bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of hydatid cyst protoscolex somatic antigens on full‐thickness skin wound healing in mouse
Authors: Hosseinzade Sajede , Nourani Hossein , Kazemi Mehrjerdi Hossein , Lotfalizadeh Narges , Borji Hassan
Published: April 2024

Background

Wound healing has evolved in recent years, resulting in diverse therapeutic options.

Objective

This study evaluated the effects of the somatic antigen of the hydatid cyst protoscolex on wound healing in mice with full‐thickness skin wounds.

Methods

Fifty‐four adult mice, weighing 25 ± 5 g and approximately 60 days old, were divided into three groups (A, B, and C), each further divided into three subgroups. Subgroups A1, A2, and A3 were assigned negative controls. B1, B2, and B3 received hydatid cyst somatic antigen tests at 10 µg/SC, whereas C1, C2, and C3 received somatic antigen tests at 20 µg/SC. Under general anesthesia, a wound biopsy puncture of 9.8 mm in diameter was performed on the mice's back and spine. In the experimental group, antigen and alum adjuvant were administered subcutaneously around the wound, while the control group received Phosphate‐Buffered Saline (PBS). Using digital images, a geometric assessment was conducted on days 0, 1, 3, 6, 9, 12, 15, 18, and 21 post‐wounding. The obtained images were analyzed by Image J software and after analyzing the data by SPSS software.

Results

A significant difference in terms of epithelization was observed in the antigen treatment group with a dose of 20 µg on days 3 and 6 (P < 0.05). Furthermore, the 20 µg antigen group was significantly higher than the 10 µg antigen group in terms of this factor on day 3 (P < 0.05). Skin samples were taken from all wounds on days 3, 10 and 21 for microscopic evaluation. Regarding epithelization, on day 10, a significant difference was observed in the treatment group with a concentration of 10 µg with the control group and the treatment group with a concentration of 20 µg (P < 0.05).

Conclusion

Based on the results of the present study, it can be concluded that somatic antigens of protoscolex hydatid cyst are dose‐dependent and antigens with a dose of 20 µg by subcutaneous injection accelerate wound healing and epithelialization.
The Challenges Involved in Teaching Biblical Hebrew to Students With Dyslexia: Some Observations
Authors: Nicholson Sarah L.
Published: April 2024

Studying Biblical Hebrew is increasingly considered a viable option for students with dyslexia. This presents particular challenges not just for the students but also for their teachers, because the pedagogical methods for teaching ancient languages have traditionally depended on strategies that create difficulties for dyslexic students. This paper outlines the particular challenges of Biblical Hebrew for teachers of students with dyslexia and makes some proposals for addressing those challenges. Responding to dyslexia research, this paper considers the effects of phonological, morphological, and other deficits; outlines teaching and assessment strategies; and argues that learning Biblical Hebrew can be a transformative experience for students with specific learning difficulties.
Association between habitual betel quid chewing and risk of adverse cardiovascular outcomes: A systematic review
Authors: Itaki Rodney , Taufa Shalon
Published: April 2024

Introduction

Habitual betel quid chewing, a tobacco product, is a leading cause of oral cancer in Asia–Pacific countries where this practice is most prevalent. However, it is not well understood whether betel quid chewing is also a cause of adverse cardiovascular outcomes. To address this gap, we conducted a systematic literature review of peer‐reviewed published studies evaluating the association between habitual betel quid use on the risk of adverse cardiovascular outcomes.

Methods

We searched PubMed for studies assessing the correlation between betel quid chewing and cardiovascular health. We included studies if (i) they included human subjects; (ii) were peer‐reviewed articles in indexed journals; and (iii) were in English. We extracted data from eligible studies and stratified them by geographical location, study designs and cardiovascular outcomes. Finally, we did a narrative synthesis of the data to identify adverse cardiovascular outcomes associated with chronic betel quid use.

Findings

We reviewed data from 19 studies that met the inclusion criteria. Habitual betel quid chewing was associated with hypertension, atherosclerosis, inflammation and ischaemic heart disease. In addition, betel quid use was a risk factor for arrhythmias. Interestingly, betel quid use was an independent risk factor for cardiovascular disease in women. Long‐term betel quid consumption was associated with higher risks for all‐cause mortality and increased overall cardiovascular risk.

Conclusions

Habitual betel quid chewing is an important cardiovascular risk factor in populations where the practice is prevalent.
What is slough? Defining the proteomic and microbial composition of slough and its implications for wound healing
Authors: Townsend Elizabeth C. , Cheong J. Z. Alex , Radzietza Michael , Fritz Blaine , Malone Matthew , Bjarnsholt Thomas , Ousey Karen , Swanson Terry , Schultz Gregory , Gibson Angela L. F. , Kalan Lindsay R.
Published: April 2024

Slough is a well‐known feature of non‐healing wounds. This pilot study aims to determine the proteomic and microbiologic components of slough as well as interrogate the associations between wound slough components and wound healing. Ten subjects with slow‐to‐heal wounds and visible slough were enrolled. Aetiologies included venous stasis ulcers, post‐surgical site infections and pressure ulcers. Patient co‐morbidities and wound healing outcome at 3‐months post‐sample collection was recorded. Debrided slough was analysed microscopically, through untargeted proteomics, and high‐throughput bacterial 16S‐ribosomal gene sequencing. Microscopic imaging revealed wound slough to be amorphous in structure and highly variable. 16S‐profiling found slough microbial communities to associate with wound aetiology and location on the body. Across all subjects, slough largely consisted of proteins involved in skin structure and formation, blood‐clot formation and immune processes. To predict variables associated with wound healing, protein, microbial and clinical datasets were integrated into a supervised discriminant analysis. This analysis revealed that healing wounds were enriched for proteins involved in skin barrier development and negative regulation of immune responses. While wounds that deteriorated over time started off with a higher baseline Bates‐Jensen Wound Assessment Score and were enriched for anaerobic bacterial taxa and chronic inflammatory proteins. To our knowledge, this is the first study to integrate clinical, microbiome, and proteomic data to systematically characterise wound slough and integrate it into a single assessment to predict wound healing outcome. Collectively, our findings underscore how slough components can help identify wounds at risk of continued impaired healing and serves as an underutilised biomarker.
A palynological study of Viola in Korea
Authors: LEE Yun–Sun , Go Ah-reum , YOO Ki-Oug , CHUNG Young Jae
Published: April 2024

Palynological studies were conducted to investigate the interspecific relationships among 43 Korean Viola taxa. Pollen of the genus Viola in Korea was monad in terms of the cell unit, and small or medium in size. The shape of the polar view was angular or circular, and the equatorial view was divided into prolate, subprolate, and prolate-spheroidal categories. The pollen polarity was isopolar, and the aperture type was 3–5 colporate. The surface sculptures of the equatorial view were found to be punctate-scabrate, punctate-rugulate, and punctate-rugulate-fossulate-scabrate. Consequently, as the pollen of most Viola taxa have similar morphological characters, it was difficult to construct a palynological description of each species. However, the seven taxa of V. arvensis, V. tricolor, V. diamantiaca, V. patrinii, V. mirabilis, V. grypoceras var. pubescens, and V. raddeana were clearly distinguished with morphologically similar species according to the aperture number, surface patterns and pollen sizes, all of which can be used as useful pollen characters.
Discovery of Lepisorus hachijoensis (Polypodiaceae) misidentified as Lepisorus onoei on Gageodo Island, Korea
Authors: CHOI Seung Se , KIM Jonghwan , PARK Yu Cheol , AHN Jin Kap , HWANG Seung Hyun , BUM Hyun Min , LEE Seung Hoon , DRIZ Journadette , HONG Hang Hwa , MOON Myung-Ok
Published: April 2024

While preparing for a floristic study of Gageodo Island, we discovered the following unrecorded species: Lepisorus hachijoensis (Polypodiaceae). It is known to be distributed only on Hachijo Island of Japan, which was the collection site of the type specimen. However, on the basis of the findings of the Fifth National Natural Environment Survey, it has recently been established that this plant also grows on the bark of trees and on shaded rocks along ridges on Gageodo Island, Sinan-gun, Jeollanam-do, in Korea. In this study, we present a description and photographs and indicate differences between Korean L. hachijoensis and related species as well as a key to the related taxa.
Re-identification of herbarium specimens through a morphological analysis reveals two species of Murdannia (Commelinaceae) from South Korea
Authors: KANG Eun Su , LEE Kang-Hyup , JI Seong-Jin , SON Dong Chan
Published: April 2024

The previously reported alien plant Murdannia nudiflora is known to be distributed on Jejudo Island and in inland areas of South Korea. However, the species distributed in the Jejudo Island region exhibits differences in the morphology of the stems, leaves, and seeds compared to those in inland areas. Although M. loriformis is morphologically similar to M. nudiflora, it differs in terms of the development of the main stem, the formation of rosettes, and the occurrence of inflorescences that develop from branched stems. The seed testa of M. loriformis exhibits a radiating striated pattern and is not verrucose. Through the re-identification of specimens of M. nudiflora and an examination of individuals and images collected in areas of their distribution, it was determined that the individuals in the Jejudo region are M. loriformis, whereas those distributed inland were found to be M. nudiflora. This study presents revised descriptions and a taxonomic key for both species, with new Korean names designated based on the characteristics of the distribution areas and surrounding growth environments.
A new record of a Plantaginaceae alien plant in the Republic of Korea: Chaenorhinum minus
Authors: LEE Se Ryeong , PARK Beom Kyun , LEE Kang Hyup , KIM Jin Suk , SON Dong Chan , KANG Eun Su
Published: April 2024

Chaenorhinum minus (L.) Lange of the family Plantaginaceae was discovered in Dangjin-si, Chungcheongnam-do, Republic of Korea. This species is an invasive alien plant that originated in Europe and North Africa and that was introduced into North America and East Asia. The genus Chaenorhinum (DC.) Rchb., to which this species belongs, is most similar to Nuttallanthus D. A. Sutton among related genera of the tribe Antirrhineae distributed in the Republic of Korea. While the two genera share common morphological features in the leaf and flower, Chaenorhinum is distinguished from Nuttallanthus by glandular hairs on the plant; monomorphic, fertile, and erect stems; 9.6–14.1 mm long pedicels; corolla as short as 5.6–7.9 mm; white corolla lower lips; and widely ovoid or oblong seeds. This study presents morphological descriptions and a genus key for the tribe Antirrhineae of the Republic of Korea for the identification of C. minus together with distribution information, voucher specimens, and photographs of this species.
Characterization of the complete chloroplast genome sequence of Hypericum petiolulatum (Hypericaceae)
Authors: ZOU Le , BA Rui-Zhu , XIANG Chun-Lei , LI Lu
Published: April 2024

Hypericum L. (Hypericaceae) is one of the best-selling herbal medicines in the world comprising ca. 500 species of herbs, shrubs, and small trees. Hypericum petiolulatum Hook. f. & Thomson ex Dyer is widely distributed in China, Vietnam, Myanmar, Nepal, India, Malaysia, and Bhutan and is used as a traditional herb to treat hemoptysis and inflammation. In this study, we sequenced and assembled the complete chloroplast (cp) genome of H. petiolulatum. The complete plastome of H. petiolulatum was 136,105 bp in length, with a large single copy region (LSC) of 93,709 bp, a small single copy region (SSC) of 11088 bp and two identical inverted repeats (IRs) of 15,654 bp. The overall GC content of the plastome was 37.0%, while GC contents of the LSC, SSC, and each IR were 35.5%, 31.0%, and 43.8%, respectively. In addition, 116 genes consisting of 76 protein-coding genes, six ribosomal RNA genes, and 34 transfer RNA genes were identified. A phylogenetic analysis of 14 taxa inferred based on cp genome sequences revealed a close relationship between H. petiolulatum and H. perforatum. The complete cp genome sequence of H. petiolulatum reported in this paper will facilitate population and phylogenomics studies of this medicinal plant group.
A Simple Predictive Method for Estimating Boil-Off Rate Over Time in a Cryogenic Container
Authors: Kim Changhyun , Kim Taehoon , You Hwalong , Kim Minchang , Han Yong-Shik , Choi Byung-Il , Do Kyu Hyung
Published: April 2024

Recently, cryogenic fluids are widely transported via cargo ships as energy sources. The generation of boil-off gas (BOG) is inevitable in a cryogenic container due to the large temperature difference. Therefore, accurately analyzing the boil-off gas over time is essential to increase delivery efficiency and ensure tank safety. However, predicting the boil-off rate (BOR) is not a simple task, as both experiment and calculation require a significant amount of time. In this study, a simple predictive method is developed for simulating a 1/50 scaled model tank. The method consists of steady and quasi-unsteady calculations. Steady calculations are performed to establish a correlation between LN2 level and inner-wall temperature. Quasi-unsteady calculations simulate BOG over time by changing the inner-wall boundary conditions. This method can help engineers effectively evaluate the insulation performance of a cryogenic container in a short time and provide guidelines for simulating a real scale tank.
Effect of Level of Competition and Drill Typology on Internal and External Load in Male Volleyball Players During the Preseason Period
Authors: Kerpe Gilbertas , Zuoza Aurelijus Kazys , Conte Daniele
Published: April 2024

Purpose: This study aimed at evaluating the effect of level of competition and drill typology on loads during the preseason period in male volleyball players. Methods: Internal (percentage of peak heart rate [HR] and summated HR zone) and external (PlayerLoad per minute, total and high accelerations per minute [tACCmin and hACCmin], decelerations per minute [tDECmin and hDECmin], and jumps per minute [tJUMPmin and hJUMPmin]) loads were monitored across a 5-week preseason period in 12 Division 1 (age: 22.5 [3.9] y; stature: 188 [6.2] cm; body mass: 85 [11.6] kg; training experience: 9.4 [4.2] y) and 12 Division 2 (age: 20.7 [2.9] y; stature: 186 [6.2] cm; body mass: 77.8 [9.6] kg; training experience: 5.6 [2.3] y) male volleyball players. Furthermore, differences in load were assessed for each drill typology (warm-up, conditioning, technical, tactical, and integral). Results: No effects (P > .05) of level of competition on the internal (except for summated HR zone, P = .05) and external loads (except for tJUMPmin, P = .002) were found. Differently, drill typologies showed an effect (P < .001) on all the investigated internal- and external-load measures. The main post hoc results revealed higher (P < .05) percentage of peak HR, summated HR zone, PlayerLoad per minute, and tACCmin in warm-up and conditioning drills, while higher (P < .05) hDECmin and hJUMPmin were found in tactical and integral drills. Conclusions: These results suggest that volleyball coaches use warm-up and conditioning drills when aiming at increasing the internal loads, PlayerLoad per minute, and tACCmin, while tactical and integral drills should be preferred to enhance the number of hDECmin and hJUMPmin.
Ibrexafungerp is efficacious in a neutropenic murine model of pulmonary mucormycosis as monotherapy and combined with liposomal amphotericin B
Authors: Gebremariam Teclegiorgis , Alkhazraji Sondus , Gu Yiyou , Najvar Laura K. , Borroto-Esoda Katyna , Patterson Thomas F. , Filler Scott G. , Wiederhold Nathan P. , Ibrahim Ashraf S.
Published: April 2024

Ibrexafungerp (formerly SCY-078) is the first member of the triterpenoid class that prevents the synthesis of the fungal cell wall polymer β-(1,3)-D-glucan by inhibiting the enzyme glucan synthase. We evaluated the
in vivo
efficacy of ibrexafungerp against pulmonary mucormycosis using an established murine model. Neutropenic mice were intratracheally infected with either
Rhizopus delemar
or
Mucor circinelloides
. Treatment with placebo (diluent control), ibrexafungerp (30 mg/kg, PO BID), liposomal amphotericin B (LAMB 10 mg/kg IV QD), posaconazole (PSC 30 mg/kg PO QD), or a combination of ibrexafungerp plus LAMB or ibrexafungerp plus PSC began 16 h post-infection and continued for 7 days for ibrexafungerp or PSC and through day 4 for LAMB. Ibrexafungerp was as effective as LAMB or PSC in prolonging median survival (range: 15 days to >21 days) and enhancing overall survival (30%–65%) vs placebo (9 days and 0%;
P
< 0.001) in mice infected with
R. delemar
. Furthermore, median survival and overall percent survival resulting from the combination of ibrexafungerp plus LAMB were significantly greater compared to all monotherapies (
P
≤ 0.03). Similar survival results were observed in mice infected with
M. circinelloides
. Monotherapies also reduce the lung and brain fungal burden by ~0.5–1.0log
10
conidial equivalents (CE)/g of tissue vs placebo in mice infected with
R. delemar
(
P
< 0.05), while a combination of ibrexafungerp plus LAMB lowered the fungal burden by ~0.5–1.5log
10
CE/g compared to placebo or any of the monotherapy groups (
P
< 0.03). These results are promising and warrant continued investigation of ibrexafungerp as a novel treatment option against mucormycosis.
PDCD4 restricts PRRSV replication in an eIF4A-dependent manner and is antagonized by the viral nonstructural protein 9
Authors: Wei Ruiping , Zhang Xiaoxiao , Wang Xiaoying , Li Lu , Fu Yajie , Chen Yaosheng , Liu Xiaohong , Guo Chunhe
Published: April 2024

As obligate parasites, viruses have evolved multiple strategies to evade the host immune defense. Manipulation of the host proteasome system to degrade specific detrimental factors is a common viral countermeasure. To identify host proteins targeted for proteasomal degradation by porcine reproductive and respiratory syndrome virus (PRRSV), we conducted a quantitative proteomics screen of PRRSV-infected Marc-145 cells under the treatment with proteasome inhibitor MG132. The data revealed that the expression levels of programmed cell death 4 (PDCD4) were strongly downregulated by PRRSV and significantly rescued by MG132. Further investigation confirmed that PRRSV infection induced the translocation of PDCD4 from the nucleus to the cytoplasm, and the viral nonstructural protein 9 (Nsp9) promoted PDCD4 proteasomal degradation in the cytoplasm by activating the Akt-mTOR-S6K1 pathway. The C-terminal domain of Nsp9 was responsible for PDCD4 degradation. As for the role of PDCD4 during PRRSV infection, we demonstrated that PDCD4 knockdown favored viral replication, while its overexpression significantly attenuated replication, suggesting that PDCD4 acts as a restriction factor for PRRSV. Mechanistically, we discovered eukaryotic translation initiation factor 4A (eIF4A) was required for PRRSV. PDCD4 interacted with eIF4A through four sites (E249, D253, D414, and D418) within its two MA3 domains, disrupting eIF4A-mediated translation initiation in the 5′-untranslated region of PRRSV, thereby inhibiting PRRSV infection. Together, our study reveals the antiviral function of PDCD4 and the viral strategy to antagonize PDCD4. These results will contribute to our understanding of the immune evasion strategies employed by PRRSV and offer valuable insights for developing new antiviral targets.

IMPORTANCE

Porcine reproductive and respiratory syndrome virus (PRRSV) infection results in major economic losses in the global swine industry and is difficult to control effectively. Here, using a quantitative proteomics screen, we identified programmed cell death 4 (PDCD4) as a host protein targeted for proteasomal degradation by PRRSV. We demonstrated that PDCD4 restricts PRRSV replication by interacting with eukaryotic translation initiation factor 4A, which is required for translation initiation in the viral 5′-untranslated region. Additionally, four sites within two MA3 domains of PDCD4 are identified to be responsible for its antiviral function. Conversely, PRRSV nonstructural protein 9 promotes PDCD4 proteasomal degradation in the cytoplasm by activating the Akt-mTOR-S6K1 pathway, thus weakening the anti-PRRSV function. Our work unveils PDCD4 as a previously unrecognized host restriction factor for PRRSV and reveals that PRRSV develops countermeasures to overcome PDCD4. This will provide new insights into virus-host interactions and the development of new antiviral targets.
A CRM1-dependent nuclear export signal in
Autographa californica
multiple nucleopolyhedrovirus Ac93 is important for the formation of intranuclear microvesicles
Authors: Chen Guoqing , Yang Jing , Wu Yihong , Wang Haoran , Zhang Xinxin , Feng Guozhong
Published: April 2024

Autographa californica
multiple nucleopolyhedrovirus (AcMNPV) Ac93 is highly conserved in all sequenced baculovirus genomes, and it plays important roles in both the nuclear egress of nucleocapsids and the formation of intranuclear microvesicles. In this study, we characterized a cellular CRM1-dependent nuclear export signal (NES) of AcMNPV Ac93. Bioinformatic analysis revealed that AcMNPV Ac93 may contain an NES at amino acids 115–125. Green fluorescent protein (GFP) fused to the NES (GFP:NES) of AcMNPV Ac93 is localized to the cytoplasm of transfected cells. Multiple point mutation analysis demonstrated that NES is important for the nuclear export of GFP:NES. Bimolecular fluorescence complementation experiments and co-immunoprecipitation assays confirmed that Ac93 interacts with
Spodoptera frugiperda
CRM1 (SfCRM1). However, AcMNPV Ac34 inhibits cellular CRM1-dependent nuclear export of GFP:NES. To determine whether the NES in AcMNPV Ac93 is important for the formation of intranuclear microvesicles, an
ac93
-null AcMNPV bacmid was constructed; the wild-type and NES-mutated Ac93 were reinserted into the
ac93
-null AcMNPV bacmid. Immunofluorescence analysis showed that Ac93 and SfCRM1 were predominantly colocalized at intranuclear microvesicles in infected cells, while the construct containing point mutations at residues 123 and 125 of Ac93 resulted in a defect in budded virus production and the abolishment of intranuclear microvesicles. Together, these data demonstrate that Ac93 contains a functional NES, which is required for the production of progeny viruses and the formation of intranuclear microvesicles.

IMPORTANCE

Autographa californica
multiple nucleopolyhedrovirus (AcMNPV) Ac93 is important for the formation of intranuclear microvesicles. However, how the baculovirus manipulates Ac93 for the formation of intranuclear microvesicles is unclear. In this study, we identified a nuclear export signal (NES) at amino acids 115–125 of AcMNPV Ac93. Our results showed that the NES is required for the interaction between Ac93 and
Spodoptera frugiperda
CRM1 (SfCRM1). However, AcMNPV Ac34 inhibits the nuclear export of green fluorescent protein fused to the NES. Our analysis revealed that Ac93 and SfCRM1 were predominantly colocalized at intranuclear microvesicles in AcMNPV-infected cells. Together, our results indicate that Ac93 participates in the formation of intranuclear microvesicles via the Ac93 NES-mediated CRM1 pathway.
Decoding host-microbiome interactions through co-expression network analysis within the non-human primate intestine
Authors: Uehara Mika , Inoue Takashi , Hase Sumitaka , Sasaki Erika , Toyoda Atsushi , Sakakibara Yasubumi
Published: April 2024

The gut microbiome affects the health status of the host through complex interactions with the host’s intestinal wall. These host-microbiome interactions may spatially vary along the physical and chemical environment of the intestine, but these changes remain unknown. This study investigated these intricate relationships through a gene co-expression network analysis based on dual transcriptome profiling of different intestinal sites—cecum, transverse colon, and rectum—of the primate common marmoset. We proposed a gene module extraction algorithm based on the graph theory to find tightly interacting gene modules of the host and the microbiome from a vast co-expression network. The 27 gene modules identified by this method, which include both host and microbiome genes, not only produced results consistent with previous studies regarding the host-microbiome relationships, but also provided new insights into microbiome genes acting as potential mediators in host-microbiome interplays. Specifically, we discovered associations between the host gene
FBP1
, a cancer marker, and polysaccharide degradation-related genes (
pfkA
and
fucI
) coded by
Bacteroides vulgatus
, as well as relationships between host B cell-specific genes (
CD19
,
CD22
,
CD79B
, and
PTPN6
) and a tryptophan synthesis gene (
trpB
) coded by
Parabacteroides distasonis
. Furthermore, our proposed module extraction algorithm surpassed existing approaches by successfully defining more functionally related gene modules, providing insights for understanding the complex relationship between the host and the microbiome.

IMPORTANCE

We unveiled the intricate dynamics of the host-microbiome interactions along the colon by identifying closely interacting gene modules from a vast gene co-expression network, constructed based on simultaneous profiling of both host and microbiome transcriptomes. Our proposed gene module extraction algorithm, designed to interpret inter-species interactions, enabled the identification of functionally related gene modules encompassing both host and microbiome genes, which was challenging with conventional modularity maximization algorithms. Through these identified gene modules, we discerned previously unrecognized bacterial genes that potentially mediate in known relationships between host genes and specific bacterial species. Our findings underscore the spatial variations in host-microbiome interactions along the colon, rather than displaying a uniform pattern throughout the colon.
Metagenomic next-generation sequencing of nasopharyngeal microbiota in COVID-19 patients with different disease severities
Authors: Aljabr Waleed , Dandachi Iman , Abbas Basma , Karkashan Alaa , Al-Amari Ahod , AlShahrani Dayel
Published: April 2024

Throughout the COVID-19 pandemic, extensive research has been conducted on SARS-COV-2 to elucidate its genome, prognosis, and possible treatments. However, few looked at the microbial markers that could be explored in infected patients and that could predict possible disease severity. The aim of this study is to compare the nasopharyngeal microbiota of healthy subjects, moderate, under medication, and recovered SARS-COV-2 patients. In 2020, 38 nasopharyngeal swabs were collected from 6 healthy subjects, 14 moderates, 10 under medication and 8 recovered SARS-COV-2 patients at the Prince Mohammed Bin Abdulaziz Hospital Riyadh. Metatranscriptomic sequencing was performed using Minion Oxford nanopore sequencing. No significant difference in alpha as well as beta diversity was observed among all four categories. Nevertheless, we have found that
Streptococcus
spp including
Streptococcus pneumoniae
and
Streptococcus thermophilus
were among the top 15 most abundant species detected in COVID-19 patients but not in healthy subjects. The genus
Staphylococcus
was found to be associated with COVID-19 patients compared to healthy subjects. Furthermore, the abundance of
Leptotrichia
was significantly higher in healthy subjects compared to recovered patients.
Corynebacterium
on the other hand, was associated with under-medication patients. Taken together, our study revealed no differences in the overall microbial composition between healthy subjects and COVID-19 patients. Significant differences were seen only at specific taxonomic level. Future studies should explore the nasopharyngeal microbiota between controls and COVID-19 patients while controlling for confounders including age, gender, and comorbidities; since these latter could affect the results and accordingly the interpretation.

IMPORTANCE

In this work, no significant difference in the microbial diversity was seen between healthy subjects and COVID-19 patients. Changes in specific taxa including
Leptotrichia
,
Staphylococcus,
and
Corynebacterium
were only observed.
Leptotrichia
was significantly higher in healthy subjects, whereas
Staphylococcus
and
Corynebacterium
were mostly associated with COVID-19, and specifically with under-medication SARS-COV-2 patients, respectively. Although the COVID-19 pandemic has ended, the SARS-COV-2 virus is continuously evolving and the emergence of new variants causing more severe disease should be always kept in mind. Microbial markers in SARS-COV-2 infected patients can be useful in the early suspicion of the disease, predicting clinical outcomes, framing hospital and intensive care unit admission as well as, risk stratification. Data on which microbial marker to tackle is still controversial and more work is needed, hence the importance of this study.
Effective Influence of an Electric Current on Brillouin Spectra in the NiFe/IrMn Structure
Authors: Morgunov R. B. , Bakhmetiev M. V. , Chernov A. I. , Khutieva A. B. , Sadovnikov A. V.
Published: April 2024

When an electric current flows through the NiFe/IrMn structure, a significant redistribution of the intensities of the direct Stokes and inverse anti-Stokes lines in spectra of Brillouin scattering on thermal spin waves is observed. This is due to a change in the orientation of uniaxial anisotropy and the corresponding easy axis of the exchange shift under the action of the spin–orbit torque in the IrMn antiferromagnet, which in turn affects the dynamics of spin waves in the neighboring ferromagnetic NiFe layer. The detected effect indicates that spin-wave processes in a ferromagnet can be controlled by applying a spin current to change the magnetic anisotropy of the NiFe/IrMn interface.
Lanka Mahila Samiti, Mary Rutnam and girls’ education
Authors: Albrecht Jessica Annette
Published: April 2024

This article engages with the maternal education politics in late colonial Sri Lanka by looking at the implementation of maternal health in the gendered syllabus of middle-class girls’ schools. After decades of gender-specific education, the 1930s saw a homogenisation of teachings in these schools through the impact of Mary Rutnam’s health manuals. Rutnam was a Canadian doctor who had been living in Sri Lanka for most of her adult life and was seen as a local. She was also active in establishing women’s and girls’ organisations and political groups. Especially the Lanka Mahila Samiti (LMS) was greatly influential and still is today. The LMS specifically aims at educating the rural women in maternal health and other forms of hygiene with the goal to increase their political and cultural agency. This article examines the relationship between Rutnam’s handbooks for girls’ schools and the globality of the discourse of motherhood, on the one hand, and the hierarchical divide between the urban middle-class woman and the rural woman, on the other hand. I will argue that by applying the classist discourse of eugenics and hygiene, the teaching of maternal health was transformed in Sri Lanka to create a notion of motherhood that was detached from religion, as it previously was so often framed by it but was highly racialised and classist. This notion of motherhood continues to exist and informs the teaching of sexuality in contemporary Sri Lankan middle-class girls’ schools.
PTME: A Regular Expression Matching Engine Based on Speculation and Enumerative Computation on FPGA
Authors: Sun Mingqian , Xie Guangwei , Zhang Fan , Guo Wei , Fan Xitian , Li Tianyang , Chen Li , Du Jiayu
Published: April 2024

Fast regular expression matching is an essential task for deep packet inspection. In previous works, the regular expression matching engine on FPGA struggled to achieve an ideal balance between resource consumption and throughput. Speculation and enumerative computation exploits the statistical properties of deterministic finite automata, allowing for more efficient pattern matching. Existing related designs mostly revolve around vector instructions and multiple processors/cores or SIMD instruction sets, with a lack of implementation on FPGA platforms. We design a parallelized two-character matching engine on FPGA for efficiently fast filtering off fields with no pattern features. We transform the state transitions with sequential dependencies to the existing problem of elements in one set, enabling the proposed design to achieve high throughput with low resource consumption and support dynamic updates. Results show that compared with the traditional DFA matching, with a maximum resource consumption of 25% for on-chip FFs (74323/1045440) and LUTs (123902/522720), there is an improvement in throughput of 8.08–229.96×
speedup
and 87.61–99.56%
speed-up(percentage improvement)
for normal traffic, and 11.73–39.59×
speedup
and 91.47–97.47%
speed-up(percentage improvement)
for traffic with high-frequency match hits. Compared with the state-of-the-art similar implementation, our circuit on a single FPGA chip is superior to existing multi-core designs.
Is Copyright Law the New Turing Test?
Authors: Blumenthal Richard
Published: April 2024

In December 2023, the New York Times Company filed a lawsuit against OpenAI and Microsoft for the "defendants' unlawful use of The Time's work to create artificial intelligence products..." [8]. While this lawsuit alone should interest the
Computers and Society
community, it struck me that its eventual judgment might serve as an interesting exhibit as to whether computers are creative in their intelligent thinking?
1
This Parting Opinion focuses on this question. As usual, I'll present some background context to
set the stage
, before diving into the primary question at hand. As a bit of nostalgia, let's begin with the early days of Artificial Intelligence (AI) and quickly move to the present.
Specific circulating miRNAs are associated with plasma lipids in a healthy American cohort
Authors: Evans Levi W. , Durbin-Johnson Blythe , Sutton Kristen J. , Yam Phoebe , Bouzid Yasmine Y. , Cervantes Eduardo , Bonnel Ellen , Stephenson Charles B. , Bennett Brian J.
Published: April 2024

This study explored the association between circulating microRNA (miRNA) and low-density lipoprotein cholesterol (LDL-c) in a healthy population of 353 participants. Two miRNAs, miR-15b-5p and miR-16-5p, were upregulated in individuals with at-risk LDL-c levels. Several miRNA clusters were positively and negatively correlated with LDL-c and are known to target mRNA involved in lipid metabolism. The study also investigated the influence of diet on circulating miRNA, suggesting potential biomarkers for hypercholesterolemia.
Supplemental Figure S13 from Subclonal Cancer Driver Mutations Are Prevalent in the Unresected Peritumoral Edema of Adult Diffuse Gliomas
Authors: Underhill Hunter R. , Karsy Michael , Davidson Christian J. , Hellwig Sabine , Stevenson Samuel , Goold Eric A. , Vincenti Sydney , Sellers Drew L. , Dean Charlie , Harrison Brion E. , Bronner Mary P. , Colman Howard , Jensen Randy L.
Published: April 2024

Supplemental Figure S13. Relative to the overall median read depth for each sample, the median read depth for the TERT promoter is less compared to other gene-specific regions (IDH1, IDH2, and NF1).
Supplemental Figure S12 from Subclonal Cancer Driver Mutations Are Prevalent in the Unresected Peritumoral Edema of Adult Diffuse Gliomas
Authors: Underhill Hunter R. , Karsy Michael , Davidson Christian J. , Hellwig Sabine , Stevenson Samuel , Goold Eric A. , Vincenti Sydney , Sellers Drew L. , Dean Charlie , Harrison Brion E. , Bronner Mary P. , Colman Howard , Jensen Randy L.
Published: April 2024

Supplemental Figure S12. Sample relatedness using Somalier.
Supplemental Figure S10 from Subclonal Cancer Driver Mutations Are Prevalent in the Unresected Peritumoral Edema of Adult Diffuse Gliomas
Authors: Underhill Hunter R. , Karsy Michael , Davidson Christian J. , Hellwig Sabine , Stevenson Samuel , Goold Eric A. , Vincenti Sydney , Sellers Drew L. , Dean Charlie , Harrison Brion E. , Bronner Mary P. , Colman Howard , Jensen Randy L.
Published: April 2024

Supplemental Figure S10. Comparison of True2 sensitivity using reduced sample complexity and iterative captures.
Movie#2 from Human Tumor–Associated Macrophages and Neutrophils Regulate Antitumor Antibody Efficacy through Lethal and Sublethal Trogocytosis
Authors: Singhal Sunil , Rao Abhishek S. , Stadanlick Jason , Bruns Kyle , Sullivan Neil T. , Bermudez Andres , Honig-Frand Adam , Krouse Ryan , Arambepola Sachinthani , Guo Emily , Moon Edmund K. , Georgiou George , Valerius Thomas , Albelda Steven M. , Eruslanov Evgeniy B.
Published: April 2024

Suppl movie 2, trogocytosis Mph A431
Supplementary Fig.S8 from PRMT1 Sustains De Novo Fatty Acid Synthesis by Methylating PHGDH to Drive Chemoresistance in Triple-Negative Breast Cancer
Authors: Yamamoto Takehiro , Hayashida Tetsu , Masugi Yohei , Oshikawa Kiyotaka , Hayakawa Noriyo , Itoh Mai , Nishime Chiyoko , Suzuki Masami , Nagayama Aiko , Kawai Yuko , Hishiki Takako , Matsuura Tomomi , Naito Yoshiko , Kubo Akiko , Yamamoto Arisa , Yoshioka Yujiro , Kurahori Tomokazu , Nagasaka Misa , Takizawa Minako , Takano Naoharu , Kawakami Koji , Sakamoto Michiie , Wakui Masatoshi , Yamamoto Takushi , Kitagawa Yuko , Kabe Yasuaki , Horisawa Kenichi , Suzuki Atsushi , Matsumoto Masaki , Suematsu Makoto
Published: April 2024

Fig.S8
Supplementary Fig.S19 from PRMT1 Sustains De Novo Fatty Acid Synthesis by Methylating PHGDH to Drive Chemoresistance in Triple-Negative Breast Cancer
Authors: Yamamoto Takehiro , Hayashida Tetsu , Masugi Yohei , Oshikawa Kiyotaka , Hayakawa Noriyo , Itoh Mai , Nishime Chiyoko , Suzuki Masami , Nagayama Aiko , Kawai Yuko , Hishiki Takako , Matsuura Tomomi , Naito Yoshiko , Kubo Akiko , Yamamoto Arisa , Yoshioka Yujiro , Kurahori Tomokazu , Nagasaka Misa , Takizawa Minako , Takano Naoharu , Kawakami Koji , Sakamoto Michiie , Wakui Masatoshi , Yamamoto Takushi , Kitagawa Yuko , Kabe Yasuaki , Horisawa Kenichi , Suzuki Atsushi , Matsumoto Masaki , Suematsu Makoto
Published: April 2024

Fig.S19
Figure S2 from The Imipridone ONC213 Targets α-Ketoglutarate Dehydrogenase to Induce Mitochondrial Stress and Suppress Oxidative Phosphorylation in Acute Myeloid Leukemia
Authors: Su Yongwei , Carter Jenna L. , Li Xinyu , Fukuda Yu , Gray Ashley , Lynch John , Edwards Holly , Ma Jun , Schreiner Patrick , Polin Lisa , Kushner Juiwanna , Dzinic Sijana H. , Buck Steven A. , Pruett-Miller Shondra M. , Hege-Hurrish Katie , Robinson Camenzind , Qiao Xinan , Liu Shuang , Wu Shuangshuang , Wang Guan , Li Jing , Allen Joshua E. , Prabhu Varun V. , Schimmer Aaron D. , Joshi Dhananjay , Kalhor-Monfared Shiva , Watson Iain D. G. , Marcellus Richard , Isaac Methvin B. , Al-awar Rima , Taub Jeffrey W. , Lin Hai , Schuetz John D. , Ge Yubin
Published: April 2024

Supplementary Figure S2
Supplementary Fig.S11 from PRMT1 Sustains De Novo Fatty Acid Synthesis by Methylating PHGDH to Drive Chemoresistance in Triple-Negative Breast Cancer
Authors: Yamamoto Takehiro , Hayashida Tetsu , Masugi Yohei , Oshikawa Kiyotaka , Hayakawa Noriyo , Itoh Mai , Nishime Chiyoko , Suzuki Masami , Nagayama Aiko , Kawai Yuko , Hishiki Takako , Matsuura Tomomi , Naito Yoshiko , Kubo Akiko , Yamamoto Arisa , Yoshioka Yujiro , Kurahori Tomokazu , Nagasaka Misa , Takizawa Minako , Takano Naoharu , Kawakami Koji , Sakamoto Michiie , Wakui Masatoshi , Yamamoto Takushi , Kitagawa Yuko , Kabe Yasuaki , Horisawa Kenichi , Suzuki Atsushi , Matsumoto Masaki , Suematsu Makoto
Published: April 2024

Fig.S11
Supplementary Fig.S1 from PRMT1 Sustains De Novo Fatty Acid Synthesis by Methylating PHGDH to Drive Chemoresistance in Triple-Negative Breast Cancer
Authors: Yamamoto Takehiro , Hayashida Tetsu , Masugi Yohei , Oshikawa Kiyotaka , Hayakawa Noriyo , Itoh Mai , Nishime Chiyoko , Suzuki Masami , Nagayama Aiko , Kawai Yuko , Hishiki Takako , Matsuura Tomomi , Naito Yoshiko , Kubo Akiko , Yamamoto Arisa , Yoshioka Yujiro , Kurahori Tomokazu , Nagasaka Misa , Takizawa Minako , Takano Naoharu , Kawakami Koji , Sakamoto Michiie , Wakui Masatoshi , Yamamoto Takushi , Kitagawa Yuko , Kabe Yasuaki , Horisawa Kenichi , Suzuki Atsushi , Matsumoto Masaki , Suematsu Makoto
Published: April 2024

Fig.S1
Table S2C from Osteosarcoma Cells Secrete CXCL14 That Activates Integrin α11β1 on Fibroblasts to Form a Lung Metastatic Niche
Authors: Xu Yanyang , Deng Chuangzhong , Chen Hongmin , Song YiJiang , Xu Huaiyuan , Song Guohui , Wang Xinliang , Luo Tianqi , Chen Weiqing , Ma Jiahui , Zeng Anyu , Huang Shujing , Chen Zhihao , Fu Jianchang , Gong Ming , Tai Yi , Huang Anfei , Feng Huixiong , Hu Jinxin , Zhu Xiaojun , Tang Qinglian , Lu Jinchang , Wang Jin
Published: April 2024

Differential expressed genes in fibroblast (Metastatic vs nonmetastatic samples).
Figure S8 from Osteosarcoma Cells Secrete CXCL14 That Activates Integrin α11β1 on Fibroblasts to Form a Lung Metastatic Niche
Authors: Xu Yanyang , Deng Chuangzhong , Chen Hongmin , Song YiJiang , Xu Huaiyuan , Song Guohui , Wang Xinliang , Luo Tianqi , Chen Weiqing , Ma Jiahui , Zeng Anyu , Huang Shujing , Chen Zhihao , Fu Jianchang , Gong Ming , Tai Yi , Huang Anfei , Feng Huixiong , Hu Jinxin , Zhu Xiaojun , Tang Qinglian , Lu Jinchang , Wang Jin
Published: April 2024

ITGα11β1 heterodimer is a functional cell-surface receptor for CXCL14.
Data from Chromatin Remodelers Are Regulators of the Tumor Immune Microenvironment
Authors: Chaudhri Apoorvi , Lizee Gregory , Hwu Patrick , Rai Kunal
Published: April 2024

Abstract
Immune checkpoint inhibitors show remarkable responses in a wide range of cancers, yet patients develop adaptive resistance. This necessitates the identification of alternate therapies that synergize with immunotherapies. Epigenetic modifiers are potent mediators of tumor-intrinsic mechanisms and have been shown to regulate immune response genes, making them prime targets for therapeutic combinations with immune checkpoint inhibitors. Some success has been observed in early clinical studies that combined immunotherapy with agents targeting DNA methylation and histone modification; however, less is known about chromatin remodeler-targeted therapies. Here, we provide a discussion on the regulation of tumor immunogenicity by the chromatin remodeling SWI/SNF complex through multiple mechanisms associated with immunotherapy response that broadly include IFN signaling, DNA damage, mismatch repair, regulation of oncogenic programs, and polycomb-repressive complex antagonism. Context-dependent targeting of SWI/SNF subunits can elicit opportunities for synthetic lethality and reduce T-cell exhaustion. In summary, alongside the significance of SWI/SNF subunits in predicting immunotherapy outcomes, their ability to modulate the tumor immune landscape offers opportunities for therapeutic intervention.
Data from The Extracellular Niche and Tumor Microenvironment Enhance KRAS Inhibitor Efficacy in Pancreatic Cancer
Authors: Kumarasamy Vishnu , Wang Jianxin , Frangou Costakis , Wan Yin , Dynka Andrew , Rosenheck Hanna , Dey Prasenjit , Abel Ethan V. , Knudsen Erik S. , Witkiewicz Agnieszka K.
Published: April 2024

Abstract
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease that lacks effective treatment options, highlighting the need for developing new therapeutic interventions. Here, we assessed the response to pharmacologic inhibition of KRAS, the central oncogenic driver of PDAC. In a panel of PDAC cell lines, inhibition of KRASG12D with MRTX1133 yielded variable efficacy in suppressing cell growth and downstream gene expression programs in 2D cultures. On the basis of CRISPR-Cas9 loss-of-function screens, ITGB1 was identified as a target to enhance the therapeutic response to MRTX1133 by regulating mechanotransduction signaling and YAP/TAZ expression, which was confirmed by gene-specific knockdown and combinatorial drug synergy. Interestingly, MRTX1133 was considerably more efficacious in 3D cell cultures. Moreover, MRTX1133 elicited a pronounced cytostatic effect in vivo and controlled tumor growth in PDAC patient-derived xenografts. In syngeneic models, KRASG12D inhibition led to tumor regression that did not occur in immune-deficient hosts. Digital spatial profiling on tumor tissues indicated that MRTX1133-mediated KRAS inhibition enhanced IFNγ signaling and induced antigen presentation that modulated the tumor microenvironment. Further investigation of the immunologic response using single-cell sequencing and multispectral imaging revealed that tumor regression was associated with suppression of neutrophils and influx of effector CD8+ T cells. Together, these findings demonstrate that both tumor cell-intrinsic and -extrinsic events contribute to response to MRTX1133 and credential KRASG12D inhibition as a promising therapeutic strategy for a large percentage of patients with PDAC.
Significance:
Pharmacologic inhibition of KRAS elicits varied responses in pancreatic cancer 2D cell lines, 3D organoid cultures, and xenografts, underscoring the importance of mechanotransduction and the tumor microenvironment in regulating therapeutic responses.
Targeting Metabolic Dependencies Fueling the TCA Cycle to Circumvent Therapy Resistance in Acute Myeloid Leukemia
Authors: Boët Emeline , Sarry Jean-Emmanuel
Published: April 2024

Acute myeloid leukemia (AML) is one of the most prevalent blood cancers, characterized by a dismal survival rate. This poor outcome is largely attributed to AML cells that persist despite treatment and eventually result in relapse. Relapse-initiating cells exhibit diverse resistance mechanisms, encompassing genetic factors and, more recently discovered, nongenetic factors such as metabolic adaptations. Leukemic stem cells (LSC) rely on mitochondrial metabolism for their survival, whereas hematopoietic stem cells primarily depend on glycolysis. Furthermore, following treatments such as cytarabine, a standard in AML treatment for over four decades, drug-persisting leukemic cells exhibit an enhanced reliance on mitochondrial metabolism. In this issue of Cancer Research, two studies investigated dependencies of AML cells on two respiratory substrates, α-ketoglutarate and lactate-derived pyruvate, that support mitochondrial oxidative phosphorylation (OXPHOS) following treatment with the imipridone ONC-213 and the BET inhibitor INCB054329, respectively. Targeting lactate utilization by interfering with monocarboxylate transporter 1 (MCT1 or SLC16A1) or lactate dehydrogenase effectively sensitized cells to BET inhibition in vitro and in vivo. In addition, ONC-213 affected αKGDH, a pivotal NADH-producing enzyme of the TCA cycle, to induce a mitochondrial stress response through ATF4 activation that diminished the expression of the antiapoptotic protein MCL1, consequently promoting apoptosis of AML cells. In summary, targeting these mitochondrial dependencies might be a promising strategy to kill therapy-naïve and treatment-resistant OXPHOS-reliant LSCs and to delay or prevent relapse.

See related articles by Monteith et al., p. 1101 and Su et al., p. 1084