bluuebunny/crossref_metadata_2025 huggingface dataset:
Frequency and predictors of virtual hope box use in individuals experiencing suicidal ideation: An ecological momentary assessment investigation
Authors: Moscardini Emma H. , Le Thanh P. , Cowan Tovah , Gerner Jessica , Robinson Anthony , Cohen Alex S. , Tucker Raymond P.
Published: November 2023

Introduction

The Virtual Hope Box (VHB) is a smartphone application designed to support emotion regulation when one is distressed, in a crisis, or experiencing suicidal ideation (SI). Initial proof of concept studies indicate that individuals are more likely to use the VHB than traditional hope boxes, and find it both easy to setup and helpful. To our knowledge, no studies have harnessed ambulatory assessment methodology to assess VHB use as it relates to incidence of suicidal thinking.

Methods

As such, we recruited N = 50 undergraduates who endorsed SI either the past year or past 2 weeks to complete a 10‐day investigation. At baseline, participants were oriented to the VHB and instructed on how to use the application. Over the next 10 days, participants responded to prompts five times per day on their personal smartphones regarding their current experiences of SI and stress as well as VHB usage.

Results

Results found that most participants used the VHB at least once, rated its usefulness as high, and rated their perceived likelihood of future use as high. In addition, increases in state SI severity were related to subsequent VHB use.

Conclusion

The VHB may be a useful tool for managing crises in undergraduates experiencing suicidal thoughts.
Storytelling as Inverse Inverse Planning
Authors: Chandra Kartik , Li Tzu‐Mao , Tenenbaum Joshua B. , Ragan‐Kelley Jonathan
Published: November 2023

Great storytelling takes us on a journey the way ordinary reality rarely does. But what exactly do we mean by this “journey?” Recently, literary theorist Karin Kukkonen proposed that storytelling is “probability design:” the art of giving an audience pieces of information bit by bit, to craft the journey of their changing beliefs about the fictional world. A good “probability design” choreographs a delicate dance of certainty and surprise in the reader's mind as the story unfolds from beginning to end. In this paper, we computationally model this conception of storytelling. Building on the classic Bayesian inverse planning model of human social cognition, we treat storytelling as inverse inverse planning: the task of choosing actions to manipulate an inverse planner's inferences, and therefore a human audience's beliefs. First, we use an inverse inverse planner to depict social and physical situations, and present behavioral studies indicating that inverse inverse planning produces more expressive behavior than ordinary “naïve planning.” Then, through a series of examples, we demonstrate how inverse inverse planning captures many storytelling elements from first principles: character, narrative arcs, plot twists, irony, flashbacks, and deus ex machina are all naturally encoded in the flexible language of probability design.
Estimation of the number of single-photon emitters for multiple fluorophores with the same spectral signature
Authors: Li Wenchao , Li Shuo , Brown Timothy C. , Sun Qiang , Wang Xuezhi , Yakovlev Vladislav V. , Kealy Allison , Moran Bill , Greentree Andrew D.
Published: November 2023

Fluorescence microscopy is of vital importance for understanding biological function. However, most fluorescence experiments are only qualitative inasmuch as the absolute number of fluorescent particles can often not be determined. Additionally, conventional approaches to measuring fluorescence intensity cannot distinguish between two or more fluorophores that are excited and emit in the same spectral window, as only the total intensity in a spectral window can be obtained. Here we show that, by using photon number resolving experiments, we are able to determine the number of emitters and their probability of emission for a number of different species, all with the same measured spectral signature. We illustrate our ideas by showing the determination of the number of emitters per species and the probability of photon collection from that species, for one, two and three otherwise unresolvable fluorophores. The convolution binomial model is presented to represent the counted photons emitted by multiple species. Then, the expectation-maximization (EM) algorithm is used to match the measured photon counts to the expected convolution binomial distribution function. In applying the EM algorithm, to leverage the problem of being trapped in a sub-optimal solution, the moment method is introduced to yield an initial guess for the EM algorithm. Additionally, the associated Cramér–Rao lower bound is derived and compared with the simulation results.
Atomic diffraction from single-photon transitions in gravity and Standard-Model extensions
Authors: Bott Alexander , Di Pumpo Fabio , Giese Enno
Published: November 2023

Single-photon transitions are one of the key technologies for designing and operating very-long-baseline atom interferometers tailored for terrestrial gravitational-wave and dark-matter detection. Since such setups aim at the detection of relativistic and beyond-Standard-Model physics, the analysis of interferometric phases as well as of atomic diffraction must be performed to this precision and including these effects. In contrast, most treatments focused on idealized diffraction so far. Here, we study single-photon transitions, both magnetically induced and direct ones, in gravity and Standard-Model extensions modeling dark matter as well as Einstein-equivalence-principle violations. We take into account relativistic effects like the coupling of internal to center-of-mass degrees of freedom, induced by the mass defect, as well as the gravitational redshift of the diffracting light pulse. To this end, we also include chirping of the light pulse required by terrestrial setups, as well as its associated modified momentum transfer for single-photon transitions.
Modification of discharge sequences to control the random dispersion of flake particles during wafer etching
Authors: Ku Ching Ming , Jang Wen Yea , Cheng Stone
Published: November 2023

During the etching of the dielectric layer of semiconductors through plasma etching, numerous flake particles are generated in the etching equipment. These particles cause layout defects on the wafer and engender reduced yield on production lines. Accordingly, this study investigated how such flake particles could form in a chamber involving varying levels of deterioration on the electrostatic chuck surface and varying levels of by-product deposition. Moreover, we tested the effect of various electrostatic chuck discharge sequences and voltages on the deposition of these flake particles. Our experimental results revealed that selecting an appropriate radiofrequency power and a voltage discharge sequence protocol for the electrostatic chuck and using a low-frequency radiofrequency power supply could minimize the number of flake particles adhering to a wafer surface. In the proposed method, wafer contamination is controlled by suppressing unstable electric stress that arises when the etching chamber is coated with deposited by-products and the electrostatic chuck has a deteriorated surface.
The Move2Smile Online Hub for Parents to Support Aspects of Preschoolers’ Physical Literacy at Home: A Feasibility Study
Authors: James Maeghan E. , Cairney John , Odorico Nikoleta , Finlay-Watson Tracia , Arbour-Nicitopoulos Kelly P.
Published: November 2023

This study aimed to develop and evaluate the acceptability and feasibility of a web-based platform for parents to support preschoolers’ development of physical literacy. Specifically, this intervention focused on children’s motor and social-emotional skill development. Twenty parents (Mage = 35.7, SD = 4.2) of preschool-aged children (Mage = 4.1, SD = 0.6) were assigned three intervention modules and completed weekly usage and feedback questionnaires (1 = strongly disagree, 5 = strongly agree). Parents (n = 15) also completed a follow-up interview. Parents indicated the modules were useable (4.5/5), useful (4.5/5), feasible (4.4/5), enjoyable (4.5/5), and acceptable (4.5/5). Five themes underlying parental engagement were generated: (a) activity organization and planning, (b) (de)motivators, (c) parent knowledge and skills, (d) experience with the platform, and (e) application to everyday routines. The online modules under investigation were deemed both acceptable and feasible by parents. However, factors such as time and knowledge may impact parental engagement at home. Future research is needed to better understand the antecedents to parent physical literacy support behaviors in the early years.
The Effects of Spectators on National Basketball Association Free Throw Performance
Authors: Markwell Logan T. , Singh Harjiv , Strick Andrew J. , Porter Jared M.
Published: November 2023

Free throw shooting percentage has averaged around 75% for nearly five decades. However, free throw percentages significantly increased to 79% during the 2020 spectator-less National Basketball Association season. The current study investigated if the elevated free throw shooting percentage observed during the spectator-less season has returned to the 50-year average now that spectators have returned to National Basketball Association arenas. Moreover, home and away free throw percentages were examined to determine if a potential home-field advantage contributed to this phenomenon. Analyses revealed that the free throw shooting percentage from the spectator-less season was significantly higher than the two spectator-filled seasons preceding and following the spectator-less season. Furthermore, the analyses found no differences in free throw percentages between home and away games. While the free throw shooting percentage increased to 79% during the spectator-less season, the free throw shooting percentage returned to the 50-year average (i.e., ∼75%), following the spectator-less season. Additionally, it does not appear that a perceived home-field advantage influenced the increased free throw performance observed in the spectator-less season. Multiple factors likely contributed to this free throw phenomenon, including the environmental characteristics shaped by the lack of spectators.
Proinflammatory apoptosis
Authors: VanHook Annalisa M.
Published: November 2023

Apoptotic cells that cannot be expelled from the epithelium provoke inflammation by releasing ATP.
Adenovirus E1A binding to DCAF10 targets proteasomal degradation of RUVBL1/2 AAA+ ATPases required for quaternary assembly of multiprotein machines, innate immunity, and responses to metabolic stress
Authors: Zemke Nathan R. , Hsu Emily , Barshop William D. , Sha Jihui , Wohlschlegel James A. , Berk Arnold J.
Published: November 2023

Adenovirus small e1a protein modifies host cell physiology to optimize virus replication. The N-terminal ~140 aa of e1a interacts with RB-family proteins to derepress dNTP and DNA synthesis and with EP300/CREBBP lysine acetyltransferases and EP400-TIP60 chromatin-modifying complexes to inhibit host anti-viral innate immune responses. However, the e1a N-terminal region activates a late host anti-viral response due to stabilization and activation of IRF3. The E1A C-terminal region counteracts IRF3 stabilization through interactions with three host nuclear proteins with seemingly unrelated functions. All three C-terminal interactions are required for e1a-association into a multi-protein complex with scaffold subunits of a CRL4 E3 ubiquitin ligase and DCAF10, a presumed specificity subunit. This e1a-DCAF10-CRL4 prevents IRF3 stabilization indirectly by targeting the essential AAA+ ATPases RUVBL1/2, subunits of several HSP90 co-chaperones required for quaternary assembly of cellular protein machines required for anti-viral defenses and responses to genotoxic and metabolic stress.

IMPORTANCE

Inactivation of EP300/CREBB paralogous cellular lysine acetyltransferases (KATs) during the early phase of infection is a consistent feature of DNA viruses. The cell responds by stabilizing transcription factor IRF3 which activates transcription of scores of interferon-stimulated genes (ISGs), inhibiting viral replication. Human respiratory adenoviruses counter this by assembling a CUL4-based ubiquitin ligase complex that polyubiquitinylates RUVBL1 and 2 inducing their proteasomal degradation. This inhibits accumulation of active IRF3 and the expression of anti-viral ISGs, allowing replication of the respiratory HAdVs in the face of inhibition of EP300/CBEBBP KAT activity by the N-terminal region of E1A.
Complete genome sequence of
Actinoplanes sichuanensis
strain 03-723
T
Authors: Kawashima Taketsugu , Watanabe Yasuha , Arakawa Kazuharu
Published: November 2023

A mesophilic bacterium
Actinoplanes sichuanensis
strain 03-723

T

was previously isolated from soil by Sun et al. Here, we present a complete and annotated genome sequence of this strain, which has a total size of 12.1 Mbp with a G + C content of 70.1%.
A novel botybirnavirus with a unique satellite dsRNA causes latent infection in
Didymella theifolia
isolated from tea plants
Authors: Ye Liangchao , Shi Xinyu , He Yunqiang , Chen Jiao , Xu Qingeng , Shafik Karim , Fu Lanning , Yin Yumeng , Kotta-Loizou Ioly , Xu Wenxing
Published: November 2023

The unique, recently discovered fungus
Didymella theifolia
specifically infects local varieties of tea plant
Camellia sinensis
in China, and therefore, the characterization of its mycoviruses is important. Three double-stranded (ds) RNAs (1, 2, and 3, with 6,338, 5,910, and 727 bp in size, respectively) were identified in the avirulent
D. theifolia
strain CJP4-1, which exhibits normal growth and morphology. Characterization of these double-stranded RNAs (dsRNAs) revealed that the two largest elements are the genomic components of a novel botybirnavirus, tentatively named Didymella theifolia botybirnavirus 1 (DtBRV1). Conversely, dsRNA3 shares no detectable similarity with sequences deposited in public databases but has high similarity with the 5′-terminal regions of dsRNAs 1 and 2 and contains a duplicated region encoding a putative small peptide. All three dsRNAs are encapsidated in isometric virions
ca
. 40 nm in diameter, supporting the notion that dsRNA3 is a DtBRV1 satellite. SDS-polyacrylamide gel electrophoresis in combination with peptide mass fingerprint analysis revealed that the DtBRV1 capsid protein consists of polypeptides encoded by the 5′-terminal regions of both genomic components dsRNA1 and dsRNA2. Vertical transmission of DtBRV1 through conidia is efficient, while its horizontal transmission from CJP4-1 to other strains was not detected. DtBRV1, with or without dsRNA3, has no obvious effects on fungal growth and virulence, as illustrated following transfection of the virulent
D. theifolia
strain JYC1-6. In summary, DtBRV1 exhibits unique molecular traits and contributes to our understanding of mycovirus diversity.

IMPORTANCE

A novel botybirnavirus, infecting the tea plant pathogen
Didymella theifolia
and tentatively named Didymella theifolia botybirnavirus 1 (DtBRV1), together with an additional double-stranded RNA (dsRNA), was characterized. DtBRV1 comprises two dsRNAs (1 and 2) encapsidated in isometric virions, while dsRNA3 is a satellite. The satellite represents a unique specimen since it contains a duplicated region and has high similarity to the two botybirnavirus dsRNAs, supporting the notion that it most likely originated from a deficient genomic component. The biological characteristics of DtBRV1 were further determined. With their unique molecular traits, DtBRV1 and its related dsRNA expand our understanding of virus diversity, taxonomy, and evolution.
Identification of common fungal extracellular membrane (CFEM) proteins inFusarium saccharithat inhibit plant immunity and contribute to virulence
Authors: Huang Zhen , Zhou Yuming , Li Huixue , Bao Yixue , Duan Zhenzhen , Wang Caixia , Powell Charles A. , Wang Kai , Hu Qin , Chen Baoshan , Zhang Jisen , Zhang Muqing , Yao Wei
Published: November 2023

Fusarium sacchariis one of the primary pathogens causing pokkah boeng disease in sugarcane in China. Common fungal extracellular membrane (CFEM) domain-containing proteins only exist in fungi and play a significant role in the interaction of pathogens and plants. However, the CFEM proteins inF. sacchariwere not identified and functionally resolved. Of the 20 FsCFEM proteins identified from the genome ofF. sacchari, 16 FsCFEM genes were cloned, while 4 FsCFEM proteins (Fs06761, Fs08184, Fs10706, and Fs13617) were identified as effector proteins that could suppress the programmed cell death triggered by BCL2-associated X protein inNicotiana benthamiana. Subcellular localization analysis revealed that these four effectors could enter plant cells and are mainly located in the cell membrane and nucleus. By the yeast YTK12 secretion system, the signal peptides of four CFEM proteins were functionally verified. The expression levels of these four effector proteins were significantly increased in theF. sacchari-infected sugarcane plants. Through fungal gene knockout, three genes (Fs06761, Fs08184, and Fs13617) were found to be important pathogenic factors for pathogens. Our results support that the FsCFEM effector proteins were virulence effectors and might be involved in regulating plant immunity.

IMPORTANCE

Common fungal extracellular membrane (CFEM) domain-containing protein has long been considered an essential effector, playing a crucial role in the interaction of pathogens and plant. Strategies aimed at understanding the pathogenicity mechanism ofF. sacchariare eagerly anticipated to ultimately end the spread of pokkah boeng disease. Twenty FsCFEM proteins in the genome ofF. saccharihave been identified, and four FsCFEM effector proteins have been found to suppress BCL2-associated X protein-triggered programmed cell death inN. benthamiana. These four effector proteins have the ability to enter plant cells and inhibit plant immunity. Furthermore, the expression of these four FsCFEM effector proteins significantly increases during the infection stage, with the three of them playing an essential role in achieving full virulence. These study findings provide a direction toward further exploration of the immune response in sugarcane. By applying these discoveries, we can potentially control the spread of disease through techniques such as host-induced gene silencing.
Honduras HIV cohort: HLA class I and CCR5-Δ32 profiles and their associations with HIV disease outcome
Authors: Valenzuela-Ponce Humberto , Carbajal Candy , Soto-Nava Maribel , Tapia-Trejo Daniela , García-Morales Claudia , Murillo Wendy , Lorenzana Ivette , Reyes-Terán Gustavo , Ávila-Ríos Santiago
Published: November 2023

Human leukocyte antigen (HLA) polymorphisms represent the strongest genetic modifier of HIV disease progression. Diverse HLA distributions can lead to distinct HIV control landscapes at the population level. We aimed to describe HLA allele and haplotype frequencies (linkage disequilibrium, LD), CCR5-Δ32 frequency, and the impact of these variants on HIV disease outcome. HLA class I loci were typed at 4-digit resolution, and CCR5 variants were determined in 402 HIV clade B-infected, antiretroviral treatment-naïve individuals from Honduras. HLA LD was assessed using Fisher’s exact test. Using univariable and multivariable analyses, we evaluated HLA associations with HIV plasma viral load (pVL) and CD4 counts. We did not find any effect on HIV control between CCR5 genotypes. The previously defined HLA associations were found to be
B*57:01/03
,
B*42:01
,
A*25:01
, and
C*12:03
(protective) and
B*53:01
and
A*68:01
(risk). Consistent with our previous research in a Mesoamerican HIV cohort, Amerindian
B*35:12
was associated with poor HIV control. Other HLA-HIV associations not previously described were
C*03:04
and
B*08:01
, which were associated with higher pVL. Overall, this first report highlights the immunogenetic uniqueness of the Honduras population that expresses Amerindian, Caucasian, and African HLA subtypes. These findings not only support this cohort as ideal for identifying HLA correlates of HIV control but also may improve future research regarding allotransplantation and disease association.

IMPORTANCE

We identify both canonical and novel human leukocyte antigen (HLA)-HIV associations, providing a first step toward improved understanding of HIV immune control among the understudied Honduras Mestizo population. Our results are relevant to understanding the protective or detrimental effects of HLA subtypes in Latin America because their unique HLA diversity poses challenges for designing vaccines against HIV and interpreting results from such vaccine trials. Likewise, the description of the HLA profile in an understudied population that shows a unique HLA immunogenetic background is not only relevant for HIV immunology but also relevant in population genetics, molecular anthropology, susceptibility to other infections, autoimmune diseases, and allograft transplantation.
Environmental factors influencing the diversity and distribution of dictyostelid cellular slime molds in forest and farmland soils of western China
Authors: Zhang Zhaojuan , Yang Yingkun , Zhao Jing , Li Yu , Stephenson Steven L. , Qiu Junzhi , Liu Pu
Published: November 2023

Dictyostelid cellular slime molds (dictyostelids) are one of the major groups of eukaryotic amoeboid protists occurring in the soil microhabitat. The past few decades have witnessed an unprecedented interest in the ecology of dictyostelids, stimulated in part by the hidden soil protist diversity that has long been overlooked. However, a better understanding of the impact of various environmental factors on the biodiversity of dictyostelids is needed to understand the critical functional role of these organisms in the soil ecosystem. Species diversity of dictyostelids has been surveyed in some provinces of China, but little data exist for Gansu and Guizhou Provinces in western China. In this paper, we report data on the distribution and occurrence of dictyostelids in the soils of these two provinces. Samples were collected from 13 localities in central Gansu and the southeastern and southcentral portions of Guizhou Province. Eleven species of dictyostelids were recovered from 99 samples of soil. Six new records of dictyostelids are reported from Gansu Province and six species from Guizhou Province, respectively.
Polysphondylium violaceum
is a common species in both regions, while
Dictyostelium sphaerocephalum
and
Dictyostelium mucoroides
are widely distributed in Lanzhou, Gansu Province. The total number of species (seven) and the number of endemic species (three) of dictyostelids in mixed forests were higher than those in other forest types. Redundancy analysis indicated that soil pH, temperature, and elevation were the primary factors that affected dictyostelid occurrence. Nonmetric multidimensional scaling and principal component analysis indicated that the dictyostelid communities were significantly different between Gansu and Guizhou Provinces.

IMPORTANCE

Soil protists are an essential yet seriously understudied component of the soil microbiome. In this study, 11 new records of dictyostelids belonging to 2 orders, 3 families, and 4 genera were identified from 99 soil samples collected from different elevations and habitats in central Gansu and the southeastern and southcentral portions of Guizhou Province, China. We found that dictyostelid communities were significantly different between Gansu and Guizhou Provinces, apparently in response to different environmental factors. Moreover, dictyostelids were found to have the highest species diversity in mixed forests. Soil pH, temperature, and elevation were determined to be the primary factors that affect the distribution and occurrence of dictyostelids in Guizhou and Gansu Provinces. This work supplements the survey data available for dictyostelids elsewhere in China. These new findings have significant implications for our understanding of the diversity of soil microorganisms.
Development of a touchdown droplet digital PCR assay for the detection and quantitation of human papillomavirus 16 and 18 from self-collected anal samples
Authors: Haqshenas Gholamreza , Garland Suzanne M. , Balgovind Prisha , Cornall Alyssa , Danielewski Jennifer , Molano Monica , Machalek Dorothy A. , Murray Gerald
Published: November 2023

Broad-spectrum droplet digital polymerase chain reaction (ddPCR) assays can be used to quantitate multiple human papillomavirus (HPV) types. However, the presence of nucleotide mismatches at the primer binding sites may result in different optimal annealing temperatures and, consequently, under detection of some HPV types. Touchdown PCR uses decreasing annealing temperature over the first PCR cycles allowing for specific and efficient amplification of the target sequence. Here, as a proof-of-concept, we assessed if touchdown ddPCR (TD-ddPCR) using broad-spectrum oligonucleotides and genotype-specific probes targeting HPV L1 can be used to quantitate HPV. We tested our hypothesis using HPV positive cell lines and anal samples which potentially contain PCR inhibitors. Using serial dilutions of HPV16 and HPV18 DNA, the TD-ddPCR assays were performed with linearity across the dilution series (Pearson’s correlation
r
= 0.9999) and detected one copy of both HPV types, with no cross-reactivity to 27 other low-risk and high-risk HPV types. The PCRs were highly reproducible, with inter- and intra-assay coefficient of variations ranging 2.0–6.3% for HPV16 and 4.9–11.6% for HPV18. Testing self-collected anal samples positive for HPV16 (
n
= 29) or HPV18 (
n
= 33) and those negative for both HPV types (
n
= 22) with the ddPCR assay and Seegene Anyplex II HPV28 (Seegene, TD-ddPCR) showed high agreements between the two assays. In conclusion, HPV broad-spectrum primers containing mismatches at their target binding sites and a touchdown thermal cycling approach resulted in sensitive and specific amplification of HPV genome using ddPCR. The assay has potential clinical diagnostic applications for detection, quantitation, and monitoring of anal HPV infections.

IMPORTANCE

The quantity of the human papillomavirus (HPV) is associated with disease outcome. We designed an accurate and precise digital PCR assay for quantitating HPV in anal samples, a sample type that is typically problematic due to the presence of PCR inhibitors.
The phage-encoded PIT4 protein affects multiple two-component systems of
Pseudomonas aeruginosa
Authors: Schroven Kaat , Putzeys Leena , Kerremans Alison , Ceyssens Pieter-Jan , Vallino Marta , Paeshuyse Jan , Haque Farhana , Yusuf Ahmed , Koch Matthias D. , Lavigne Rob
Published: November 2023

Two-component systems (TCSs) control a large proportion of virulence factors in
Pseudomonas aeruginosa
. Yet, investigations on inhibitors of regulatory pathways of TCSs remain scarce, despite their potential in anti-virulence strategies. This work elucidates the molecular mechanism of PIT4, a protein encoded by the lytic
P. aeruginosa
phage LSL4. Single-copy expression of this early phage gene inhibits bacterial motility, in particular twitching motility, and reduces the virulence of
P. aeruginosa
in HeLa cells. Differential gene expression and a yeast two-hybrid screen showed that PIT4 interacts with components of different two-component systems. In one-on-one interaction assays, it was confirmed that PIT4 specifically interacts with the histidine kinase domains of FleS, PilS, and PA2882. This identified phage mechanism therefore demonstrates the ability of phage proteins to simultaneously target and impact multiple pathways and hints toward a biological function as an infection-exclusion mechanism. This work highlights the potential of previously unknown phage proteins in virulence regulation of multidrug resistant pathogens that could in future be exploited for anti-virulence strategies and biotechnological applications.

IMPORTANCE

More and more
Pseudomonas aeruginosa
isolates have become resistant to antibiotics like carbapenem. As a consequence,
P. aeruginosa
ranks in the top three of pathogens for which the development of novel antibiotics is the most crucial. The pathogen causes both acute and chronic infections, especially in patients who are the most vulnerable. Therefore, efforts are urgently needed to develop alternative therapies. One path explored in this article is the use of bacteriophages and, more specifically, phage-derived proteins. In this study, a phage-derived protein was studied that impacts key virulence factors of the pathogen via interaction with multiple histidine kinases of TCSs. The fundamental insights gained for this protein can therefore serve as inspiration for the development of an anti-virulence compound that targets the bacterial TCS.
Porcine deltacoronavirus enters ST cells by clathrin-mediated endocytosis and does not require Rab5, Rab7, or Rab11
Authors: Li Shiqian , Xiao Dai , Zhang Luwen , Chen Rui , Song Daili , Wen Yiping , Wu Rui , Zhao Qin , Du Senyan , Yan Qigui , Cao Sanjie , Huang Xiaobo
Published: November 2023

Porcine deltacoronavirus (PDCoV) is a newly emerged enteric pathogen that causes diarrhea, dehydration, vomiting, and in suckling piglets, a high rate of death. Here, we used endocytosis inhibitors, dominant-negative mutants, and small interfering RNA (siRNA) interference to investigate PDCoV entry into swine testicle (ST) cells. Results showed that chlorpromazine, dynasore, and methyl-β-cyclodextrin (MβCD) inhibited PDCoV internalization; immunofluorescence assay (IFA) of dominant-negative (DN) mutants and siRNA interference further demonstrated these results, indicating that PDCoV utilizes clathrin-mediated endocytosis and requires dynamin and cholesterol to enter ST cells. The role of endosomes in PDCoV infection was also investigated and we found that PDCoV does not require Rab5, Rab7, or Rab11 for productive infection, indicating that the transport of PDCoV in ST cells does not require the participation of the endosomal system. Our findings will provide additional understanding of the entry mechanisms of PDCoV and possible antiviral targets.

IMPORTANCE

Porcine deltacoronavirus (PDCoV) is a newly emerged enteric virus threatening pig industries worldwide. Our previous work showed that PDCoV enters porcine kidney (PK-15) cells through a caveolae-dependent pathway, but the entry mechanism for PDCoV into swine testicle (ST) cells remains unclear. Mechanisms of virus entry can be different with different virus isolates and cell types. Here, we determined that PDCoV enters ST cells via clathrin-mediated endocytosis. Additionally, we found that PDCoV entry does not require Rab5, Rab7, or Rab11. These findings provide additional understanding of the entry mechanisms of PDCoV and possible antiviral targets.
Real-world evaluation of the Lucira Check-It COVID-19 loop-mediated amplification (LAMP) test
Authors: Simms Elizabeth , McCracken Gregory R. , Hatchette Todd F. , McNeil Shelly A. , Davis Ian , Whelan Noella , Keenan Angela , LeBlanc Jason J. , Patriquin Glenn
Published: November 2023

In hospitals during the COVID-19 pandemic, laboratory testing was important to reduce SARS-CoV-2 transmissions, particularly for high-risk settings like the emergency department and pre-operative settings and for the safe return to work of exposed healthcare workers (HCWs). For these applications, delayed test results from laboratory nucleic acid amplification tests (NAATs) posed a barrier to maximizing efficient patient flow and minimizing staffing shortages. This quality improvement project sought to evaluate the performance of the Lucira Check-It COVID-19 Test, a rapid diagnostic test that used NAAT technology (NAAT-RDT). Using 10-fold serial dilutions of SARS-CoV-2, the analytical sensitivity of the NAAT-RDT was assessed against standard NAATs used for routine diagnostic testing. Clinical performance was assessed at two Nova Scotia hospitals in 405 cases with paired swabs tested by NAAT-RDT and laboratory-based NAATs. These represented three distinct populations: patients presenting to the emergency department (
n
= 208), patients in the pre-operative setting (
n
= 158), and patients presenting to community testing sites (
n
= 38). The analytical sensitivity of the NAAT-RDT and other laboratory NAATs was comparable. During clinical evaluation, the overall sensitivity and specificity were 92.9% and 98.3%, respectively, with little variation between settings. The Lucira NAAT-RDT is a portable and self-contained device that provides an easily interpreted result within 30 minutes following a bilateral nasal swab collection. Its performance was shown to be acceptable for use in three settings in this quality improvement project, facilitating patient flow and management.

IMPORTANCE

In hospitals during the COVID-19 pandemic, laboratory testing was important to reduce SARS-CoV-2 transmissions, while facilitating patient flow in the emergency department and pre-operative settings, and allowing for the safe return to work of exposed healthcare workers. Delayed test results from laboratory nucleic acid amplification tests (NAATs) posed a barrier to maximizing efficient patient flow and minimizing staffing shortages. This quality improvement project sought to evaluate the analytical and clinical performance of the Lucira Check-It COVID-19 Test, a point-of-care test that used NAAT technology, in the perioperative setting, emergency department, and community testing sites. We found the Lucira Check-It to have comparable performance to laboratory NAATs. It can be employed with little training for specimen collection, processing, and interpretation, and at a cost justifiable from the resources saved from avoiding sample transport and laboratory testing.
The diagnostic accuracy of the GeneXpert ESBL-
ampC
prototype assay for rapid PCR-based detection of extended-spectrum beta-lactamase genes directly from urine
Authors: Tops Sofie C. M. , Schapendonk Claire E. P. , Coolen Jordy P. M. , Tenover Fred C. , Tickler Isabella A. , Melchers Willem J. G. , Wertheim Heiman F. L.
Published: November 2023

The emerging prevalence of extended-spectrum beta-lactamase (ESBL) producing Enterobacterales has implications for the empirical treatment of common infections, such as complicated urinary tract infections. To provide adequate treatment, while avoiding empirical therapy with last resort carbapenems, rapid identification of ESBL-containing pathogens is desirable. Routine urine samples were collected between February and July 2021 in two Dutch clinical medical microbiology laboratories according to a predefined list containing certain culture characteristics. All urine samples were screened for the presence of ESBL genes (
bla
CTX-M2
,
bla
CTX-M14
, and
bla
CTX-M15
) with random-access quantitative PCR (qPCR) using the Cepheid GeneXpert ESBL-
ampC
prototype assay. The qPCR and microbiological culture results were compared. After the calculation of the sensitivity and specificity, discrepancies were investigated by whole-genome sequencing. In total, 276 urine samples were available for ESBL analysis (94 ESBL culture positive and 182 ESBL culture negative). The sensitivity and specificity for detection of ESBL genes were 90.4% and 98.4%, respectively. In nine samples (9.6%), no ESBL genes were detected with GeneXpert, while in the microbiological culture, an ESBL-positive organism was isolated. This was mainly explained by non-GeneXpert ESBL genes:
bla
SHV
-family (
n
= 6; 75.0%),
bla
TEM
-family (
n
= 1; 12.5%), and
bla
SRT
-family (
n
= 1; 12.5%). The positive and negative predictive values in a hypothetical clinical scenario with a 15% ESBL prevalence were 0.91 and 0.98, respectively. Regarding
ampC
, the specificity appears to be satisfactory, but the sensitivity is low. The Cepheid GeneXpert ESBL assay could be beneficial for the fast and accurate detection of ESBL genes in regions where the epidemiology of ESBL genes coincides with the targets in the panel.

IMPORTANCE

Early identification of complicated urinary tract infections caused by ESBL-producing Enterobacterales has the potential to limit the use of carbapenems to those patients without alternative antibiotic options and avoid the empirical use of carbapenems in patients without ESBL-producing bacteria. The purpose for such a test will differ by setting and ESBL prevalence rates. Countries with low ESBL rates and cephalosporins as empiric treatment (e.g., The Netherlands) will need a rule-in test to decide to use carbapenems, while countries with high ESBL rates and empiric carbapenem treatment will need a rule-out test for ESBLs to de-escalate therapy early. Anyway, such as a test would—at least theoretically—improve patient care and reduce selective pressure for the emergence of carbapenem resistance.
An Effective Synthetic Approach to of 2-([5'-Aryl-2,2'-bipyridin]-6-yl)-5-aryl-1,3,4-oxadiazoles
Authors: Valieva M. I. , Starnovskaya E. S. , Kopchuk D. S. , Sharafieva E. R. , Slovesnova N. V. , Kovalev I. S. , Nosova E. V. , Zyryanov G. V. , Chupakhin O. N.
Published: November 2023

A convenient synthetic approach to 2-(2,2'-bipyridin-6-yl)-1,3,4-oxadiazole derivatives is proposed, which involves the preparation of 5-aryl-2,2'-bipyridine-6-carboxylic acid esters by the “1,2,4-triazine” methodology and the subsequent construction of the 1,3,4-oxadiazole ring via the modification of the ester group.
Rare case of central congenital hypothyroidism due to aTSHβmutation presenting with macro-orchidism
Authors: Karguppikar Madhura Bharat , Schoenmakers Nadia , Khadilkar Vaman , Khadilkar Anuradha
Published: November 2023

A male infant was brought to our paediatric endocrine unit with typical clinical features of congenital hypothyroidism (CH) and striking macro-orchidism. On evaluation, free T3, free T4 and thyroid stimulating hormone (TSH) were found to be low, suggestive of congenital CH. Cortisol was within reference range and prolactin was mildly elevated. No suspicious lesions were encountered on neurosonography. On commencing treatment with thyroxine, clinical features of hypothyroidism showed dramatic improvement with regression of testicular enlargement. Genetic analysis revealed deletion of theTSHβgene.

Our case highlights a rare presentation of central CH with macro-orchidism in a genetically proven deletion ofTSHβgene. Macro-orchidism has been widely reported inIGSF-1mutations leading to central CH; however, central CH and macro-orchidism have not been reported in association withTSHβdeletions.
Minimally invasive fenestration for decompression of C2-C3 spinal stenosis
Authors: Hebda Patrycja Weronika , Majewski Olaf
Published: November 2023

Conventional techniques in neurosurgery such as laminectomy have been extensively displaced by minimally invasive types, owing to the character of complexity of cervical spinal region. Spinal canal stenosis at C2-C3 level is documented in the literature with the majority being caused by intervertebral disc herniations.

This case reports a patient who presented with classical myelopathy symptoms and significant thickening of ligamentum flavum, while minimal spondylosis was detected at C2-C3 level. The decompression was performed from posterior approach and limited to the removal of ligamentum flavum with minimal resection of adjacent laminae, no fixation and no disc evacuation. After surgery, there was a significant improvement with preserved spinal stability.

Although the anterior approach is more common for cervical spine, universal access site has not been defined in literature. We suggest that minimal decompression produces desirable effects with no need for fusion and preserving adequate stability of spinal complex.
Atypical hypertrophy of retinal pigment epithelium manifesting as the first sign of familial adenomatous polyposis
Authors: Ponces Ramalhão João , Afonso Miguel , Macedo Mafalda , Araújo Maria
Published: November 2023

A female patient in her 20s presented to a routine ophthalmology appointment. Medical history was unremarkable. Family history was notable for intestinal cancer of a second-degree relative, diagnosed in her late 60s. Fundus examination revealed bilateral, multiple, flat, oval, pigmented lesions with an irregular halo of atrophy. The patient was diagnosed with atypical congenital hypertrophy of retinal pigmented epithelium. Investigation of extraocular associations was performed, including upper and lower endoscopy, which revealed 500–1000 colonic polyps with a maximum size 25 mm. Pathology did not reveal submucosal invasion. Genetic testing detected an adenomatous polyposis coli mutation (heterozygotic variant c.3183_3187delACAAA p.(Gln1062*)).
Retrieval of a retained umbilical vein catheter at 6 months
Authors: Rawat Jiledar , Singh Sudhir , Tyagi Nirpex , Pant Nitin
Published: November 2023

Umbilical venous catheterisation is carried out for the care of neonates who have very low birth weight and are critically ill. It is uncommon for catheter fragments to become fractured and retained. Here, we describe a case of a retained fractured umbilical vein catheter in an infant. An endovascular procedure to retrieve a catheter is the usual management option when the catheter has been accidentally cut and has moved proximally into a major vessel or inside the heart. It is rare to need open exploration and retrieval.
Tibial lengthening for massive distal femoral bone loss
Authors: Rathod Tushar Narayan , Kolur Shivaprasad Sharangouda , Rai Abhishek Kumar , Paul Dhruv
Published: November 2023

A man in his 30s was involved in a road traffic accident (RTA) and sustained a grade-IIIA distal femur fracture with acute loss of distal two-third of the femur. Initially, damage control surgery was done by an external fixator application. Later, staged limb reconstruction surgery was undertaken as a definitive procedure that involved bifocal distraction osteogenesis involving the proximal tibia and femur along with docking of the corticotomised femoral fragment onto the tibial plateau to achieve knee arthrodesis. The tibial and femoral regenerate together measured 25.8 cm at the end of distraction phase leaving behind a limb length discrepancy of 5 cm. Acute traumatic large bone loss is a rare presentation and is beset with unique management challenges. Limb reconstruction surgery (LRS) with LRS system provides flexibility to tackle individual case-based scenarios and helps achieve limb length, maintain alignment and restore function.
Brachial artery aneurysm and bilateral posterior circulation strokes in a young child with tuberous sclerosis complex
Authors: Meyer Juliette A , Graydon Andrew , Muthukumaraswamy Carl , Jones Hannah F
Published: November 2023

Although tuberous sclerosis (TS) may affect many organs, vascular manifestations involving medium- and large-size vessels are rare. We present a young child with known TS who presented with bilateral posterior circulation infarcts and subsequently was found to have right-hand ischaemia secondary to a thrombosed brachial artery aneurysm. A wound on his right middle finger failed to heal with conservative management, and digital subtraction angiography and MR angiogram demonstrated a lack of bypass target with microcollateral supply of the forearm only. The right middle digit ischaemia was initially managed with right middle finger disarticulation at the metacarpophalangeal joint, but the wound failed to heal and the patient proceeded to a thumb-sparing carpo-metacarpal amputation. Aneurysms, stenotic-occlusive disease and embolic stroke are rare but important complications of TS.
Amantadine withdrawal in a patient with spinocerebellar ataxia
Authors: Pak Andrew , Chang Emiley
Published: November 2023

We report a case of a man with spinocerebellar ataxia (SCA) on high-dose amantadine who was admitted for acute on chronic dysphagia secondary to progression of SCA. Four days after oral medications were held due to patient’s dysphagia, he developed fever, tachycardia and mild rigidity in extremities and became obtunded. Despite antibiotics treatment, the vitals and mental status changes persisted for 8 days. When amantadine was resumed, the patient’s vital signs and encephalopathy improved within 2 days. This is among the first reports of amantadine withdrawal syndrome (AWS) in a patient without Parkinson’s disease. Our case reinforces the importance of careful medication review at admission and consideration of pharmacologic side effects with not only medication initiation but also discontinuation.
Building upon the sugar beverage tax in Mexico: a modelling study of tax alternatives to increase benefits
Authors: Salgado Hernández Juan Carlos , Basto-Abreu Ana , Junquera-Badilla Isabel , Moreno-Aguilar Luis Alberto , Barrientos-Gutiérrez Tonatiuh , Colchero M. Arantxa
Published: November 2023

Introduction

In 2014, Mexico implemented a one peso-per-litre tax to sugar-sweetened beverage (SSB). Even though this tax reduced household purchases and predicted population health gains, the magnitude is lower compared with taxes implemented in other settings. In this study, we assessed what would happen if Mexico modified its existing tax to get higher benefits based on currently implemented taxes elsewhere.

Methods

For each tax scenario, we estimated net benefits as the difference between healthcare savings and lost jobs. We created hypothetical scenarios in which the current tax doubled or would be modified based on existing tax designs around the world including specific taxes (sugar-density or volumetric) and ad-valorem taxes.

Results

We found that the largest benefits would correspond to a tax increase of 7.4 Mexican pesos (0.45 US dollars (USD)) per SSB litre, following the current tax in Bahrain (the highest tax rate option). This tax is predicted to yield net benefits equivalent to USD 24.7 billion after 10 years of the tax redesign. We also found that sugar-density taxes can result in larger net benefits since, in addition to reductions in consumption associated with responses to prices, they induce product reformulation. Middle-income households are the most benefited group because they reported the highest baseline prevalence of obesity and the largest price elasticity.

Conclusion

Policymakers should consider pursuing a tax reform adding to the current tax, with significant increases in prices linked to a sugar-density strategy to reach a higher benefit.
National hospital costing systems matter for universal healthcare: the India PM-JAY experience
Authors: Prinja Shankar , Chugh Yashika , Garg Basant , Guinness Lorna
Published: November 2023

India envisions achieving universal health coverage to provide its people with access to affordable quality health services. A breakthrough effort in this direction has been the launch of the world’s largest health assurance schemeAyushman Bharat Pradhan Mantri Jan Arogya Yojana, the implementation of which resides with the National Health Authority. Appropriate provider payment systems and reimbursement rates are an important element for the success of PM-JAY, which in turn relies on robust cost evidence to support pricing decisions. Since the launch of PM-JAY, the health benefits package and provider payment rates have undergone a series of revisions. At the outset, there was a relative lack of cost data. Later revisions relied on health facility costing studies, and now there is an initiative to establish a national hospital costing system relying on provider-generated data. Lessons from PM-JAY experience show that the success of such cost systems to ensure regular and routine generation of evidence is contingent on integrating with existing billing or patient information systems or management information systems, which digitise similar information on resource consumption without any additional data entry effort. Therefore, there is a need to focus on building sustainable mechanisms for setting up systems for generating accurate cost data rather than relying on resource-intensive studies for cost data collection.