bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potentielle Nephrotoxizität der Kombinationstherapie von Vancomycin
und Piperacillin-Tazobactam: Empfehlungen der AG ABS der DGPI unter Beteiligung
von Experten der GPN
Authors: Martin Luise , Pecar Alenka , Baltaci Yeliz , Simon Arne , Kohl Stefan , Müller Dominik , Forster Johannes 
Published: March 2024

ZusammenfassungDie Kombination von Vancomycin und Piperacillin/Tazobactam (V+P/T) kommt in der
empirischen Therapie von schweren Infektionen zum Einsatz, insbesondere, wenn
patientenseitige Risikofaktoren wie Immunsuppression oder Kolonisation mit
multiresistenten Erregern vorliegen. Die Nephrotoxizität von Vancomycin ist
bekannt, das Risiko der Nephrotoxizität wird durch adaptierte Dosierungen sowie
therapeutisches Drug-Monitoring vermindert. Piperacillin/Tazobactam (P/T) kann
sehr selten eine interstitielle Nephritis auslösen. Die Resultate retrospektiver
Kohortenstudien bei Kindern zeigen überwiegend eine geringe, klinisch wenig
relevante, additive Nephrotoxizität (definiert als Kreatinin-Anstieg im Serum)
beider Substanzen. Präklinische Studien und eine prospektive Studie mit
erwachsenen Patienten, die weitere Nierenretentionsparameter sowie das klinische
Outcome untersuchten, zeigten keinen Zusammenhang zwischen einer Therapie mit
V+P/T und akuter Nierenfunktionseinschränkung. Aufgrund der Limitationen der
vorhandenen Publikationen sprechen sich die Arbeitsgruppe ABS der DGPI und die
Experten der GPN nicht gegen den Einsatz von P/T plus Vancomycin aus. Dennoch
sollte durch den zeitlich restriktiven Einsatz der Kombination V+P/T die
Exposition gegenüber V+P/T und ein mögliches Nephrotoxizitätsrisiko minimiert
werden. Auch die alternativ infrage kommenden Substanzen sind dabei sowohl im
Hinblick auf ihr antimikrobielles Spektrum, auf mögliche Nebenwirkungen sowie
auf den durch sie ausgeübten Selektionsdruck kritisch zu hinterfragen.
Indikationen für den empirischen sowie gezielten Einsatz von P/T und V+P/T
sollten in Zusammenarbeit mit dem lokalen ABS-Team in hausinternen Leitlinien
festgelegt werden. Wird die Kombinationstherapie V+P/T verwendet, sollte eine
über das Serum-Kreatinin hinausgehende sowohl laborchemische (BGA, Cystatin C)
als auch klinische Überwachung (Bilanzierung, Blutdruck) der Nierenfunktion
erfolgen.
Production of positronium chloride: A study of the charge exchange reaction between Ps and Cl−
Authors: Lévêque-Simon K. , Camper A. , Taïeb R. , Caillat J. , Lévêque C. , Giner E. 
Published: March 2024

We present cross sections for the formation of positronium chloride (PsCl) in its ground state from the charge exchange between positronium (Ps) and chloride (Cl−) in the range of 10 meV–100 eV Ps energy. We have used theoretical models based on the first Born approximation in its three-body formulation. We simulated the collisions between Ps and Cl− using ab initio binding energies and positronic wave functions at both the mean-field and correlated levels extrapolated to the complete basis set limit. The accuracy of these ab initio data was benchmarked on the PsF system with the existing highly accurate results, including the very recent quantum Monte Carlo results. We have investigated Ps excited states up to n = 4. The results suggest that the channel Ps(n = 2) is of particular interest for the production of PsCl in the ground state and shows that an accurate treatment of correlation effects (i.e., electron–electron and electron–positron correlations) leads to a significant change in the magnitude of the PsCl production cross section with respect to the mean-field level.
Interactional multimodal metadiscourse in public health posters during the COVID-19 pandemic
Authors: Al-Subhi Aisha Saadi 
Published: March 2024

Abstract
While language remains a constant channel of communication, visual information also plays a significant role in
contemporary communication. This study explores the application of interactional metadiscourse and meaning-making in public health
posters issued during the COVID-19 crisis. It examines both the textual and visual communicative strategies adopted in the
multimodal texts of 60 COVID-19 posters published on the official websites of the World Health Organization and the Ministry of
Health in Saudi Arabia. Principally, the study is framed within the theories of interactional metadiscourse by Hyland (2005b) and multimodality by Kress and van Leeuwen (1996/ 2006/ 2010), as investigated through their work on
visual grammar. The frequency and functions of interactional metadiscourse resources and socio-semiotic resources were scrutinized
and analyzed. The findings reveal that reader pronouns and directives were the most frequently used interactional metadiscourse to
explicitly engage the target audience and guide them toward physical acts that maintain the application of health-protective
procedures. The results further demonstrate that framing, salience, and images were the socio-semiotic resources most commonly
utilized to achieve compositional meaning, explain content visually, and make information more readily comprehensible to the
public.
Soliton dynamics and stability in the ABS spinor model with a
PT
-symmetric periodic complex potential
Authors: Mertens Franz G , Sánchez-Rey Bernardo , Quintero Niurka R 
Published: March 2024

Abstract
We investigate the effects on solitons dynamics of introducing a

PT

-symmetric complex potential in a specific family of the cubic Dirac equation in (1+1)-dimensions, called the Alexeeva–Barashenkov–Saxena model. The potential is introduced taking advantage of the fact that the nonlinear Dirac equation admits a Lagrangian formalism. As a consequence, the imaginary part of the potential, associated with gains and losses, behaves as a spatially periodic damping (changing from positive to negative, and back) that acts at the same time on the two spinor components. A collective coordinates (CCs) theory is developed by making an ansatz for a moving soliton where the position, rapidity, momentum, frequency, and phase are all functions of time. We consider the complex potential as a perturbation and verify that numerical solutions of the equation of motions for the CCs are in agreement with simulations of the nonlinear Dirac equation. The main effect of the imaginary part of the potential is to induce oscillations in the charge and energy (they are conserved for real potentials) with the same frequency and phase as the momentum. We find long-lived solitons even with very large charge and energy oscillations. Additionally, we extend to the nonlinear Dirac equation an empirical stability criterion, previously employed successfully in the nonlinear Schrödinger equation.
Emotion recognition with reduced channels using CWT based EEG feature representation and a CNN classifier
Authors: Mahmud Md Sultan , Fattah Shaikh Anowarul , Saquib Mohammad , Saha Oishy 
Published: March 2024

Abstract

Objective. Although emotion recognition has been studied for decades, a more accurate classification method that requires less computing is still needed. At present, in many studies, EEG features are extracted from all channels to recognize emotional states, however, there is a lack of an efficient feature domain that improves classification performance and reduces the number of EEG channels. Approach. In this study, a continuous wavelet transform (CWT)-based feature representation of multi-channel EEG data is proposed for automatic emotion recognition. In the proposed feature, the time-frequency domain information is preserved by using CWT coefficients. For a particular EEG channel, each CWT coefficient is mapped into a strength-to-entropy component ratio to obtain a 2D representation. Finally, a 2D feature matrix, namely CEF2D, is created by concatenating these representations from different channels and fed into a deep convolutional neural network architecture. Based on the CWT domain energy-to-entropy ratio, effective channel and CWT scale selection schemes are also proposed to reduce computational complexity. Main results. Compared with previous studies, the results of this study show that valence and arousal classification accuracy has improved in both 3-class and 2-class cases. For the 2-class problem, the average accuracies obtained for valence and arousal dimensions are 98.83% and 98.95%, respectively, and for the 3-class, the accuracies are 98.25% and 98.68%, respectively. Significance. Our findings show that the entropy-based feature of EEG data in the CWT domain is effective for emotion recognition. Utilizing the proposed feature domain, an effective channel selection method can reduce computational complexity.
Importance profiles. Visualization of atomic basis set requirements
Authors: Lehtola Susi 
Published: March 2024

Abstract
Recent developments in fully numerical methods promise interesting opportunities for new, compact atomic orbital (AO) basis sets that maximize the overlap to fully numerical reference wave functions, following the pioneering work of Richardson and coworkers from the early 1960s. Motivated by this technique, we suggest a way to visualize the importance of AO basis functions employing fully numerical wave functions computed at the complete basis set limit: the importance of a normalized AO basis function

|
α
⟩

centered on some nucleus can be visualized by projecting

|
α
⟩

on the set of numerically represented occupied orbitals

|

ψ

i

⟩

as

I

0

(
α
)
=

∑

i

⟨
α

|

ψ

i

⟩
⟨

ψ

i

|

α
⟩

. Choosing α to be a continuous parameter describing the AO basis, such as the exponent of a Gaussian-type orbital or Slater-type orbital basis function, one is then able to visualize the importance of various functions. The proposed visualization

I

0

(
α
)

has the important property

0
⩽

I

0

(
α
)
⩽
1

which allows unambiguous interpretation. We also propose a straightforward generalization of the importance profile for polyatomic applications

I
(
α
)

, in which the importance of a test function

|
α
⟩

is measured as the increase in projection from the atomic minimal basis. We exemplify the methods with importance profiles computed for atoms from the first three rows, and for a set of chemically diverse diatomic molecules. We find that the importance profile offers a way to visualize the atomic basis set requirements for a given system in an a priori manner, provided that a fully numerical reference wave function is available.
Quasi-experimental methods for pharmacoepidemiology: difference-in-differences and synthetic control methods with case studies for vaccine evaluation
Authors: Kennedy-Shaffer Lee 
Published: March 2024

Abstract
Difference-in-differences and synthetic control methods have become common study designs for evaluating the effects of changes in policies, including health policies. They also have potential for providing real-world effectiveness and safety evidence in pharmacoepidemiology. To effectively add to the toolkit of the field, however, designs—including both their benefits and drawbacks—must be well understood. Quasi-experimental designs provide an opportunity to estimate the average treatment effect on the treated without requiring the measurement of all possible confounding factors, and to assess population-level effects. This requires, however, other key assumptions, including the parallel trends or stable weighting assumptions, a lack of other concurrent events that could alter time trends, and an absence of contamination between exposed and unexposed units. The targeted estimands are also highly specific to the settings of the study, and combining across units or time periods can be challenging. Case studies are presented for 3 vaccine evaluation studies, showcasing some of these challenges and opportunities in a specific field of pharmacoepidemiology. These methods provide feasible and valuable sources of evidence in various pharmacoepidemiologic settings and can be improved through research to identify and weigh the advantages and disadvantages in those settings.
This article is part of a Special Collection on Pharmacoepidemiology.
Oligofluorene main-chain length-dependence on one-pot extraction of chirality-selective semiconducting single-walled carbon nanotubes
Authors: Shindome Shoichiro , Shiraki Tomohiro , Toshimitsu Fumiyuki , Fujigaya Tsuyohiko , Nakashima Naotoshi 
Published: March 2024

Abstract
Polyfluorene and their derivatives are noted for being fascinating dispersants for single-walled carbon nanotubes (SWCNTs) because they selectively solubilize semiconducting (sem-) SWCNTs. However, the selective extraction mechanism of this unique behavior has not yet been fully clarified. In this paper, we describe a unique SWCNT solubilization behavior using 12 fluorene oligomers with different main-chain lengths (FOn, n = 2∼30), in which n is the number of fluorene-repeating unit. Sonication of SWCNTs using these oligofluorenes in toluene was found to solubilize SWCNTs when the main-chain length was longer than n = 12. Raman spectra revealed that selective sem-SWCNT extraction occurred when using the FOn with n ≥ 18, while, when using FOn (n = 12, 15), both sem- and metallic (met-) SWCNTs were solubilized. The (n,m)chiralites of the extracted SWCNTs using the fluorene oligomers differed from those using a homopolymer, poly(9,9′-di-n-octylfluorene) (PFO); that is, PFO extracted (9,7)SWCNTs well, while only FO30 slightly dissolved the (9,7)tubes, and when using other FOn (n = 12∼27), no (9,7)tubes were solubilized. The present study demonstrated the importance of the main-chain length of the oligofluorenes on selected chirality extraction of sem-SWCNTs, which is useful for designing fluorene-based compounds with selective extraction of sem-SWCNTs with a specific (n,m) chirality.
GPVI inhibition: Advancing antithrombotic therapy in cardiovascular disease
Authors: Slater Alexandre , Khattak Sophia , Thomas Mark R 
Published: March 2024

Abstract
Glycoprotein (GP) VI (GPVI) plays a major role in thrombosis but not haemostasis, making it a promising antithrombotic target. The primary role of GPVI on the surface of platelets is a signalling receptor for collagen, which is one of the most potent thrombotic sub-endothelial components that is exposed by atherosclerotic plaque rupture. Inhibition of GPVI has therefore been investigated as a strategy for treatment and prevention of atherothrombosis, such as during stroke and acute coronary syndromes. A range of specific GPVI inhibitors have been characterized, and two of these inhibitors, glenzocimab and revacept, have completed Phase II clinical trials in ischaemic stroke. In this review, we summarize mechanisms of GPVI activation and the latest progress of clinically tested GPVI inhibitors, including their mechanisms of action. By focusing on what is known about GPVI activation, we also discuss whether alternate strategies could be used to target GPVI.
A genome-wide cytotoxicity screen of cluster F1 mycobacteriophage Girr reveals novel inhibitors of Mycobacterium smegmatis growth
Authors: Pollenz Richard S , Barnhill Kaylee , Biggs Abbigail , Bland Jackson , Carter Victoria , Chase Michael , Clark Hayley , Coleman Caitlyn , Daffner Marshall , Deam Caitlyn , Finocchiaro Alyssa , Franco Vanessa , Fuller Thomas , Pinera Juan Gallardo , Horne Mae , Howard Zoe , Kanahan Olivia , Miklaszewski Christopher , Miller Sydney , Morgan Ryan , Onalaja Oluwatobi , Otero Louis , Padhye Shivani , Rainey Emily , Rasul Fareed , Robichaux Kobe , Rodier Alexandra , Schlosser Sydni , Sciacchitano Ava , Stewart Emma , Thakkar Rajvi , Heller Danielle M 
Published: March 2024

Abstract
Over the past decade, thousands of bacteriophage genomes have been sequenced and annotated. A striking observation from this work is that known structural features and functions cannot be assigned for &gt;65% of the encoded proteins. One approach to begin experimentally elucidating the function of these uncharacterized gene products is genome-wide screening to identify phage genes that confer phenotypes of interest like inhibition of host growth. This study describes the results of a screen evaluating the effects of overexpressing each gene encoded by the temperate Cluster F1 mycobacteriophage Girr on the growth of the host bacterium Mycobacterium smegmatis. Overexpression of 29 of the 102 Girr genes (~28% of the genome) resulted in mild to severe cytotoxicity. Of the 29 toxic genes described, 12 have no known function and are predominately small proteins of &lt;125 amino acids. Overexpression of the majority of these 12 cytotoxic no known functions proteins resulted in moderate to severe growth reduction and represent novel antimicrobial products. The remaining 17 toxic genes have predicted functions, encoding products involved in phage structure, DNA replication/modification, DNA binding/gene regulation, or other enzymatic activity. Comparison of this dataset with prior genome-wide cytotoxicity screens of mycobacteriophages Waterfoul and Hammy reveals some common functional themes, though several of the predicted Girr functions associated with cytotoxicity in our report, including genes involved in lysogeny, have not been described previously. This study, completed as part of the HHMI-supported SEA-GENES project, highlights the power of parallel, genome-wide overexpression screens to identify novel interactions between phages and their hosts.
Comparative analysis of in-silico tools in identifying pathogenic variants in dominant inherited retinal diseases
Authors: Brock Daniel C , Wang Meng , Hussain Hafiz Muhammad Jafar , Rauch David E , Marra Molly , Pennesi Mark E , Yang Paul , Everett Lesley , Ajlan Radwan S , Colbert Jason , Porto Fernanda Belga Ottoni , Matynia Anna , Gorin Michael B , Koenekoop Robert K , Lopez Irma , Sui Ruifang , Zou Gang , Li Yumei , Chen Rui 
Published: March 2024

Abstract
Inherited retinal diseases (IRDs) are a group of rare genetic eye conditions that cause blindness. Despite progress in identifying genes associated with IRDs, improvements are necessary for classifying rare autosomal dominant (AD) disorders. AD diseases are highly heterogenous, with causal variants being restricted to specific amino acid changes within certain protein domains, making AD conditions difficult to classify. Here, we aim to determine the top-performing in-silico tools for predicting the pathogenicity of AD IRD variants. We annotated variants from ClinVar and benchmarked 39 variant classifier tools on IRD genes, split by inheritance pattern. Using area-under-the-curve (AUC) analysis, we determined the top-performing tools and defined thresholds for variant pathogenicity. Top-performing tools were assessed using genome sequencing on a cohort of participants with IRDs of unknown etiology. MutScore achieved the highest accuracy within AD genes, yielding an AUC of 0.969. When filtering for AD gain-of-function and dominant negative variants, BayesDel had the highest accuracy with an AUC of 0.997. Five participants with variants in NR2E3, RHO, GUCA1A, and GUCY2D were confirmed to have dominantly inherited disease based on pedigree, phenotype, and segregation analysis. We identified two uncharacterized variants in GUCA1A (c.428T&gt;A, p.Ile143Thr) and RHO (c.631C&gt;G, p.His211Asp) in three participants. Our findings support using a multi-classifier approach comprised of new missense classifier tools to identify pathogenic variants in participants with AD IRDs. Our results provide a foundation for improved genetic diagnosis for people with IRDs.
Development and utility of a clinical research informatics application for participant recruitment and workflow management for a return of results pilot trial in familial hypercholesterolemia in the Million Veteran Program
Authors: Brunette Charles A , Yi Thomas , Danowski Morgan E , Cardellino Mark , Harrison Alicia , Assimes Themistocles L , Knowles Joshua W , Christensen Kurt D , Sturm Amy C , Sun Yan V , Hui Qin , Pyarajan Saiju , Shi Yunling , Whitbourne Stacey B , Gaziano J Michael , Muralidhar Sumitra , Vassy Jason L 
Published: March 2024

Abstract

Objective
The development of clinical research informatics tools and workflow processes associated with re-engaging biobank participants has become necessary as genomic repositories increasingly consider the return of actionable research results.

Materials and Methods
Here we describe the development and utility of an informatics application for participant recruitment and enrollment management for the Veterans Affairs Million Veteran Program Return Of Actionable Results Study, a randomized controlled pilot trial returning individual genetic results associated with familial hypercholesterolemia.

Results
The application is developed in Python-Flask and was placed into production in November 2021. The application includes modules for chart review, medication reconciliation, participant contact and biospecimen logging, survey recording, randomization, and documentation of genetic counseling and result disclosure. Three primary users, a genetic counselor and two research coordinators, and 326 Veteran participants have been integrated into the system as of February 23, 2023. The application has successfully handled 3367 task requests involving greater than 95 000 structured data points. Specifically, application users have recorded 326 chart reviews, 867 recruitment telephone calls, 158 telephone-based surveys, and 61 return of results genetic counseling sessions, among other available study tasks.

Conclusion
The development of usable, customizable, and secure informatics tools will become increasingly important as large genomic repositories begin to return research results at scale. Our work provides a proof-of-concept for developing and using such tools to aid in managing the return of results process within a national biobank.
Evaluating cross-reactivity of new psychoactive substances (NPS) in human whole blood by enzyme-linked immunosorbent assay (ELISA)
Authors: Cieri Grace , Mohr Amanda L A , Mastrovito Rebecca , Logan Barry K 
Published: March 2024

Abstract
Due to the increase in the use of novel psychoactive substances (NPS) and their overall prevalence, it is important to have effective and reliable screening technologies to detect NPS in biological matrices. Enzyme-linked immunosorbent assays (ELISA) are among the most popular screening methods. To evaluate the effectiveness of ELISA for NPS detection, five subclasses of NPS (novel synthetic opioids, fentanyl analogs, stimulants, benzodiazepines and hallucinogens) were evaluated in whole blood for their cross-reactivity on commercially available ELISA kits. A variety of novel synthetic opioids were tested at concentrations of 1–80 ng/mL and 50–2000 ng/mL and demonstrated no cross-reactivity to a morphine ELISA plate at either concentration range. Fentanyl analogs were tested at concentrations ranging from 0.01 to 1 ng/mL and had cross-reactivities ranging from 8% to 178% on the fentanyl ELISA kit used. Both para-chloro fentanyl (178%) and acryl fentanyl (164%) showed cross-reactivities well above that of fentanyl. Novel stimulants were tested at concentrations of 0.5–40 ng/mL and 20–2,000 ng/mL. 4-Fluoroamphetamine was the only novel stimulant with cross-reactivity (3,354%) to the amphetamine ELISA plate. Novel benzodiazepines were tested at concentrations of 1–40 ng/mL on a benzodiazepine plate. Cross-reactivities ranged from 36.1% to 263%, with desalkylflurazepam having the highest cross-reactivity. Finally, novel hallucinogens were tested at concentrations of 0.5–10 ng/mL on a phencyclidine (PCP) ELISA plate, which produced no cross-reactivity and then with 10–1,000 ng/mL, which gave results from 56.6% to 151%. Both hydroxy-PCP (151%) and chloro-PCP (137%) showed cross-reactivities above that of PCP. This research has demonstrated the utility of using ELISA-based screening for novel benzodiazepines, hallucinogens and for fentanyl analogs; however, there is limited application and risk of false-negative results for the other drug classes due to low or non-existent cross-reactivities.