bluuebunny/crossref_metadata_2025 huggingface dataset:
Epistasis and pleiotropy‐induced variation for plant breeding
Authors: Dwivedi Sangam L. , Heslop‐Harrison Pat , Amas Junrey , Ortiz Rodomiro , Edwards David
Published: June 2024

Epistasis refers to nonallelic interaction between genes that cause bias in estimates of genetic parameters for a phenotype with interactions of two or more genes affecting the same trait. Partitioning of epistatic effects allows true estimation of the genetic parameters affecting phenotypes. Multigenic variation plays a central role in the evolution of complex characteristics, among which pleiotropy, where a single gene affects several phenotypic characters, has a large influence. While pleiotropic interactions provide functional specificity, they increase the challenge of gene discovery and functional analysis. Overcoming pleiotropy‐based phenotypic trade‐offs offers potential for assisting breeding for complex traits. Modelling higher order nonallelic epistatic interaction, pleiotropy and non‐pleiotropy‐induced variation, and genotype × environment interaction in genomic selection may provide new paths to increase the productivity and stress tolerance for next generation of crop cultivars. Advances in statistical models, software and algorithm developments, and genomic research have facilitated dissecting the nature and extent of pleiotropy and epistasis. We overview emerging approaches to exploit positive (and avoid negative) epistatic and pleiotropic interactions in a plant breeding context, including developing avenues of artificial intelligence, novel exploitation of large‐scale genomics and phenomics data, and involvement of genes with minor effects to analyse epistatic interactions and pleiotropic quantitative trait loci, including missing heritability.
The dynamics of issue attention in policy process scholarship
Authors: Fagan E. J. , Furnas Alexander , Koski Chris , Thomas Herschel , Workman Samuel , Connor Corinne
Published: June 2024

This article examines the policy topics and theoretical debates found in Policy Studies Journal (PSJ) articles over the last three decades. PSJ is the premier journal for scholars studying policy processes, seeking to create generalizable theories across the spectrum of specific policy areas. To examine trends in PSJ over time, we collected 1314 abstracts from PSJ articles. We identified abstracts that mention major theories of the policy process and stages of the policy cycle. Next, we measured their policy content using the Comparative Agendas Project codebook, as well as their citations in academic journals and policy documents. We then explore these data, finding that changes in the content of PSJ articles over time correspond with other trends in the policy process field and PSJ's increased impact factor.
What is critical history of philosophy?
Authors: Sandford Stella
Published: June 2024

In the past half‐century critical historiographies of philosophy have challenged the exclusionist Eurocentric and masculinist presumptions of “history of philosophy,” and we have witnessed the multiplication of philosophical worlds in the relation of indigenous to Western scholarship and in critical philosophical anthropologies. Does this mean that there is, or can be, no unity to the history of philosophy? In this article, I argue that these challenges are not incompatible with our thinking the unity of the history of philosophy, so long as we understand it to be an historical “distributive unity,” constitutively related to other histories and to social, political, and institutional realities, and open to continuous transformation. The idea of a “critical history of philosophy” emerges from this. I argue that a critical history of philosophy proceeds via the problematizations of contemporary thought, which are then themselves challenged by that critical history and that it can and must include what remains marginal to its canonical history, working in conjunction with the theory and practices of other disciplines. These general claims are illustrated by showing how a critical history of philosophy could proceed in practice in relation to the contemporary problematization of the concept of “sex.”
Artifactually increased serum bicarbonate in a cat with rhabdomyolysis
Authors: Wynter Zoe R. , Ruane Emily , Kortum Andre J. , Hare Cassia H. Z.
Published: June 2024

A 3‐year‐old male neutered domestic shorthair cat presented with lethargy, hyporexia, and pyrexia of unknown origin. Biochemical analysis using a Beckman Coulter AU480 demonstrated marked increases in creatine kinase and aspartate aminotransferase, indicative of severe muscle injury, with concurrent presumptive myoglobinuria on urinalysis. A marked, non‐physiologic increase in measured bicarbonate and resultant negative anion gap was documented; however, calculated bicarbonate obtained via a point‐of‐care blood gas analyzer was within normal limits. Laboratory error due to interference by lactate dehydrogenase was suspected and supported by the results of subsequent biochemical testing. Artifactual increases in bicarbonate have been documented in cases of rhabdomyolysis in horses, cows, and a bird. However, to the best of the authors' knowledge, this is the first report to demonstrate this spurious change in a cat.
On the diameter of semigroups of transformations and partitions
Authors: East James , Gould Victoria , Miller Craig , Quinn‐Gregson Thomas , Ruškuc Nik
Published: June 2024

For a semigroup whose universal right congruence is finitely generated (or, equivalently, a semigroup satisfying the homological finiteness property of being type right‐), the right diameter of is a parameter that expresses how ‘far apart’ elements of can be from each other, in a certain sense. To be more precise, for each finite generating set for the universal right congruence on , we have a metric space where is the minimum length of derivations for as a consequence of pairs in ; the right diameter of with respect to is the diameter of this metric space. The right diameter of is then the minimum of the set of all right diameters with respect to finite generating sets. We develop a theoretical framework for establishing whether a semigroup of transformations or partitions on an arbitrary infinite set has a finitely generated universal right/left congruence, and, if it does, determining its right/left diameter. We apply this to prove results such as the following. Each of the monoids of all binary relations on , of all partial transformations on , and of all full transformations on , as well as the partition and partial Brauer monoids on , have right diameter 1 and left diameter 1. The symmetric inverse monoid on has right diameter 2 and left diameter 2. The monoid of all injective mappings on has right diameter 4, and its minimal ideal (called the Baer–Levi semigroup on ) has right diameter 3, but neither of these two semigroups has a finitely generated universal left congruence. On the other hand, the semigroup of all surjective mappings on has left diameter 4, and its minimal ideal has left diameter 2, but neither of these semigroups has a finitely generated universal right congruence.
Myths and methodologies: Considerations for evaluating the time course of thermoregulatory adaptation during heat acclimation
Authors: Tyler Christopher J. , Notley Sean R.
Published: June 2024

Since the early 1900s, repeated heat exposure has been used as a method to induce physiological adaptations that enhance our ability to tolerate heat stress during athletic and occupational pursuits. Much of this work has been dedicated to quantifying the time course of adaptation and identifying the minimum duration of acclimation required to optimise performance or enhance safety. To achieve this, investigators have typically applied classical (constant load) heat acclimation, whereby 60–90 min exercise is performed at the same absolute or relative intensity in a hot environment for 3–24 days, with adaptations evaluated using an identical forcing function test before and after. This approach has provided a foundation from which to develop our understanding of changes in thermoregulatory function, but it has several, frequently overlooked shortcomings, which have resulted in misconceptions concerning the time course of adaptation. It is frequently suggested that most of the thermoregulatory adaptations during heat acclimation occur within a week, but this is an oversimplification and a predictable artefact of the experimental designs used. Consequently, the time course of complete human adaptation to heat remains poorly understood and appears to vary considerably due to numerous individual factors. The purpose of this communication is to highlight the key methodological considerations required when interpreting the existing literature documenting adaptation over time. We also propose potential means by which to improve the way we induce and quantify the magnitude of adaptation to expedite discovery.
Review of Passenger Railroad EMU and MU Rolling Stock in the US and Canada – Part I, New York State Region
Authors: Donohue Brian P.
Published: June 2024

Since the invention of the first electrified, self-propelled rail vehicles by Siemens & Halske in 1879 followed by the pioneering innovations of Frank Sprague starting in 1886, self-propelled, passenger, electric traction rail vehicles have evolved into an amazing variety of use cases, shapes and sizes to the present date. With the amelioration of each generation, the electrical and mechanical engineering disciplines have developed a high degree of cooperation and integration to what has evolved into a seamless systems approach that allows agencies and railroads to enjoy record breaking, yet safe commuter and short-haul passenger railroad service with an array of amenities and technical advancements. The core of these rail vehicles are and were humble looking Electric Multiple Unit (EMU) (also referred to as Multiple Unit (MU)) trains that unceremoniously ply the rails around major cities with hundreds of daily riders on board. These otherwise, non-descript vehicles often have mundane identifications such as “MP-54” or “M-9.” Once in a while, one of these workhorses garners brief notoriety that leads to a full name such as “Metroliner.” But these full names, more often than not, are simply duplicated by analogy much in the same way the term “Watergate” has been overused. The identification of each fleet and the uniqueness / advancements that each have brought to the passenger rail industry since 1904 is the goal of this paper series.

This paper is the first in a short series that will present a simple historic review of the electric, self-propelled railroad vehicles (EMUs) that were or are currently in service in the United States and Canada. The review begins with the transition away from wooden cars when steel cars were necessary by design. These early cars helped to define the EMU (and MU) benchmark and how they differ from other rail rolling stock of the early 1900s such as elevated / subway cars, interurbans, and locomotive-drawn coach cars. Regulation was part of the progress, but ever-increasingly heavy passenger, mail and cargo loads, tunnel designs and general progress of design evolution helped to define this classification of rolling stock that eventually has folded into the United States-defined FRA (Federal Railroad Administration) Tier 1 passenger fleet. This first paper will begin with a focus on EMUs of the New York State region, starting with Long Island and Westchester, New York branch lines. A future, second history paper will feature equipment from the States of Connecticut and New Jersey. The third history paper will feature equipment serving the cities of Philadelphia and Chicago. And the fourth and final history paper will feature other regions of the United States and Canada.
Multiscale Computational Modeling of Subsurface Cracking in Railhead: Insights Into Fatigue Life
Authors: Saberi Sina , Whetstone Gavin , Allen David H.
Published: June 2024

Railways, crucial to national transport, constantly face rolling contact loads that lead to subsurface cracking. This study examines how these cracks impact the fatigue life of railheads. The focus is on modeling the progressive growth of these cracks, which is crucial to preventing severe failures. A finite element model simulates stress from wheel contact, considering the steel’s ductility. A multiscale computational method enhances modeling efficiency, focusing on local scale crack behavior influenced by global scale stress tractions. This approach aims to predict when a railhead might fail. An advanced non-linear cohesive zone model is used for more accurate predictions of crack growth behavior. This involves developing sophisticated rail testing protocols for model calibration and validation, ensuring real-world applicability. The research employs phased array ultrasonic testing for non-destructive internal crack analysis. This methodology, illustrate the experimental results by measures the internal crack geometry under long-term cyclic loading. These insights are crucial for understanding railhead life expectancy post-crack detection, enhancing railway safety, reliability, and efficiency.
Powering Onboard Bearing Health Monitoring Sensors With Thermoelectric Generators Under Non-Uniform Temperatures
Authors: Capitanachi Danna , de Leon Gael , Rodriguez Carlos , Tarawneh Constantine , Foltz Heinrich
Published: June 2024

Wireless onboard health monitoring devices are a promising preventive technology that can detect the early stages of bearing defects. However, the nature of the continuous monitoring requires an energy source sufficient to record and transmit data. Thermoelectric energy harvesting is an effective solution to power onboard wireless condition monitoring sensors during railroad operations. Thermoelectric Generators (TEGs) are considered to be environmentally safe, do not contain moving parts or complex structures, and require little maintenance. The TEGs play a crucial role in providing energy to run vibration and temperature sensors, as well as supporting LoRa communications. However, TEGs may be subjected to non-uniform temperature differentials caused by the forced convection generated by air motion relative to the vehicle when mounted on the railcar. It can be shown that non-homogeneous temperatures of two TEGs connected in series lead to reduced power output in comparison to the available power from each alone, and if the temperature difference of the underperforming TEG is lower than 41.4% of the other TEG, even less power than one TEG alone. This paper presents analysis and experimental data comparing several possible design solutions: (1) a simple series connection, (2) a series connection with bypass diodes, and (3) isolated TEGS with separate boost converters for each module.
EPS Geofoam In-Filled Ground Vibration Barriers for Environmental Sustainability of Ballasted High-Speed Railway Tracks: State of the Art
Authors: Karalikkadan Suhail , Khan M. Roshan
Published: June 2024

The transportation industry has rapidly evolved in recent decades, with high-speed railways (HSR) having substantially contributed to fulfilling the growing transportation needs of the global population. It is often referred to as the transport mode of the future since it provides four key attributes to consumers: safety, speed, capacity, and sustainability. Although HSR lines offer numerous benefits, increased ground vibrations and noise from faster train speeds and heavier axle loads have become a challenging railway operation issue. These ground-borne railway vibrations adversely affect the structural performance of the railway infrastructure, the vibration-sensitivity of buildings near the track, and the productivity and comfort of the residents in the buildings close to the railway tracks. The vibration mitigation strategies for railway tracks align with similar sources of cyclic dynamic loads since elastic wave propagation in soils is mostly analogous. The generation, propagation, and mitigation of ground vibrations highly depend on the embankment soil properties, subsurface conditions, and train characteristics (operational speed and axle load). Broadly, ground-borne vibrations from railways can be reduced by implementing control measures at the source or receptor, or by impeding the transmission path using wave barriers. More often, damping material in-filled trenches positioned at varied distances from the railway embankment (along the track) is used to attenuate vibrations due to their low cost and relatively high performance. It performs as a discontinuity in the path of the surface waves, causing them to reflect, refract, damp and then propagate an attenuated wave. This paper reviews the utilization of Expanded Polystyrene (EPS) geofoam as an in-fill material for vibration mitigation trenches, specifically for attenuation of high-speed train-induced ground vibrations. EPS geofoam infilled wave barrier trenches with higher depth, higher width, and placement close to the track exhibit maximum vibration attenuation efficiencies, up to 60–70%. Using lower-density EPS geofoam for in-filling the trench also delivers a higher vibration attenuation efficiency. Moreover, deploying an EPS geofoam layer at the slope of railway formations is found to be yet another effective method for mitigating ground-borne railway vibrations. Incorporating a hybrid combination of EPS geofoam in-filled trenches and EPS geofoam blocks at the slope of the railway formations exhibits a substantially high potential for attenuation of railway vibrations, irrespective of the underlying embankment soil. Investigating mitigation strategies using different EPS geofoam layouts reveals that significant vibration reduction can be achieved using EPS geofoam in-filled trenches as passive vibration wave barriers next to the railway tracks.
Spectral Clustering in Railway Crossing Accidents Analysis
Authors: Villalobos Ethan , Lugo Hector , Cheng Biqian , Gutierrez Miguel , Tarawneh Constantine , Xu Ping , Chen Jia , Papalexakis Evangelos E.
Published: June 2024

This study employs graph mining and spectral clustering to analyze patterns in railway crossing accidents, utilizing a comprehensive dataset from the US Department of Transportation. By constructing a graph of implicit relationships between railway companies based on shared accident localities, we apply spectral clustering to identify distinct clusters of companies with similar accident patterns. This offers nuanced insight into the underlying structure of these incidents. Our results indicate that “Highway User Position” and “Equipment Involved” play pivotal roles in accident clustering, while temporal elements like “Date” and “Time” exert a diminished impact. This research not only sheds light on potential accident causation factors but also sets the stage for subsequent predictive safety analyses. It aims to serve as a cornerstone for future studies that aspire to leverage advanced data-driven techniques for improving railway crossing safety protocols.
Kernel Ridge Regression in Predicting Railway Crossing Accidents
Authors: Villalobos Ethan , Tarawneh Constantine , Chen Jia , Papalexakis Evangelos E. , Xu Ping
Published: June 2024

Expanding on the insights from our initial investigation into railway accident patterns, this paper delves deeper into the predictive capabilities of machine learning to forecast potential accident trends in railway crossings. Focusing on critical factors such as “Highway User Position” and “Equipment Involved,” we integrate Kernel Ridge Regression (KRR) models tailored to distinct clusters, as well as a global model for the entire dataset. These models, trained on historical data, discern patterns and correlations that might elude traditional statistical methods. Our findings are compelling: certain clusters, despite limited data points, showcase remarkably Root Mean Squared Error (RMSE) values between predictions and real data, indicating superior model performance. However, certain clusters hint at potential overfitting, given the disparities between model predictions and actual data. Conversely, clusters with vast datasets underperform compared to the global model, suggesting intricate interactions within the data that might challenge the model’s capabilities. The performance nuances across clusters emphasize the value of specialized, cluster-specific models in capturing the intricacies of each dataset segment. This study underscores the efficacy of KRR in predicting future railway crossing incidents, fostering the implementation of data-driven strategies in public safety.
Superconductivity due to fluctuating loop currents
Authors: Palle Grgur , Ojajärvi Risto , Fernandes Rafael M. , Schmalian Jörg
Published: June 2024

Orbital magnetism and the loop currents (LCs) that accompany it have been proposed to emerge in many systems, including cuprates, iridates, and kagome superconductors. In the case of cuprates, LCs have been put forward as the driving force behind the pseudogap, strange-metal behavior, and
d

x
2
−
y
2

-wave superconductivity. Here, we investigate whether fluctuating intra-unit-cell LCs can cause unconventional superconductivity. For odd-parity LCs, we find that they are repulsive in all pairing channels near the underlying quantum-critical point (QCP). For even-parity LCs, their fluctuations give rise to unconventional pairing, which is not amplified in the vicinity of the QCP, in sharp contrast to pairing mediated by spin-magnetic, nematic, or ferroelectric fluctuations. Applying our formalism to the cuprates, we conclude that fluctuating intra-unit-cell LCs are unlikely to yield
d

x
2
−
y
2

-wave superconductivity. If LCs are to be relevant for the cuprates, they must break translation symmetry.
Symbionts out of sync: Decoupled physiological responses are widespread and ecologically important in lichen associations
Authors: Meyer Abigail R. , Koch Natália M. , McDonald Tami , Stanton Daniel E.
Published: June 2024

A core vulnerability in symbioses is the need for coordination between the symbiotic partners, which are often assumed to be closely physiologically integrated. We critically re-examine this assumed integration between symbionts in lichen symbioses, recovering a long overlooked yet fundamental physiological asymmetry in carbon balance. We examine the physiological, ecological, and transcriptional basis of this asymmetry in the lichen
Evernia mesomorpha
. This carbon balance asymmetry depends on hydration source and aligns with climatic range limits. Differences in gene expression across the
E. mesomorpha
symbiosis suggest that the physiologies of the primary lichen symbionts are decoupled. Furthermore, we use gas exchange data to show that asymmetries in carbon balance are widespread and common across evolutionarily disparate lichen associations. Using carbon balance asymmetry as an example, we provide evidence for the wide-ranging importance of physiological asymmetries in symbioses.
Schlafen 11 triggers innate immune responses through its ribonuclease activity upon detection of single-stranded DNA
Authors: Zhang Peng , Hu Xiaoqing , Li Zekun , Liu Qian , Liu Lele , Jin Yingying , Liu Sizhe , Zhao Xiang , Wang Jianqiao , Hao Delong , Chen Houzao , Liu Depei
Published: June 2024

Nucleic acids are major structures detected by the innate immune system. Although intracellular single-stranded DNA (ssDNA) accumulates during pathogen infection or disease, it remains unclear whether and how intracellular ssDNA stimulates the innate immune system. Here, we report that intracellular ssDNA triggers cytokine expression and cell death in a CGT motif–dependent manner. We identified Schlafen 11 (SLFN11) as an ssDNA-activated RNase, which is essential for the innate immune responses induced by intracellular ssDNA and adeno-associated virus infection. We found that SLFN11 directly binds ssDNA containing CGT motifs through its carboxyl-terminal domain, translocates to the cytoplasm upon ssDNA recognition, and triggers innate immune responses through its amino-terminal ribonuclease activity that cleaves transfer RNA (tRNA). Mice deficient in Slfn9, a mouse homolog of SLFN11, exhibited resistance to CGT ssDNA–induced inflammation, acute hepatitis, and septic shock. This study identifies CGT ssDNA and SLFN11/9 as a class of immunostimulatory nucleic acids and pattern recognition receptors, respectively, and conceptually couples DNA immune sensing to controlled RNase activation and tRNA cleavage.
Waking the sleeping giant: Single-stranded DNA binds Schlafen 11 to initiate innate immune responses
Authors: Ragland Stephanie A. , Kagan Jonathan C.
Published: June 2024

Single-stranded DNA containing CGT/A motifs binds to the helicase domain of Schlafen 11 (SLFN11) to initiate cell death and cytokine production via SLFN11 ribonuclease activity (see related Research Article by Zhang
et al.
).
Long-term changes in the phenotype and cytokine production of monocytes in COVID-19 recovered and vaccinated individuals
Authors: Ostapchuk Yekaterina O. , Lushova Anzhelika V. , Kan Sofia A. , Abdolla Nurshat , Kali Aikyn , Tleulieva Raikhan , Perfilyeva Anastassiya V. , Perfilyeva Yuliya V.
Published: June 2024

Monocytes play a crucial role in the immune response against pathogens. Here, we sought to determine COVID-19 and the vaccine Gam-COVID-Vac induce long-term changes in the phenotype and cytokine production of circulating monocytes. Monocytes were purified from peripheral blood mononuclear cells of healthy donors who had not had COVID-19 or vaccination, who had received two doses of Gam-COVID-Vac, and who had mild/moderate COVID-19 in the last 6 months and evaluated by flow cytometry. To investigate the effect of SARS-CoV-2 proteins, monocytes were cultured for 2 days with or without stimulation with recombinant SARS-CoV-2 S1 and N peptides. Monocytes obtained from vaccinated and recovered individuals showed increased basal expression of HLA-DR, CD63, CXCR2, and TLR7. We also observed an increased frequency of CD63
+
classical monocytes in both groups, as well as an increased frequency of HLA-DR
+
non-classical monocytes in the COVID-19-recovered group compared to the control group. Monocytes from vaccinated and recovered donors produced higher basal levels of IL-6, IL-1β, and TNF-α cytokines.
Ex vivo
stimulation with SARS-CoV-2 antigens induced increased expression of HLA-DR and TLR7 on monocytes obtained from the control group. The challenge with SARS-CoV-2 antigens had no effect on the production of IL-6, IL-1β, and TNF-α cytokines by monocytes. The acquired data offer compelling evidence of enduring alterations in both the phenotype and functional status of circulating monocytes subsequent to vaccination with Gam-COVID-Vac and mild/moderate COVID-19 infection. At least some of these changes appear to be a consequence of exposure to SARS-CoV-2 S1 and N antigens.
Non-interchangeable functions of efflux transporters of
Pseudomonas aeruginosa
in survival under infection-associated stress
Authors: Adamiak Justyna W. , Ajmal Laiba , Zgurskaya Helen I.
Published: June 2024

Pseudomonas aeruginosa
is a challenging opportunistic pathogen due to its intrinsic and acquired mechanisms of antibiotic resistance. A large repertoire of efflux transporters actively expels antibiotics, toxins, and metabolites from cells and enables growth of
P. aeruginosa
in diverse environments. In this study, we analyzed the roles of representative efflux pumps from the Resistance-Nodulation-Division (RND), Major Facilitator Superfamily (MFS), and Small Multidrug Resistance (SMR) families of proteins in the susceptibility of
P. aeruginosa
to antibiotics and bacterial growth under stresses imposed by human hosts during bacterial infections: an elevated temperature, osmotic stress, low iron, bile salts, and acidic pH. We selected five RND pumps MexAB-OprM, MexEF-OprN, MexCD-OprJ, MuxABC-OpmB, and TriABC-OpmH that differ in their substrate specificities and expression profiles, two MFS efflux pumps PA3136-3137 and PA5158-5160 renamed here into MfsAB and MfsCD-OpmG, respectively, and an SMR efflux transporter PA1540-1541 (MdtJI). We found that the most promiscuous RND pumps such as MexEF-OprN and MexAB-OprM are integrated into diverse survival mechanisms and enable
P. aeruginosa
growth under various stresses. MuxABC-OpmB and TriABC-OpmH pumps with narrower substrate spectra are beneficial only in the presence of the iron chelator 2,2′-dipyridyl and bile salts, respectively. MFS pumps do not contribute to antibiotic efflux but play orthogonal roles in acidic pH, low iron, and in the presence of bile salts. In contrast, MdtJI protects against polycationic antibiotics but does not contribute to survival under stress. Thus, efflux pumps play specific, non-interchangeable functions in
P. aeruginosa
cell physiology and bacterial survival under stresses.

IMPORTANCE

The role of multidrug efflux pumps in the intrinsic and clinical levels of antibiotic resistance in
Pseudomonas aeruginosa
and other gram-negative bacteria is well-established. Their functions in bacterial physiology, however, remain unclear. The
P. aeruginosa
genome comprises an arsenal of efflux pumps from different protein families, the substrate specificities of which are typically assessed by measuring their impact on susceptibility to antibiotics. In this study, we analyzed how deletions and overproductions of efflux pumps affect
P. aeruginosa
growth under human-infection-induced stresses. Our results show that the physiological functions of multidrug efflux pumps are non-redundant and essential for the survival of this important human pathogen under stress.
Targeted eradication of EBV-positive cancer cells by CRISPR/dCas9-mediated EBV reactivation in combination with ganciclovir
Authors: Sugiokto Febri Gunawan , Li Renfeng
Published: June 2024

Epstein-Barr virus (EBV) is a ubiquitous human tumor virus that establishes lifelong, persistent infections in B cells. The presence of EBV in cancer cells presents an opportunity to target these cells by reactivating the virus from latency. In this study, we developed a novel approach for EBV reactivation termed clustered regularly interspaced short palindromic repeats (CRISPR)/dCas9-mediated EBV reactivation (CMER) strategy. Using modified CRISPR-associated protein 9 (dCas9) fused with VP64, we designed 10 single guide RNAs (sgRNAs) to target and activate the EBV immediate-early gene promoter. In Akata Burkitt lymphoma cells, 9 out of 10 CMER sgRNAs effectively reactivated EBV. Among these, CMER sgRNA-5 triggered robust reactivation across various cell types, including lymphoma, gastric cancer, and nasopharyngeal carcinoma cells. Importantly, the combination of CMER and ganciclovir selectively eliminated EBV-positive cells, regardless of their cell origin. These findings indicate that targeted virus reactivation by CMER, combined with nucleoside analog therapy, holds promise for EBV-associated cancer treatment.

IMPORTANCE

This study explores a novel strategy called clustered regularly interspaced short palindromic repeats (CRISPR)/dCas9-mediated Epstein-Barr virus (EBV) reactivation (CMER) to reactivate the Epstein-Barr virus in cancer cells. EBV is associated with various cancers, and reactivating EBV from latency offers a potential therapeutic strategy. We utilized an enzymatically inactive CRISPR-associated protein 9 (dCas9) fused with VP64 and designed 10 single guide RNAs to target the EBV immediate-early gene promoter. Nine of these sgRNAs effectively reactivated EBV in Burkitt lymphoma cells, with CMER sgRNA-5 demonstrating strong reactivation across different cancer cell types. Combining CMER with ganciclovir selectively eliminated EBV-positive cells, showing promise for EBV-associated cancer treatment.
Iron limitation induces motility in uropathogenic
E. coli
CFT073 partially through action of LpdA
Authors: Frick-Cheng A. E. , Shea A. E. , Roberts J. R. , Smith S. N. , Ohi M. D. , Mobley H. L. T.
Published: June 2024

More than half of women will experience a urinary tract infection (UTI) with most cases caused by uropathogenic
Escherichia coli
(UPEC). Bacterial swimming motility enhances UPEC pathogenicity, resulting in more severe disease outcomes including kidney infection. Surprisingly, the connection between motility and iron limitation is mostly unexplored despite the lack of free iron available in the host. We sought to investigate a potential connection between iron restriction and regulation of motility in UPEC. We cultured
E. coli
CFT073, a prototypical UPEC strain, under iron limitation and observed that CFT073 had elevated
fliC
(flagella) promoter activity, and this iron-specific response was repressed by the addition of exogenous iron. We confirmed increased flagellar expression in CFT073 by measuring
fliC
transcript, FliC protein, and surface-expressed flagella under iron-limited conditions. Interestingly, known motility regulator
flhDC
did not have altered transcription under these conditions. To define the regulatory mechanism of this response, we constructed single knockouts of eight master regulators and found the iron-regulated response was lost in
crp, arcA,
and
fis
mutants. Thus, we focused on the five genes regulated by all three regulators. Of the five genes knocked out, the iron-regulated motility response was most strongly dysregulated in the
lpdA
mutant, which also resulted in significantly lowered fitness in the murine model of ascending UTI, both against the WT and a non-motile
fliC
mutant. Collectively, we demonstrated that iron-mediated motility in CFT073 is partially regulated by
lpdA
, which contributes to the understanding of how uropathogens differentially regulate motility mechanisms in the iron-restricted host.

IMPORTANCE

Urinary tract infections (UTIs) are ubiquitous and responsible for over five billion dollars in associated health care costs annually. Both iron acquisition and motility are highly studied virulence factors associated with uropathogenic
Escherichia coli
(UPEC), the main causative agent of uncomplicated UTI. This work is innovative by providing mechanistic insight into the synergistic relationship between these two critical virulence properties. Here, we demonstrate that iron limitation has pleiotropic effects with consequences that extend beyond metabolism and impact other virulence mechanisms. Indeed, targeting iron acquisition as a therapy may lead to an undesirable enhancement of UPEC pathogenesis through increased motility. It is vital to understand the full breadth of UPEC pathogenesis to adequately respond to this common infection, especially with the increase of antibiotic-resistant pathogens.
Cellular endosomal potassium ion flux regulates arenavirus uncoating during virus entry
Authors: Shaw Amelia B. , Tse Hiu Nam , Byford Owen , Plahe Grace , Moon-Walker Alex , Hover Samantha E. , Saphire Erica Ollmann , Whelan Sean P. J. , Mankouri Jamel , Fontana Juan , Barr John N.
Published: June 2024

Lymphocytic choriomeningitis virus (LCMV) is an enveloped and segmented negative-sense RNA virus classified within the
Arenaviridae
family of the
Bunyavirales
order. LCMV is associated with fatal disease in immunocompromised populations and, as the prototypical arenavirus member, acts as a model for the many highly pathogenic members of the
Arenaviridae
family, such as Junín, Lassa, and Lujo viruses, all of which are associated with devastating hemorrhagic fevers. To enter cells, the LCMV envelope fuses with late endosomal membranes, for which two established requirements are low pH and interaction between the LCMV glycoprotein (GP) spike and secondary receptor CD164. LCMV subsequently uncoats, where the RNA genome-associated nucleoprotein (NP) separates from the Z protein matrix layer, releasing the viral genome into the cytosol. To further examine LCMV endosome escape, we performed an siRNA screen which identified host cell potassium ion (K

+

) channels as important for LCMV infection, with pharmacological inhibition confirming K
+
channel involvement during the LCMV entry phase completely abrogating productive infection. To better understand the K
+
-mediated block in infection, we tracked incoming virions along their entry pathway under physiological conditions, where uncoating was signified by separation of NP and Z proteins. In contrast, K
+
channel blockade prevented uncoating, trapping virions within Rab7 and CD164-positive endosomes, identifying K
+
as a third LCMV entry requirement. K
+
did not increase GP-CD164 binding or alter GP-CD164-dependent fusion. Thus, we propose that K
+
mediates uncoating by modulating NP-Z interactions within the virion interior. These results suggest K
+
channels represent a potential anti-arenaviral target.

IMPORTANCE

Arenaviruses can cause fatal human disease for which approved preventative or therapeutic options are not available. Here, using the prototypical LCMV, we identified K

+

channels as critical for arenavirus infection, playing a vital role during the entry phase of the infection cycle. We showed that blocking K

+

channel function resulted in entrapment of LCMV particles within late endosomal compartments, thus preventing productive replication. Our data suggest K

+

is required for LCMV uncoating and genome release by modulating interactions between the viral nucleoprotein and the matrix protein layer inside the virus particle.
Postlaryngectomy pharyngoplasty with melolabial flap
Authors: Gupta Devendra Kumar , Patel Bhaumik , Tanwar Deepika
Published: June 2024

To the best of our knowledge, this is the largest case series describing the use of a melolabial flap for postlaryngectomy pharyngoplasty. It is an excellent alternative for pharyngoplasty, especially in cases post chemoradiotherapy. It accomplishes the goal while removing the restrictions of local and distant flaps. Although donor site morbidity is acceptable, specific consent is required due to the possibility of functional and cosmetic impairment. Additional cases with a larger sample size and a longer follow-up period can assist corroborate our first findings. In addition, because we tend to protect facial vessels for this flap, a follow-up about the compromise of oncological safety at level IB is required. In our case series, however, there was no recurrence until the final follow-up. As a result, it is a better option to pharyngoplasty post laryngectomy.
Pigmented villonodular synovitis and rheumatoid arthritis: diagnostic challenges and therapeutic considerations in a case of knee pain
Authors: Barlas Nur , Barlas Sait , Adalier Emre , Basnyat Shristi
Published: June 2024

We present a case of a woman in her 30s who visited the rheumatology clinic due to her persistent knee pain for 5 years, which spread to multiple joints. She was diagnosed with seropositive rheumatoid arthritis (RA). While most joints responded well to methotrexate and subsequently etanercept, persistent unilateral knee pain prompted further investigation. Imaging revealed synovitis and joint effusion in her knee, prompting arthroscopy and synovial biopsy, revealing pigmented villonodular synovitis (PVNS). Despite initial success with a tricompartmental synovectomy, her disease recurred. The decision was made to pursue medical therapy, with pexidartinib initiated by the oncology team. Our case report highlights the importance of considering other underlying conditions in patients with RA who do not achieve full clinical improvement despite standard treatment. Physicians should remain vigilant for atypical presentations and imaging features in patients with RA, for early recognition of PVNS can significantly impact treatment decisions and patient outcomes.
Coexisting presentation of two rare genetic variants of autosomal dominant polycystic kidney disease and Alport syndrome
Authors: Venda João , Henriques Andreia , Leal Rita , Alves Rui
Published: June 2024

Alport syndrome and autosomal dominant polycystic kidney disease are monogenic causes of chronic kidney disease and end-stage kidney failure. We present a case of a man in his 60s with progressive chronic kidney disease, bilateral sensorineural hearing loss and multiple renal cysts. Genetic analysis revealed a heterozygous variant inCOL4A3(linked to Alport syndrome) and in theGANABgene (associated with a milder form of autosomal dominant polycystic kidney disease). Although each variant confers a mild risk of developing end-stage kidney disease, the patient presented a pronounced and accelerated progression of chronic kidney disease, which goes beyond what would be predicted by adding up their individual effects. This suggests a potential synergic effect of both variants, which warrants further investigation.
Novel biomarker profiles to improve individual diagnosis and prognosis in patients with suspected inflammatory bowel disease: protocol for the Nordic inception cohort study (NORDTREAT)
Authors: Fejrskov Anja , Füchtbauer Johannes David , Davíðsdóttir Lóa G , Halfvarson Jonas , Høivik Marte Lie , Jensen Michael Dam , Mortensen Joachim Høg , Nielsen Lene Nyholm , Rejler Martin , Repsilber Dirk , Söderholm Johan D , Aalykke Claus , Andersen Vibeke , Christensen Robin , Kjeldsen Jens
Published: June 2024

Introduction

Inflammatory bowel disease (IBD), including ulcerative colitis and Crohn’s disease, can be challenging to diagnose, and treatment outcomes are difficult to predict. In the NORDTREAT cohort study, a Nordic prospective multicentre study, we aim to identify novel molecular biomarkers of diagnostic value by assessing the diagnostic test accuracy (cross-sectionally), as well as the prognostic utility when used as prognostic markers in the long-term (cohort study). In the diagnostic test accuracy study, the primary outcome is a successful diagnosis using one or more novel index tests at baseline compared with the ECCO criteria as the reference standard. The composite outcome of the prognostic utility study is ‘severe IBD’ within 52 weeks from inclusion, defined as one or more of the following three events: IBD-related surgery, IBD-related hospitalisation or IBD-related death.

Methods and analysis

We aim to recruit 800 patients referred on suspicion of IBD to this longitudinal observational study, a collaboration between 11 inclusion sites in Denmark, Iceland, Norway and Sweden. Inclusion will occur from February 2022 until December 2023 with screening and baseline visits for all participants and three outcome visits at weeks 12, 26 and 52 after baseline for IBD-diagnosed patients. Biological material (blood, faeces, biopsies, urine and hair), clinical data and lifestyle information will be collected during these scheduled visits.

Ethics and dissemination

This study will explore novel biomarkers to improve diagnostic accuracy and prediction of disease progression, thereby improving medical therapy and the quality of life for patients with IBD.

The study is approved by the Ethics Committee (DK: S-20200051, v1.4, 16.10.2021; IS: VSNb2021070006/03.01, NO: 193064; SE: DNR 2021-05090) and the Danish Data Protecting Agency (20/54594). Results will be disseminated through peer-reviewed journals, patient associations and presentations at international conferences.

Clinical trial registration number

NCT05414578.
Transcutaneous auricular vagal nerve stimulation for consciousness recovery in patients with prolonged disorders of consciousness (TAVREC): study protocol for a multicenter, triple-blind, randomized controlled trial in China
Authors: Zhou Long-yun , Peng Li-jun , Liu Ya-feng , Wang Shu-wei , Qiu Yue , Chen Si-jing , Feng Ming-ming , Liu Jin , Wu Shan-shan , Luo Ting , Liu Zhen-yu , Wu Hui-juan , Ge Jiang-ping , Reinhardt Jan D , Lu Xiao
Published: June 2024

Introduction

Prolonged disorders of consciousness (pDoC) are a catastrophic condition following brain injury with few therapeutic options. Transcutaneous auricular vagal nerve stimulation (taVNS), a safe, non-invasive intervention modulating thalamo-cortical connectivity and brain function, is a possible treatment option of pDoC. We developed a protocol for a randomised controlled study to evaluate the effectiveness of taVNS on consciousness recovery in patients with pDoC (TAVREC).

Methods and analysis

The TAVREC programme is a multicentre, triple-blind, randomised controlled trial with 4 weeks intervention followed by 4 weeks follow-up period. A minimum number of 116 eligible pDoC patients will be recruited and randomly receive either: (1) conventional therapy plus taVNS (30 s monophasic square current of pulse width 300 μs, frequency of 25 Hz and intensity of 1 mA followed by 30 s rest, 60 min, two times per day, for 4 weeks); or (2) conventional therapy plus taVNS placebo. Primary outcome of TAVREC is the rate of improved consciousness level based on the Coma Recovery Scale-Revised (CRS-R) at week 4. Secondary outcomes are CRS-R total and subscale scores, Glasgow Coma Scale score, Full Outline of UnResponsiveness score, ECG parameters, brainstem auditory evoked potential, upper somatosensory evoked potential, neuroimaging parameters from positron emission tomography/functional MRI, serum biomarkers associated with consciousness level and adverse events.

Ethics and dissemination

This study was reviewed and approved by the Research Ethics Committee of the First Affiliated Hospital of Nanjing Medical University (Reference number: 2023-SR-392). Findings will be disseminated in a peer-reviewed journal and presented at relevant conferences.

Trial registration number

ChiCTR2300073950.
Ultrasound-based comparative analysis and nomogram development for predicting triple-negative and non-triple-negative breast cancer: a 4-year institutional study in Quanzhou First Hospital
Authors: Su Liyang , Xie Qiaojie , Chen Jiaohong , Zhang Qingquan , Li Nian , Hong Chuntian
Published: June 2024

Objective

The objective of this study was to compare ultrasound features and establish a predictive nomogram for distinguishing between triple-negative breast cancer (TNBC) and non-TNBC.

Design

A retrospective cohort study.

Setting

This study was conducted at Quanzhou First Hospital, a grade A tertiary hospital in Quanzhou, China, with the research data set covering the period from September 2019 to August 2023.

Participants

The study included a total of 205 female patients with confirmed TNBC and 574 female patients with non-TNBC, who were randomly divided into a training set and a validation set at a ratio of 7:3.

Main outcome measures

All patients underwent ultrasound examination and received a confirmatory pathological diagnosis. Nodules were classified according to the Breast Imaging-Reporting and Data System standard. Subsequently, the study conducted a comparative analysis of clinical characteristics and ultrasonic features.

Results

A statistically significant difference was observed in multiple clinical and ultrasonic features between TNBC and non-TNBC. Specifically, in the logistic regression analysis conducted on the training set, indicators such as posterior echo, lesion size, presence of clinical symptoms, margin characteristics, internal blood flow signals, halo and microcalcification were found to be statistically significant (p<0.05). These significant indicators were then effectively incorporated into a static and dynamic nomogram model, demonstrating high predictive performance in distinguishing TNBC from non-TNBC.

Conclusion

The results of our study demonstrated that ultrasound features can be valuable in distinguishing between TNBC and non-TNBC. The presence of posterior echo, size, clinical symptoms, margin, internal flow, halo and microcalcification was identified as predictive factors for this differentiation. Microcalcification, hyperechoic halo, internal flow and clinical symptoms emerged as the strongest predictive factors, indicating their potential as reliable indicators for identifying TNBC and non-TNBC.