOFAR observations and other projects similar in the observing frequency. We also discuss the advantages of using individual LOFAR stations (or similar instruments) for this kind of research.
Multiplex gene editing reveals cucumber MILDEW RESISTANCE LOCUS O family roles in powdery mildew resistance
Authors: Ma Mingru , Yang Li , Hu Zhenzhu , Mo Changjuan , Geng Shouyu , Zhao Xin , He Qiuyu , Xiao Li , Lu Liurong , Wang Dan , Li Shanggui , Kong Qiusheng , Li Dawei , Bie Zhilong
Published: February 2024

Powdery mildew (PM) is one of the most widespread and prevalent diseases that affects a wide range of crops. In cucumber (Cucumis sativus L.), previous forward genetic studies have identified MILDEW RESISTANCE LOCUS O 8 (CsMLO8) as necessary but alone insufficient for cucumber PM resistance (PMR) and suggested the involvement of other members of the CsMLO family. However, the function of other CsMLO family members in cucumber remains largely unknown. Here, we developed a highly efficient multiplex gene editing system in cucumber to generate a series of Csmlo mutants from all the 13 family members. Systematic analysis of these mutants revealed growth effects of these CsMLO family members on development and PMR. Importantly, we obtained the Csmlo1/8/11 triple mutant with complete resistance to PM. Transcriptome and proteome analysis of PM-resistant Csmlo mutants suggested that the kinesin-like calmodulin-binding protein (KCBP)-interacting Ca2+-binding protein (CsKIC), calmodulin-like protein 28 (CsCML28), and Ca2+-dependent protein kinase 11 (CsCPK11)-mediated calcium signaling pathway is involved in PMR. CsMLO8 interacted directly with CsKIC, and the simultaneous silencing of both genes resulted in a phenotype that resembled the silencing of CsKIC alone. Silencing CsCML28 and CsCPK11 increased susceptibility to PM, whereas overexpressing CsCPK11 through genetic transformation enhanced cucumber's PMR, demonstrating their positive regulatory roles in PMR. Given the importance of PMR for cucurbit crops, this research provides unprecedented insights into the function of the proteins encoded by the CsMLO gene family as well as the plant defense response to PM pathogen.
Gene inversion led to the emergence of brackish archaeal heterotrophs in the aftermath of the Cryogenian Snowball Earth
Authors: Fan Lu , Xu Bu , Chen Songze , Liu Yang , Li Fuyan , Xie Wei , Prabhu Apoorva , Zou Dayu , Wan Ru , Li Hongliang , Liu Haodong , Liu Yuhang , Kao Shuh-Ji , Chen Jianfang , Zhu Yuanqing , Rinke Christian , Li Meng , Zhu Maoyan , Zhang Chuanlun
Published: February 2024

Land–ocean interactions greatly impact the evolution of coastal life on earth. However, the ancient geological forces and genetic mechanisms that shaped evolutionary adaptations and allowed microorganisms to inhabit coastal brackish waters remain largely unexplored. In this study, we infer the evolutionary trajectory of the ubiquitous heterotrophic archaea Poseidoniales (Marine Group II archaea) presently occurring across global aquatic habitats. Our results show that their brackish subgroups had a single origination, dated to over 600 million years ago, through the inversion of the magnesium transport gene corA that conferred osmotic-stress tolerance. The subsequent loss and gain of corA were followed by genome-wide adjustment, characterized by a general two-step mode of selection in microbial speciation. The coastal family of Poseidoniales showed a rapid increase in the evolutionary rate during and in the aftermath of the Cryogenian Snowball Earth (∼700 million years ago), possibly in response to the enhanced phosphorus supply and the rise of algae. Our study highlights the close interplay between genetic changes and ecosystem evolution that boosted microbial diversification in the Neoproterozoic continental margins, where the Cambrian explosion of animals soon followed.