bluuebunny/crossref_metadata_2025_split huggingface dataset:
You Cannot Escape from People: Why Institutional Reasons Are Necessary for Arguing for Judicial Review
Authors: Vitaliani Emiliano Martin 
Published: December 2024

AbstractOne set of arguments on judicial review states that this is a necessary consequence of understanding rights as limits to democracy. This paper brings some nuances to this argument, arguing that the answer to the problem of judicial review should rely not only on rights‐based arguments, but also on institutional arguments. In order to do so, the first part will present the idea that links rights as trumps to judicial review. In the second part, the article will show it is possible to split the conception of rights as limits into two questions, one regarding what the state should or should not do and the other regarding who should be the one to give content to this set of decisions. The third part will show that all rights‐based arguments fail because they cannot deal with the fact of disagreement. The last part will show that rights still have a part to play in the discussion on judicial review, though without the final word.
Abnormalities of teeth and jaws in thalassemia pediatric patients
Authors: Lertsirivorakul Jinda , Sukanindr Parichamon , Jetsrisuparb Arunee , Pitiphat Waranuch , Sutthiprapaporn Pipop 
Published: December 2024

AbstractAimsTo assess the prevalence of abnormalities of teeth and jaws in thalassemia patients and their association with the severity and type of thalassemia.Methods and ResultsThis cross‐sectional study was conducted among thalassemia patients, attending the Pediatric Outpatient Clinic at a university hospital in Thailand. Data were collected from medical records, clinical and orthopantomographic examinations. Descriptive statistics, Fisher's exact test, and binary logistic regression were employed for data analyses. The study included 163 patients, aged 1.9−28.6 years, with 148 accepting panoramic radiographic examination. Dental caries, convex profile, malocclusion, abnormal teeth, small maxillary sinus, absent inferior alveolar canal, and eroded mandibular cortex presented in 93.9%, 76.7%, 86.3%, 22.9%, 52.7%, 49.3%, and 29.7% of the participants, respectively. Severe thalassemia patients had a higher prevalence of malocclusion (p < .01) and small maxillary sinus (p = .02) than non‐severe group. Compared to patients with β‐thalassemia, those with coinheritance of α‐ and β‐thalassemia demonstrated less malocclusion (p = .03) and small maxillary sinus (p < .001). No significant associations were found between the severity and type of thalassemia with other abnormalities.ConclusionThalassemia pediatric patients manifested several dental and jaw abnormalities, with malocclusion and small maxillary sinuses being associated with severe thalassemia and β‐thalassemia.
Numerical Simulation Method for the Rain-Wind Induced Vibration of the Three-Dimensional Flexible Stay Cable
Authors: Zichen Pan , Jian Guan , Jian Wang , Canchen Wang , Xiaoyu Guo 
Published: December 2024

Abstract
Under specific wind and rain conditions, the cable may exhibit low frequency and large amplitude phonomenon, which is called the rain-wind induced vibration (RWIV). Because the RWIV phenomenon encompasses interactions among gas, liquid, and solid phases, make it difficult to reproduce through numerical simulation method. In the previous research, based on lubrication theory, researchers have established theory models of two-dimensional (2D) coupled and rigid segment of three-dimensional (3D) cables for RWIV. Based on the previous research, the new numerical simulation method for RWIV of 3D flexible cable is proposed in this paper, which can reflect the interaction among the gas, liquid, and solid phases. The aerodynamics forces are calculated using comsol. The evolution of water film is calculated using matlab. In the previous studies, the cable deformation was not considered. Hence, cable vibration is derived from the solution of a single-degree-of-freedom vibration equation. In this study, the cable is treated as a deformable body. The vibration response of the cable under external force is solved using ansys. The bidirectional coupling effect between the cable and the water film is considered. The morphology of water film on the cable surface is changing with time, which causes the variation of the lift over time. Therefore, it is necessary to discretize the time so that the lift acted on the cable at each time-step can be obtained. The Restart technique in ansys is used for this purpose. Additionally, the transmission of information can be achieved by using matlab is used to control comsol and ansys. The rain-wind induced vibration phenomenon of 3D flexible cable is reproduced by using the new numerical simulation method, analyzing the variation of water film, cable lift, cable vibration under the influence of cable deformation. The mechanism of rain-wind-induced vibration is revealed again by analysing the 3D model. In addition, the advantages and necessity of the 3D cable vibration model are demonstrated by comparing it with the 2D model simulating cable vibration
A KSHV RNA-binding protein promotes FOS to inhibit nuclease AEN and transactivate RGS2 for AKT phosphorylation
Authors: Majerciak Vladimir , Alvarado-Hernandez Beatriz , Ma Yanping , Duduskar Shivalee , Lobanov Alexei , Cam Maggie , Zheng Zhi-Ming 
Published: December 2024

ABSTRACT

Kaposi’s sarcoma-associated herpesvirus (KSHV) encodes an RNA-binding protein ORF57 in lytic infection. Using an optimized CLIP-seq in this report, we identified ORF57-bound transcripts from 544 host protein-coding genes. By comparing with the RNA-seq profiles from BCBL-1 cells with latent and lytic KSHV infection and from HEK293T cells with and without ORF57 expression, we identified FOS RNA as one of the major ORF57-specific RNA targets. FOS dimerizes with JUN as a transcription factor AP-1 involved in cell proliferation, differentiation, and transformation. Knockout of the ORF57 gene from the KSHV genome led BAC16-iSLK cells incapable of FOS expression in KSHV lytic infection. The dysfunctional KSHV genome in FOS expression could be rescued by Lenti-ORF57 virus infection. ORF57 protein does not regulate FOS translation but binds to the 13-nt RNA motif near the FOS RNA 5′ end and prolongs FOS mRNA half-life 7.7 times longer than it is in the absence of ORF57. This binding of ORF57 to FOS RNA is likely competitive to the binding of host nuclease AEN (ISG20L1) of which physiological RNase activity remains unknown. KSHV infection inhibits the expression of AEN, but not exosomal RNA helicase MTR4. FOS expression mediated by ORF57 inhibits
AEN
transcription through FOS binding to
AEN
promoter but transactivates
RGS2
, a regulator of G-protein-coupled receptors. FOS binds a conserved AP-1 site in the
RGS2
promoter and enhances RGS2 expression to phosphorylate AKT. Altogether, we have discovered that KSHV ORF57 specifically binds and stabilizes FOS RNA to increase FOS expression, thereby disturbing host gene expression and inducing pathogenesis during KSHV lytic infection.

IMPORTANCE

We discovered that FOS, a heterodimer component of oncogenic transcription factor AP-1, is highly elevated in KSHV-infected cells by expression of a viral lytic RNA-binding protein, ORF57, which binds a 13-nt RNA motif near the FOS RNA 5′ end to prolong FOS RNA half-life. This binding of ORF57 to FOS RNA is competitive to the binding of host RNA destabilizer(s). KSHV infection inhibits expression of host nuclease AEN, but not MTR4. FOS inhibits AEN transcription by binding to the
AEN
promoter but transactivates RGS2 by binding to a conserved AP-1 site in the RGS2 promoter, thereby enhancing RGS2 expression and phosphorylation of AKT. Thus, KSHV lytic infection controls the expression of a subset of genes for signaling, cell cycle progression, and proliferation to potentially contribute to viral oncogenesis.
Draft genome sequence of a non-human primate-derived isolate of
Candida parapsilosis
Authors: James Steve A. , Parker Aimee , Purse Catherine , Baker David J. , Funnell Simon G. P. , Carding Simon R. 
Published: December 2024

ABSTRACT

Candida parapsilosis
is a common human commensal and opportunistic fungal pathogen that is also found in non-human primates (NHPs). Here, we report the first draft sequence of
C. parapsilosis
NCYC 4418, a fecal isolate from an adult cynomolgus macaque.
Draft genome sequences of evolutionary distant
Yersinia
species representatives
Authors: Brady Amanda , Garrison Taylor M. , Ernst Robert K. , Rasko David A. , Lawrenz Matthew B. 
Published: December 2024

ABSTRACT

Yersinia pestis
is the etiological agent of human plague. However, certain evolutionarily divergent subspecies have different host specificities and virulence capacity compared to the more commonly studied strains with pandemic potential. This resource examines 10 diverse isolates representing some of the most understudied subspecies commonly referred to as
Yersinia pestis
Pestoides.
Laboratory evaluation of oral fluid for syphilis screening among clinic users from Lima, Peru
Authors: Qquellon Jazmin , Vargas Silver K. , Vasquez Francesca , Reyes-Diaz E. Michael , Konda Kelika A. , Caceres Carlos F. , Klausner Jeffrey D. 
Published: December 2024

ABSTRACT

Serological tests for syphilis require equipment unavailable in many health centers; however, point-of-care testing facilitates rapid screening using finger-prick whole blood samples. A further improvement could be oral fluid for ease of use. We evaluated the performance of treponemal antibody point-of-care testing for syphilis screening using oral fluid samples. We recruited users of STI clinics in Lima, Peru. We collected oral fluid using the OraSure collection device (OraSure Technologies Inc., USA) according to the manufacturer’s instructions and serum from each participant. Oral fluid and serum were analyzed using the SD Bioline Syphilis 3.0 rapid test (Standard Diagnostics Inc., Korea). Serum was also tested using RPR (RPR slide test, Wiener Laboratorios SAIC, Argentina) and TPPA (Serodia, Fujirebio Diagnostics Inc., Japan). We assessed oral fluid rapid test overall percent agreement, sensitivity, specificity, and Kappa coefficient against serum SD Bioline Syphilis, TPPA, and RPR. Among 323 participants, nearly half (51.3%) reported prior syphilis. The overall percent agreement, sensitivity, specificity, and Kappa coefficient of oral fluid were 71.0% (95% CI: 65.6%–75.8%), 78.1% (71.1%–83.7%), 63.5% (55.8%–70.6%), and 0.42% (0.32%–0.52%), respectively, versus serum SD Bioline Syphilis. A similar performance was obtained versus serum TPPA. When limiting the sample to TPPA-reactive with RPR titer ≥1:8, the sensitivity increased to 88.1% (75.0%–94.8%), whereas the specificity did not vary (65.3% [57.2%–72.6%]). We observed a good performance of the rapid treponemal test using oral fluid. Further investigations are needed to improve the specificity of oral fluid as a potential sample for accurate syphilis screening.

IMPORTANCE
Point-of-care tests are essential for rapid and efficient screening of syphilis, especially in low-resource settings. Oral fluid specimens offer a noninvasive, accessible, and practical alternative to traditional blood samples. Our study evaluated the performance of a rapid treponemal test using oral fluid specimens. We found that the rapid treponemal test using oral fluid had good sensitivity compared with the rapid treponemal test using serum and the non-treponemal RPR test. This suggests that oral fluid could be a viable option for syphilis screening, facilitating broader and faster access to diagnosis and treatment. However, further studies are needed to improve the specificity of this method to ensure accurate screening in diverse clinical scenarios.
Implementation and validation of a new qPCR assay to detect imported human
Plasmodium
species
Authors: Cordier Camille , Hamane Samia , Ghelfenstein-Ferreira Théo , Dellière Sarah , Da Silva Élodie , Denis Blandine , Houzé Sandrine , Joste Valentin , Alanio Alexandre 
Published: December 2024

ABSTRACT

Diagnosis of imported malaria is based on microscopic examination of blood smears (BS), detection of circulating plasmodial antigen by immunochromatography (ICT), or detection of
Plasmodium
spp. DNA by loop mediated isothermal amplification. We have developed duplex (
Plasmodium
spp. and
Plasmodium falciparum
) real-time PCR (qPCR) and species-specific qPCR assays for the identification and quantification of human
Plasmodium
species. Whole nucleic acids from 523 samples prospectively collected from 410 patients suspected of malaria between June 2016 and March 2021 were tested by qPCRs and compared to standard diagnostic procedures. All qPCRs were designed on 18S ribosomal ribonucleic acid. The limit of detection of duplex qPCR was 8 copies/reaction, and analytical specificity of species-specific qPCRs was 100%. Seventy-nine patients diagnosed for single species malaria involving
P. falciparum
,
P. vivax
,
P. ovale,
and
P. malariae
were positive with duplex and species-specific qPCRs.
P. knowlesi
qPCR detected DNA from a
P. knowlesi
culture. Of eight cases of mixed
Plasmodium
species infection, five were identified with our qPCR assays with better sensitivity as compared to BS and ICT. Eight out of 323 patients with negative BS were hospitalized for symptoms suggestive malaria after malaria-endemic area travel or known with history of malaria had a low positive duplex qPCR. Between day of diagnosis and post-treatment follow-up at D2-D4 of malaria, a 3.1-log
P. falciparum
load decrease was observed by qPCR. These new
Plasmodium
qPCRs allowing detection of human plasmodial species have excellent species specificity and allow rapid detection of
P. falciparum
cases, malaria with low parasitaemia, and mixed
Plasmodium
species infection.

IMPORTANCE

Malaria is a disease transmitted by a
Plasmodium
parasite genus. Most cases are caused by
Plasmodium falciparum
. Despite a significant drop of incidence and mortality since 2000, 249million cases and 608,000 deaths have been estimated in 2022, mainly in Africa. Due to the increasing number of travels to endemic areas, incidence of imported malaria is rising in Europe. Various techniques are used in European laboratories, such as microscopic examination of thin and thick smears and rapid diagnostic tests. However, these techniques require skilled operators to differentiate plasmodial species and have limited sensitivity. Actually, molecular diagnosis is carried out using point-of-care test for rapid results with excellent sensitivity but is unabled to determine involved species and assess parasitaemia. In this study, we developed a combined molecular tool based on both detection of all human plasmodial species (
Plasmodium
spp.) and
P. falciparum
. We have also developed specific qPCRs for each human plasmodial species.
Mode of action of silver-based perovskite against Gram-negative bacteria
Authors: Fani Fereshteh , Talebpour Cyrus , Leprohon Philippe , Salimnia Hossein , Alamdari Houshang , Ouellette Marc 
Published: December 2024

ABSTRACT

Although silver is known for its antibacterial activity, its exact mode of action remains unclear. In our previous work, we described AgNbO
3
nanoparticles (AgNbO
3
NPs) prepared using a ceramic method, followed by high-energy and low-energy ball-milling processes, which exhibited antimicrobial activity with negligible release of Ag
+
in deionized water. Here, we investigated thoroughly the mode of action of these AgNbO
3
NPs against
Escherichia coli
. Drastic morphological changes in
E. coli
were observed after their exposure to AgNbO
3
NPs. In addition to cellular damage, AgNbO
3
NPs induced the production of reactive oxygen species and lipid peroxidation, likely following the release of small amounts of Ag
+
. This was concluded from the characterization of mutants resistant to AgNbO
3
NPs that showed cross-resistance to AgNO
3
, impaired reactive oxygen species production and lipid peroxidation, and harbored a key mutation in a two-component regulatory system regulating an Ag
+
efflux pump. We calculated, however, that the quantity of Ag
+
released from AgNbO
3
NPs is not sufficient by itself to lead to bacterial death. We propose that bacterial contact with the AgNbO
3
NPs in combination with Ag
+
release is necessary for the mode of action of AgNbO
3
NPs.

IMPORTANCE

Silver is known for its antibacterial activity, but its exact mode of action remains unclear. Here, we investigated thoroughly the mode of action of AgNbO
3
nanoparticles against
Escherichia coli
. Our data suggest that AgNbO
3
nanoparticles have dual effects on the cell and that both are required for its lethal action.
Role of the two-component system AmgRS in early resistance of
Pseudomonas aeruginosa
to cinnamaldehyde
Authors: Dubois Eline , Spasovski Vladimir , Plésiat Patrick , Llanes Catherine 
Published: December 2024

ABSTRACT

Exposure of
Pseudomonas aeruginosa
to cinnamaldehyde (CNA), a natural electrophilic antimicrobial often used as self-medication to treat mild infections, triggers overproduction of the MexAB-OprM efflux system, leading to multidrug resistance. In this study, we demonstrate that CNA exposure induces expression of genes regulated by the two-component system AmgRS. AmgRS activates MexAB-OprM production, independent of repressors MexR and NalD. In addition to the essential role played by the NalC-ArmR pathway in this adaptive process, AmgRS is critical for the survival of
P. aeruginosa
challenged with CNA. Altogether, these data suggest that efflux-dependent and -independent mechanisms are activated in the early phase of CNA exposure, allowing for progressive enzymatic reduction of the biocide to non-toxic cinnamic alcohol.

IMPORTANCE

Exposure of
Pseudomonas aeruginosa
to cinnamaldehyde (CNA), an antimicrobial used in self-medication, induces overproduction of the MexAB-OprM efflux system, leading to multidrug resistance. Our study demonstrates that the AmgRS two-component system aids in the survival of
P. aeruginosa
strain PA14 under CNA exposure through both MexAB-OprM-dependent and -independent mechanisms until the enzymatic reduction of CNA into the less toxic cinnamic alcohol. This discovery highlights the pivotal role of AmgRS in mediating defense against aldehyde biocides, emphasizing its significance in the persistence of
P. aeruginosa
, a pathogen associated with hospital-acquired infections and cystic fibrosis, and underscores the potential impact on clinical treatment strategies.
Strategies for genetic manipulation of the halotolerant black yeast
Hortaea werneckii
: ectopic DNA integration and marker-free CRISPR/Cas9 transformation
Authors: Hernandez-Rodriguez Yainitza , Bullard A. Makenzie , Busch Rebecca J. , Marshall Aidan , Vargas-Muñiz José M. 
Published: December 2024

ABSTRACT

Hortaea werneckii
is a halotolerant black yeast commonly found in hypersaline environments. This yeast is also the causative agent of tinea nigra, a superficial mycosis of the palm of the hand and soles of the feet of humans. In addition to their remarkable halotolerance, this black yeast exhibits an unconventional cell division cycle, alternating between fission and budding cell division. Cell density and the salt concentration in their environment regulate which cell division cycle
H. werneckii
uses. Although
H. werneckii
have been extensively studied due to their unique physiology and cell biology, deciphering the underlying mechanisms behind these remarkable phenotypes has been limited due to the lack of genetic tools available. Here, we report a new ectopic integration protocol for
H. werneckii
using polyethylene glycol-CaCl
2
mediated protoplast transformation. This approach relies on a drug (hygromycin B) resistance gene to select for successful integration of the genetic construct. The same construct was used to express cytosolic green fluorescent protein. Finally, we developed a marker-free CRISPR/Cas9 protocol for targeted gene deletion using the melanin synthesis pathway as a visual reporter of successful transformation. These transformation strategies will allow testing hypotheses related to
H. werneckii
cell biology and physiology.

IMPORTANCE

Hortaea werneckii
is a remarkable yeast capable of growing in high salt concentration, and its cell division cycle alternates between fission-like and budding. For these unique attributes,
H. werneckii
has gathered interest in research programs studying extremophile fungi and cell division. Most of our understanding of
H. werneckii
biology comes from genomic analyses, the usage of drugs to target a particular pathway, or the heterologous expression of its genes in
S. cerevisiae
. Nonetheless,
H. werneckii
has remained genetically intractable. Here, we report on two strategies to transform
H. werneckii
: ectopic integration of a plasmid and gene deletion using CRISPR/Cas9. These approaches will be fundamental to expanding the experimental techniques available to study
H. werneckii
, including live-cell imaging of cellular processes and reverse genetic approaches.
Comparison of clinical outcomes between different combinations of hybrid multifocal, extended-depth-of-focus and enhanced monofocal intraocular lenses
Authors: Kim Bokyung , Son Hyeck-Soo , Khoramnia Ramin , Auffarth Gerd U , Choi Chul Young 
Published: December 2024

PurposeTo compare clinical outcomes of bilateral implantation of hybrid multifocal intraocular lenses (IOLs) versus mix-and-match implantation of hybrid multifocal and extended-depth-of-focus (EDOF) versus mix-and-match implantation of hybrid multifocal and enhanced monofocal IOLs.MethodsPatients with bilateral age-related cataract were randomised in one of three groups: group 1, bilateral hybrid multifocal IOL; group 2, EDOF in the dominant eye, hybrid multifocal in the non-dominant eye; group 3, enhanced monofocal in the dominant eye, hybrid multifocal in the non-dominant eye. Assessments at 6 months postoperatively included monocular and binocular uncorrected distance visual acuity (UDVA), intermediate (UIVA) and near distance (UNVA) at 40 and 33 cm, defocus curves, contrast sensitivity (CS), reading speed and questionnaires on quality of vision and dysphotopsia.Results75 patients (25 per group) were enrolled. There were no statistically significant differences in binocular UDVA and UNVA between groups (p>0.05); binocular UIVA was better for group 1 and 2 versus group 3 (p=0.030). Binocular uncorrected defocus curve showed better performance for group 1 compared with group 3 from −2.00 to −3.50 D. Significantly higher reading speed was measured for Jaeger 1 font in group 1. There were no differences in CS between groups, but higher incidence of starbursts in group 1 and higher need for near spectacles in group 3.ConclusionBilateral hybrid multifocal IOL implantation resulted in better near vision, but higher rates of photic phenomena compared with the mix-and-match groups. Combinations of IOLs may allow surgeons to fine-tune for individual patient’s needs.