bluuebunny/crossref_metadata_2025 huggingface dataset:
What’s on a prophage: analysis of
Salmonella
spp. prophages identifies a diverse range of cargo with multiple virulence- and metabolism-associated functions
Authors: Yates Caroline R. , Nguyen Anthony , Liao Jingqiu , Cheng Rachel A.
Published: May 2024

The gain of mobile elements, such as prophages, can introduce cargo to the recipient bacterium that could facilitate its persistence in or expansion to a new environment, such as a host. While previous studies have focused on identifying and characterizing the genetic diversity of prophages, analyses characterizing the cargo that prophages carry have not been extensively explored. We characterized prophage regions from 303
Salmonella
spp. genomes (representing 254 unique serovars) to assess the distribution of prophages in diverse
Salmonella
. On average, prophages accounted for 3.7% (0.1%–8.8%) of the total genomic content of each isolate. Prophage regions annotated as Gifsy 1 and Salmon Fels 1 were the most commonly identified intact prophages, suggesting that they are common throughout the
Salmonella
genus. Among 21,687 total coding sequences (CDSs) from intact prophage regions in subsp.
enterica
genomes, 7.5% (median; range: 1.1%–47.6%) were categorized as having a function not related to prophage integration or phage structure, some of which could potentially provide a functional attribute to the host
Salmonella
cell. These predicted functions could be broadly categorized into CDSs involved in: (i) modification of cell surface structures (i.e., glycosyltransferases); (ii) modulation of host responses (e.g., SodC/SodA, SopE, ArtAB, and typhoid toxin); (iii) conferring resistance to heavy metals and antimicrobials; (iv) metabolism of carbohydrates, amino acids, and nucleotides; and (v) DNA replication, repair, and regulation. Overall, our systematic analysis of prophage cargo highlights a broader role for prophage cargo in influencing the metabolic, virulence, and resistance characteristics of
Salmonella
.

IMPORTANCE

Lysogenic bacteriophages (phages) can integrate their genome into a bacterial host's genome, potentially introducing genetic elements that can affect the fitness of the host bacterium. The functions of prophage-encoded genes are important to understand as these genes could be mobilized and transferred to a new host. Using a large genomic dataset representing >300 isolates from all known subspecies and species of
Salmonella
, our study contributes important new findings on the distribution of prophages and the types of cargo that diverse
Salmonella
prophages carry. We identified a number of coding sequences (CDSs) annotated as having cell surface-modifying attributes, suggesting that prophages may have played an important role in shaping
Salmonella
's diverse surface antigen repertoire. Furthermore, our characterization of prophages suggests that they play a broader role in facilitating the acquisition and transfer of CDSs associated with metabolism, DNA replication and repair, virulence factors, and to a lesser extent, antimicrobial resistance.
Supplemental Material: Google Earth Engine web applications for investigating and teaching fundamental geoscience concepts
Authors: Hoxey Andrew K.R. , Taylor Michael H. , Walker J. Douglas , Kamola Diane L.
Published: May 2024

Supplemental Material. Table of measurements used in Plane Orientation Calculator example.
Practice ‘safe scans’: why ultrasound transducer covers should be considered best practice
Authors: Prinzbach Ariana , Gadsden Jeffrey
Published: May 2024

Single-injection, ultrasound-guided nerve block procedures involve puncturing the skin in close proximity to an ultrasound transducer, creating a potential vector for transmission of microbial organisms when skin flora and blood come into contact with the probe. Practice patterns regarding disinfection of the transducer and the use of barrier protection are inconsistent, ranging from sterile sleeve probe covers to no cover at all. Although sleeve probe covers are easy and straightforward to use and serve to protect patients, providers and medical equipment, their utilisation remains controversial. Standardisation of their use eliminates the impact of improper or haphazard probe disinfection and makes infection control practices consistent and reproducible. This position is shared by multiple societies and authorities on ultrasound and acute care medicine. In this Daring Discourse, we outline the arguments supporting the utilisation of single-use sleeve probe covers to ensure patient safety with respect to vector-borne transmission of microbes during single-injection regional anaesthesia procedures.
At-home bodyweight interval exercise in the fed versus fasted state lowers postprandial glycemia and appetite perceptions in females
Authors: Govette Alexa , Gillen Jenna B.
Published: May 2024

Limited research has characterized the metabolic health benefits of bodyweight interval exercise (BWE) performed outside of a laboratory setting. Metabolic responses to exercise can also be influenced by meal timing around exercise, but the interactive effects of BWE and nutrition are unknown. This study investigated the effects of BWE performed in the fasted or fed state on postprandial glycemia, post-exercise fat oxidation and appetite perceptions. Twelve females (23 ± 2 years; 22 ± 2 kg/m2) underwent two virtually-monitored trials that involved completing BWE (10 × 1 min, 1 min recovery) 5 min before (FastEX) or beginning BWE 10 min after (FedEX) a standardized breakfast. Heart rate and rating of perceived exertion (RPE) were measured during exercise and capillary glucose concentrations were measured for 2 h postprandial. Following exercise, appetite perceptions were assessed and Lumen expired carbon dioxide percentage (L%CO2) was measured as an index of fat oxidation. Heart rate (85 ± 5%) and RPE (14 ± 2) did not differ between conditions ( p > 0.05). Postprandial glucose mean (6.1 ± 0.6 vs. 6.8 ± 0.8 mmol/L, p = 0.03), peak (7.4 ± 1.2 vs. 8.5 ± 1.5 mmol/L, p = 0.01), and area under the curve (AUC) (758 ± 72 vs. 973 ± 82 mmol/L × 2 h, p = 0.004) were lower in FedEX versus FastEX. Appetite perceptions were lower in FedEX versus FastEX (−87.63 ± 58.51 vs. −42.06 ± 34.96 mm, p = 0.029). Post-exercise L%CO2was transiently decreased 30 min post-exercise in both conditions (4.03 ± 0.38 vs. 4.29 ± 0.34%, p = 0.0023), reflective of increased fat oxidation following BWE. These findings demonstrate that BWE performed in the fed compared to the fasted state lowered postprandial glycemia and appetite perceptions in females.
Generating and Evaluating Data of Daily Activities with an Autonomous Agent in a Virtual Smart Home
Authors: Gramoli Lysa , Cumin Julien , Lacoche Jérémy , Foulonneau Anthony , Arnaldi Bruno , Gouranton Valérie
Published: May 2024

Training machine learning models to identify human behavior is a difficult yet essential task to develop autonomous and adaptive systems such as smart homes. These models require large and diversified amounts of labeled data to be trained effectively. Due to the high variety of home environments and occupant behaviors, collecting datasets that are representative of all possible homes is a major challenge. In addition, privacy and cost are major hurdles to collect real home data. To avoid these difficulties, one solution consists of training these models using purely synthetic data, which can be generated through the simulation of home and their occupants. Two challenges arise from this approach: designing a methodology with a simulation able to generate credible simulated data and evaluating this credibility. In this article, we explain the methodology used to generate diversified synthetic data of daily activities, through the combination of an agent model to simulate an occupant and a simulated 3D house enriched with sensors and effectors to produce such data. We demonstrate the credibility of the generated synthetic data by comparing their efficacy for training human context understanding models against the efficacy generated by real data. To achieve this, we replicate a real dataset collection setting with our smart home simulator. The occupant is replaced by an autonomous agent following the same experimental protocol used for the real dataset collection. This agent is a BDI-based model enhanced with a scheduler designed to offer a balance between control and autonomy. This balance is useful in synthetic data generation since strong constraints can be imposed on the agent to simulate desired situations while allowing autonomous behaviors outside these constraints to generate diversified data. In our case, the constraints are those imposed during the real dataset collection that we want to replicate. The simulated sensors and effectors were configured to react to the agent’s behaviors similarly to the real ones. We experimentally show that data generated from this simulation are valuable for two human context understanding tasks: current human activity recognition and future human activity prediction. In particular, we show that models trained solely with simulated data can give reasonable predictions about real situations occurring in the original dataset. We also report experimental results regarding statistical analysis and C2ST to assess the credibility of generated data. We discuss the generality of our approach for evaluating the credibility of simulated data from their use as training data.
Sociology of Twitter/X: Trends, Challenges, and Future Research Directions
Authors: Murthy Dhiraj
Published: May 2024

This article provides a sociology of Twitter (now known as X) and charts the development of the study of the platform and its data in sociological venues through an analysis of 1,644 articles published since 2009. This review helps readers understand developments in the field and provides a road map for advancing future Twitter-related sociological research. The works cited in this review advance sociological research on a variety of subfields, including but not limited to race, social movements, segregation, politics, violence, and stratification. After a brief introduction of definitions as well as methodological approaches used to study the platform (computational, qualitative, and mixed), I explore how Twitter has been used in sociological research. Furthermore, using social movements and activism as a case study, I highlight what the platform's usage and communication reveal about the social world. I conclude with a road map for advancing Twitter-related sociological research in the current atmosphere in which Twitter has been renamed X. Ultimately, a sociology of Twitter does not need to be tethered to the platform per se, as it also provides a framework for understanding new platforms if they become home for what people previously posted to Twitter/X.
Electrochemical Synthesis and Performance of AgCl/Ag/Sliver Mesh Collector Composite Electrode for Seawater Batteries
Authors: Zhang Haitao , Wang Shenggui , He Xuehua , Wang Yuankui , Xu Wanli , Song Juemin , Li Zheng , Yang Guangzhou , Wang Xinyi , Zhang Qian , Li Hongxu , Yan Yang , Yu Kun
Published: May 2024

High-energy-density and easy-to-implement battery storage technologies are essential for the exploitation of marine resources. AgCl is a promising cathode material for seawater batteries due to its environmental friendliness and high capacities density, but its inherent low conductivity limits its application in specific scenarios. In this paper, AgCl was electrochemically grown on a sparsely conductive Ag/Sliver mesh collector (SMC) substrate, and an excellent performance AgCl/Ag/SMC composite electrode is obtained. The cathodic polarization curves indicate that the current density of the AgCl/Ag/SMC electrode was 208.2 mA cm−2 at 0.4 V (vs RHE) potential, which is significantly higher than that of the conventional AgCl cathode material. The AgCl/Ag/SMC electrode demonstrated a very high discharge capacity of 181.7 mAh g−1 at 30 mA cm−2, and the assembled cell was found to be in good condition at 100 mA cm−2 with a power density of up to 154.7 mW cm−2, showing very excellent performance. Furthermore, investigation of the mechanism and depth of discharge experiment reveal the kinetic and microscopic reasons for the high performance of AgCl/Ag/SMC composite electrodes. Therefore, this study provides an efficient and feasible solution for the electrochemical preparation of highly active cathode materials for Mg-AgCl seawater batteries.
In Situ Investigation of Lattice Oxygen Loss from Preferentially Faceted Electrodeposited LiCoO2 via Scanning Electrochemical Microscopy
Authors: Mishra Abhiroop , Lin Jr-Wen , Zahiri Beniamin , Braun Paul V. , Rodríguez-López Joaquín
Published: May 2024

Lattice oxygen loss from transition metal oxide cathodes in Li-ion batteries (LiBs) is a key factor responsible in their gradual capacity decline over time. Understanding and mitigating this phenomenon is crucial for the development of next-generation LiBs. The effect of various parameters on lattice oxygen loss, such as cathode chemical composition, has been studied extensively. However, there is a lack of experimental investigation into the lattice oxygen stability across different crystallographic facets within the same cathode composition. Here, we employed in situ scanning electrochemical microscopy (SECM) to investigate oxygen evolution from preferentially faceted, electrodeposited LiCoO2 cathodes. Samples predominantly exposing the (003) basal planes and the (101), (102), (110) fast Li-ion diffusing facets exhibited oxygen evolution at potentials exceeding 3.5 V vs Li+/Li. Finite element simulations helped quantify the flux of oxygen evolution on the first charge cycle to 33 ± 5 pmol cm−2s−1 for the basal plane and 37 ± 9 pmol cm−2s−1 for the faceted samples at potentials above 4 V based on single spot measurements. However, spatially resolved measurements showed that faceted samples exhibited significant heterogeneity in their oxygen evolution, reaching twofold values compared to the basal plane samples at potentials beyond 4.5 V.
Stem cells, cell therapies, and bioengineering in lung biology and diseases 2023
Authors: Hynds Robert E. , Magin Chelsea M. , Ikonomou Laertis , Aschner Yael , Beers Michael F. , Burgess Janette K. , Heise Rebecca L. , Hume Patrick S. , Krasnodembskaya Anna D. , Mei Shirley H. J , Misharin Alexander V. , Park Jin-Ah , Reynolds Susan D. , Tschumperlin Daniel J. , Tanneberger Alicia E. , Vaidyanathan Sriram , Waters Christopher M. , Zettler Patricia J. , Weiss Daniel J. , Ryan Amy L.
Published: May 2024

Repair and regeneration of a diseased lung using stem cells or bioengineered tissues is an exciting therapeutic approach for a variety of lung diseases and critical illnesses. Over the past decade, increasing evidence from preclinical models suggests that mesenchymal stromal cells, which are not normally resident in the lung, can be used to modulate immune responses after injury, but there have been challenges in translating these promising findings to the clinic. In parallel, there has been a surge in bioengineering studies investigating the use of artificial and acellular lung matrices as scaffolds for three-dimensional lung or airway regeneration, with some recent attempts of transplantation in large animal models. The combination of these studies with those involving stem cells, induced pluripotent stem cell derivatives, and/or cell therapies is a promising and rapidly developing research area. These studies have been further paralleled by significant increases in our understanding of the molecular and cellular events by which endogenous lung stem and/or progenitor cells arise during lung development and participate in normal and pathological remodeling after lung injury. For the 2023 Stem Cells, Cell Therapies, and Bioengineering in Lung Biology and Diseases Conference, scientific symposia were chosen to reflect the most cutting-edge advances in these fields. Sessions focused on the integration of “omics” technologies with function, the influence of immune cells on regeneration, and the role of the extracellular matrix in regeneration. The necessity for basic science studies to enhance fundamental understanding of lung regeneration and to design innovative translational studies was reinforced throughout the conference.
Stigmas and Petals of Crocus sativus L. (Taliouine, Morocco): Comparative Evaluation of Their Phenolic Compounds, Antioxidant, and Antibacterial Activities
Authors: Benkerroum Asmaa , Oubella Khadija , Zini Soukaina , Boussif Kaoutar , Mouhanni Hind , Achemchem Fouad
Published: May 2024

The dried stigmas of Crocus sativus L. produce saffron, a precious spice used for its culinary and medicinal properties since ancient times, while its petals are considered the main by-product of saffron production. The present study aimed to comparatively evaluate the phenolic content, antioxidant capacity, and antibacterial activity of methanolic extracts of stigmas and petals of Crocus sativus L. from Taliouine. The polyphenol content was measured using the Folin–Ciocalteu method, the antioxidant activity was determined using the DPPH free radical scavenging method, and the well-diffusion method was used to assess antibacterial activity against seven pathogenic bacterial strains (Bacillus subtilis, Escherichia coli, Listeria monocytogenes, Proteus vulgaris, Pseudomonas aeruginosa, Salmonella enterica, and Staphylococcus aureus). Furthermore, the minimum inhibitory concentration (MIC) of the extracts was determined using the microdilution broth test. Our findings revealed that stigmas and petals contained phenolic compounds at the rate of 56.11 ± 4.70 and 64.73 ± 3.42 mg GAE/g, as well as DPPH radical scavenging capacity with IC50 of 1700 µg/ml and 430 µg/ml, respectively. Petal extract showed more effective antibacterial activity, with inhibition diameters ranging from 10.66 ± 0.57 to 22.00 ± 1.00 mm and MIC values ranging from 2.81 to 5.62 mg/ml, compared to the stigma extract, which displayed inhibition diameters from 10.00 ± 0.00 to 18.67 ± 0.76 mm and MIC from 2.81 to 11.25 mg/ml, against five of the seven bacterial strains tested, including S. aureus, E. coli, P. vulgaris, P. aeruginosa, and S. enterica. Statistical analyses were performed to determine the significance of these results. Thus, stigmas and petals of Crocus sativus L. might serve as a suitable source of natural antioxidant and antimicrobial agents for application in the food and pharmaceutical industries.
Formaldehyde‐Degrading Bacteria R1 Is Effective in Removing HCHO from the Air in an Indoor Environment
Authors: Wang Ru , Wang Wenyuan , Zhang Wei , Li Zhengxue , An Zhengyang , Zhou Dongming , Min Yong
Published: May 2024

Formaldehyde (HCHO) is a widespread air pollutant in the indoor environment. Previous studies have shown that some bacteria have potential application to remove indoor HCHO. The purpose of this study is to evaluate the effectiveness of Methylobacterium sp. strain R1 (S‐R1) in removing formaldehyde (HCHO) from indoor air using biofilters. Three experiments confirmed S‐R1’s ability to degrade HCHO in the air, with 13C‐NMR analysis revealing its involvement in the metabolic process. Optimal biofilter parameters, including 35 sponge layers, 30% humidity, and 9.50 m3/min air flow, resulted in a removal efficiency of up to 90% and an elimination capability of 24111‐27000 μg/(m3∗h) during a 60‐minute test period. Long‐term (31‐day) operation of the biofilter with the optimal parameters effectively reduced HCHO levels from 1.60 mg/m3 to 0.02‐0.03 mg/m3, below China’s national standard, and maintained this level. Fluorescence microscope observation and downstream gas detection revealed stable S‐R1 cell numbers and no bacterial leakage, respectively. Two conclusions can be drawn: (1) S‐R1 is effective in removing HCHO in polluted air and (2) with optimum parameters, the S‐R1 biofilter is engineering effective in purifying the indoor air environment.
Targeting Super-Enhancer–Driven Transcriptional Dependencies Suppresses Aberrant Hedgehog Pathway Activation and Overcomes Smoothened Inhibitor Resistance
Authors: Sui Yi , Wang Teng , Mei Yanqing , Zhu Ying , Jiang Wenyan , Shen Jiayi , Yan Siyuan , Lu Wenjie , Zhao Kewen , Mo Jialin , Wang Chaochen , Tang Yujie
Published: May 2024

Aberrant activation of the Hedgehog (Hh) signaling pathway plays important roles in oncogenesis and therapeutic resistance in several types of cancer. The clinical application of FDA-approved Hh-targeted smoothened inhibitors (SMOi) is hindered by the emergence of primary or acquired drug resistance. Epigenetic and transcriptional-targeted therapies represent a promising direction for developing improved anti-Hh therapies. In this study, we integrated epigenetic/transcriptional-targeted small-molecule library screening with CRISPR/Cas9 knockout library screening and identified CDK9 and CDK12, two transcription elongation regulators, as therapeutic targets for antagonizing aberrant Hh activation and overcoming SMOi resistance. Inhibition of CDK9 or CDK12 potently suppressed Hh signaling and tumor growth in various SMOi responsive or resistant Hh-driven tumor models. Systemic epigenomic profiling elucidated the Hh-driven super-enhancer (SE) landscape and identified IRS1, encoding a critical component and cytoplasmic adaptor protein of the insulin-like growth factor (IGF) pathway, as an oncogenic Hh-driven SE target gene and effective therapeutic target in Hh-driven tumor models. Collectively, this study identifies SE-driven transcriptional dependencies that represent promising therapeutic vulnerabilities for suppressing the Hh pathway and overcoming SMOi resistance. As CDK9 and IRS inhibitors have already entered human clinical trials for cancer treatment, these findings provide comprehensive preclinical support for developing trials for Hh-driven cancers.

Significance: Dissecting transcriptional dependencies driven by super-enhancers uncovers therapeutic targets in Hedgehog-driven cancers and identifies strategies for overcoming resistance to smoothened inhibitors.
Figure S5 from Novel Spirocyclic Dimer, SpiD3, Targets Chronic Lymphocytic Leukemia Survival Pathways with Potent Preclinical Effects
Authors: Eiken Alexandria P. , Smith Audrey L. , Skupa Sydney A. , Schmitz Elizabeth , Rana Sandeep , Singh Sarbjit , Kumar Siddhartha , Mallareddy Jayapal Reddy , de Cubas Aguirre A , Krishna Akshay , Kalluchi Achyuth , Rowley M. Jordan , D'Angelo Christopher R. , Lunning Matthew A. , Bociek R. Gregory , Vose Julie M. , Natarajan Amarnath , El-Gamal Dalia
Published: May 2024

Figure S5 shows SpiD3 inhibits cap-dependent protein translation in CLL cells.
Figure S4 from Novel Spirocyclic Dimer, SpiD3, Targets Chronic Lymphocytic Leukemia Survival Pathways with Potent Preclinical Effects
Authors: Eiken Alexandria P. , Smith Audrey L. , Skupa Sydney A. , Schmitz Elizabeth , Rana Sandeep , Singh Sarbjit , Kumar Siddhartha , Mallareddy Jayapal Reddy , de Cubas Aguirre A , Krishna Akshay , Kalluchi Achyuth , Rowley M. Jordan , D'Angelo Christopher R. , Lunning Matthew A. , Bociek R. Gregory , Vose Julie M. , Natarajan Amarnath , El-Gamal Dalia
Published: May 2024

Figure S4 shows SpiD3 inhibits CLL chemotaxis and induces transcription of UPR genes.
Figure S3 from Novel Spirocyclic Dimer, SpiD3, Targets Chronic Lymphocytic Leukemia Survival Pathways with Potent Preclinical Effects
Authors: Eiken Alexandria P. , Smith Audrey L. , Skupa Sydney A. , Schmitz Elizabeth , Rana Sandeep , Singh Sarbjit , Kumar Siddhartha , Mallareddy Jayapal Reddy , de Cubas Aguirre A , Krishna Akshay , Kalluchi Achyuth , Rowley M. Jordan , D'Angelo Christopher R. , Lunning Matthew A. , Bociek R. Gregory , Vose Julie M. , Natarajan Amarnath , El-Gamal Dalia
Published: May 2024

Figure S3 shows proteomic analysis of SpiD3-treated CLL cells using TMT-labeling.
FIGURE 5 from Novel Spirocyclic Dimer, SpiD3, Targets Chronic Lymphocytic Leukemia Survival Pathways with Potent Preclinical Effects
Authors: Eiken Alexandria P. , Smith Audrey L. , Skupa Sydney A. , Schmitz Elizabeth , Rana Sandeep , Singh Sarbjit , Kumar Siddhartha , Mallareddy Jayapal Reddy , de Cubas Aguirre A , Krishna Akshay , Kalluchi Achyuth , Rowley M. Jordan , D'Angelo Christopher R. , Lunning Matthew A. , Bociek R. Gregory , Vose Julie M. , Natarajan Amarnath , El-Gamal Dalia
Published: May 2024

SpiD3 synergizes with ibrutinib and elicits cytotoxic effects in ibrutinib-resistant CLL cells. A–D, Combination assays to test synergy between SpiD3 and ibrutinib (IBR; BTK inhibitor) in preclinical CLL models. HG-3 cells (A–B; n = 3 independent experiments) or CpG ODN 2006 (CpG; 3.2 µmol/L)-stimulated patient-derived CLL cells (C–D; n = 6) were treated with SpiD3, IBR, or both (1:1 ratio) for 72 hours. MTS assay was performed to detect the dose effect. A and C, Dose-effect of the single drugs and their combination (1:1 ratio). B and D, CI of the combined doses (0.5 µmol/L SpiD3 + 0.5 µmol/L IBR = 1 µmol/L on graph). CI values were calculated using the Chou-Talalay method by the software Compusyn. CI values >1 are antagonistic, CI values = 1 are additive, and CI values <1 are synergistic. E, Mitochondrial activity in parental wild-type (WT) and ibrutinib-resistant (IR) HG-3 cell lines were assessed by MTS assay following treatment with increasing concentrations of SpiD3 or IBR (72 hours; n = 6 independent experiments/cell line). IC50 values (mean ± SEM) are noted for each cell line. F and G, Representative immunoblot analyses of p-BTK (Tyr223), total BTK, p-PRAS (Thr246), total PRAS, p-ERK1/2 (Thr202/Tyr204), total ERK1/2, MYC, PARP (total and cleaved), IKKα, IKKβ, p65, and RELB in WT- and IR-HG3 cells treated with SpiD3 (1–2 µmol/L) or IBR (1 µmol/L) for 4 hours. BCR activation was induced by adding soluble α-IgM (10 µg/mL) for the last 15 minutes of treatment (n = 5 independent experiments). GAPDH served as the loading control. H, Spleen-derived malignant B cells from terminally diseased Eµ-Myc/TCL1 mice (n = 8) were stimulated ex vivo with 1X PMA/Ionomycin and treated with SpiD3 (0.25–2 µmol/L), IBR (1 µmol/L), or JQ-1 (1 µmol/L) for 48 hours. Proliferation was assessed via MTS assay and normalized to the unstimulated vehicle (dashed line). Asterisks indicate significance versus stimulated vehicle. *, P < 0.05; **, P < 0.01; ***, P < 0.001.
FIGURE 3 from Novel Spirocyclic Dimer, SpiD3, Targets Chronic Lymphocytic Leukemia Survival Pathways with Potent Preclinical Effects
Authors: Eiken Alexandria P. , Smith Audrey L. , Skupa Sydney A. , Schmitz Elizabeth , Rana Sandeep , Singh Sarbjit , Kumar Siddhartha , Mallareddy Jayapal Reddy , de Cubas Aguirre A , Krishna Akshay , Kalluchi Achyuth , Rowley M. Jordan , D'Angelo Christopher R. , Lunning Matthew A. , Bociek R. Gregory , Vose Julie M. , Natarajan Amarnath , El-Gamal Dalia
Published: May 2024

SpiD3 induces the unfolded protein response and modulates CLL survival factors independent of TME stimuli. A, HG-3 and OSU-CLL cells were treated for 4 hours with SpiD3 (5, 10 µmol/L), thapsigargin (Thaps; 10 µmol/L), or equivalent DMSO vehicle (VEH) and then incubated with TPE-NMI dye to probe for unfolded proteins. Data are represented as fold change in TPE-NMI MFI compared with VEH (n = 3–5 independent experiments/cell line). B, Representative immunoblot analyses of IRE1α, XBP1, PERK, ATF4, CHOP, p-eIF2α (Ser51), and total eIF2α in HG-3 and OSU-CLL cells treated with VEH, SpiD3 (0.5–2 µmol/L), or Thaps (2 µmol/L) for 4 hours (n = 4–5 independent experiments/cell line). β-ACTIN served as the loading control. Blue arrow: spliced XBP1, green arrow: PERK shift. C, HG-3 cells were treated with VEH (24 hours), SpiD3 (0.5–2 µmol/L; 24 hours), or cycloheximide (CHX; 50 µg/mL; 30 minutes) and then incubated with OPP for 30 minutes. Data are represented as fold change in OPP MFI compared with VEH (n = 3–4 independent experiments). D, Representative immunoblot analyses of PDCD4, eIF4A1, p-4E-BP1 (Ser65), total 4E-BP1, eIF4E, and eIF4G1 levels in HG-3 and OSU-CLL cells treated with VEH or SpiD3 (0.5–2 µmol/L) for 4 hours (n = 4 independent experiments/cell line). β-ACTIN served as the loading control. Black arrows indicate the three isoforms of 4E-BP1. E, OSU-CLL cells were incubated with the alkyne-tagged analog 19 (10 µmol/L) for 2 hours. Cell lysates were clicked with TAMRA-biotin and biotin-tagged-19-bound proteins were isolated using streptavidin agarose beads, trypsinized, and then evaluated via mass spectrometry. Top: Pathway enrichment (EnrichR) analysis of similar proteins found in at least two of the three biological replicates. Bottom: Representative immunoblot analysis of biotin-alkyne-tagged proteins, with their corresponding input lysates for IKKα, IKKβ, p65, RELB, BTK, and GAPDH. The blue arrow indicates IKKα and IKKβ. Immunoblot analysis of the indicated proteins in whole-cell lysates of HG-3 and OSU-CLL cells treated with SpiD3 (1, 2 µmol/L) for 4 hours and cocurrently stimulated with α-IgM (10 µg/mL; F) or rhBAFF ligand (50 ng/mL; G). α-TUBULIN served as the loading control (n = 4 independent experiments/cell line). Asterisks denote significance versus VEH: *, P < 0.05; **, P < 0.01; ***, P < 0.001.
Carolina Maria de Jesus vive em nós: Reflexos e reflexões dos 10 anos de cotas da Unilab, Ceará
Authors: Silva Ana Maria Eugenia da , Silva Geyse Anne Souza da , Moreira Dayane da Silva
Published: May 2024

O trabalho traz contribuições e reflexões acerca dos dez anos de cotas e seus múltiplos desdobramentos na Universidade da Integração Internacional da Lusofonia Afro-Brasileira. Tais diálogos ocorrem a partir das produções (filme, poesias, artigos e roda de conversa) das autoras influenciadas por Carolina Maria de Jesus e seu modo de utilizar a escrita como forma de denunciar as diversas fomes a qual foi submetida. Os debates sobre a importância das cotas, desdobramentos, desafios e perspectivas no ensino superior são pautas latentes no dia a dia dos estudantes unilabianos, em particular, no cotidiano das autoras que atuam em diversas frentes como: Movimento Negro, Movimento Quilombola e nos grupos de estudo e pesquisas ao qual estão  inseridas. Assim, nós, Carolinas, também utilizamos as nossas escritas-denúncias como forma de luta e resistência para enfrentar e combater as desigualdades, alimentadas pelo modo operante do epistemicídio em nossas vidas.
Perceptual Adaptation to Noise-Vocoded Speech by Lip-Read Information: No Difference between Dyslexic and Typical Readers
Authors: Pourhashemi Faezeh , Baart Martijn , Vroomen Jean
Published: May 2024

Auditory speech can be difficult to understand but seeing the articulatory movements of a speaker can drastically improve spoken-word recognition and, on the longer-term, it helps listeners to adapt to acoustically distorted speech. Given that individuals with developmental dyslexia (DD) have sometimes been reported to rely less on lip-read speech than typical readers, we examined lip-read-driven adaptation to distorted speech in a group of adults with DD () and a comparison group of typical readers (). Participants were presented with acoustically distorted Dutch words (six-channel noise-vocoded speech, NVS) in audiovisual training blocks (where the speaker could be seen) interspersed with audio-only test blocks. Results showed that words were more accurately recognized if the speaker could be seen (a lip-read advantage), and that performance steadily improved across subsequent auditory-only test blocks (adaptation). There were no group differences, suggesting that perceptual adaptation to disrupted spoken words is comparable for dyslexic and typical readers. These data open up a research avenue to investigate the degree to which lip-read-driven speech adaptation generalizes across different types of auditory degradation, and across dyslexic readers with decoding versus comprehension difficulties.
Female Gazes in the Communist Movement: Women Photographers in the Interwar Period and World War ii
Authors: Strippoli Giulia
Published: May 2024

Women participated in communist movements and contributed to communist culture. At the intersection of women’s history, visual arts, gender studies, history of socialism, and the history of communism, this article focuses on six women photographers—Tina Modotti, Elizaveta Mikulina, Gisèle Freund, Lisette Model, Julia Pirotte, and Gerda Taro—analysing the circulation of their works in the communist press and in circles sympathetic with the communist cause. The research on women photographers’ gazes contributes to a deeper understanding of both the lager networks of communist movement and the multifaceted aesthetics of communist culture. By crossing women’s lives and works, their subjectivity and political paths, the documental and artistic legacy of the images they have produced, the article demonstrates why and how women photographers’ production intersects communist culture during the Comintern and World War ii.
Stemphylium persianum sp. nov., (Pleosporales, Ascomycota) from Iran
Authors: AHMADPOUR ABDOLLAH , GHOSTA YOUBERT , ALAVI FATEMEH , ALAVI ZAHRA , C. KARUNARATHNA SAMANTHA , TIBPROMMA SAOWALUCK
Published: May 2024

Stemphylium species are saprophytes, or plant pathogens mostly associated with economically important crops. In this study, we isolated Stemphylium strains from grey to brown lesions on the culms of Schoenoplectus sp. (Cyperaceae, Poales). Based on combined morphological characteristics and sequence data of the internal transcribed spacer (ITS‒rDNA) region, parts of glyceraldehyde-3-phosphate dehydrogenase (gapdh) and calmodulin (cmdA) genes, the studied Stemphylium strains were identified and described herein as a new species, S. persianum. The new species is phylogenetically closely related to S. halophilum and S. lycii, however, they are distinguishable based on conidiophores, conidia, and ascospores morphology. Detailed morphological descriptions, illustrations, and phylogenetic relationships with other Stemphylium species are provided herein.
Revision of Nearctic Eparces (Hymenoptera: Ichneumonidae: Ichneumoninae): description Eparces australis Claridge & Dal Pos sp. nov., nomenclatural notes, and new records of Eparces quadriceps (Cresson, 1867)
Authors: CLARIDGE BRANDON , POS DAVIDE DAL
Published: May 2024

The Nearctic species of the parasitoid wasp genus Eparces are revised. A new species, Eparces australis Claridge & Dal Pos sp. nov., is described from the southeastern USA. Additionally, nomenclatural comments on the other Nearctic species, Eparces quadriceps (Cresson, 1867) are provided, along with new records for the species from various states in the USA.
Limitations and consequences of public health models centred on hospitals and lacking connections with territorial and home-based social and health services
Authors: Gentile Lavinia , Scaramella Martina , Liotta Giuseppe , Magrini Andrea , Mulas Maria Franca , Quintavalle Giuseppe , Palombi Leonardo
Published: May 2024

Background

Delayed discharge from hospital to home or other care institutions is a significant problem and has been investigated in the international scientific literature for many years.

Behind this condition is a health care system based on a hospital-centered concept characterized by a lack of territorial health and social welfare services.

This phenomenon causes two different problems: an excessive length of hospital stay, resulting in slow turnover of bed utilization; and overcrowding in emergency rooms (ERs).

The phenomenon of frequent users assumes particular importance in this context. These patients repeatedly visit the emergency department (ED) in the same year because care needs are not met by primary care services.

The authors in this study tried to describe the Frequent users (FUs) population and the variables associated with this condition.

Materials and methods

A retrospective "single-arm" descriptive study was conducted by analysing all accesses made to the ED of Policlinico Tor Vergata (PTV) from January 1, 2022, to December 31, 2022.

FUs were defined as patients who had 4 or more accesses to PTV ER during the year.

Results

A total of 37,800 accesses occurred during the study period. A total of 31,691 users accessed the PS, with a mean age of 55.8 ± 22.2 years.

There were 359 FU patients (approximately 1%) who had a total of 1984 accesses, corresponding to 5.2% of the total accesses.

The triage codes for the FU patients were red, 2%; orange, 21%; blue, 45%; green, 26%; white, 5%; and not performed, 1%.

Considering the 1984 FU accesses, the most frequently attributed "main problems" in the ED were "other symptoms or disorders" (54%), "psychomotor agitation" (12%), "trauma or burn" (8%), "abdominal pain" (6%), "chest pain" (4%), "dyspnea" (4%) and "urological symptoms or disorders" (4%). Multivariate analysis revealed that the main determinants of FUs were psychomotor agitation (HR = 7,23; CL95%:6,194–8,443), urological disorders (HR = 2,16; CL95%:1,68–2,76) and poor socioeconomic status (HR = 2,40; CL95%:2,213–2,663).

Conclusions

The FUs phenomenon expresses an area of health and social distress where poverty and lack of territorial services oblige people to refer to the ED. Primary care interventions integrated with social support are crucial for managing access to the ED.
Spatiotemporal snowline status and climate variability impact assessment: a case study of Pindari River Basin, Kumaun Himalaya, India
Authors: Pandey Arvind , Parashar Deepanshu , Palni Sarita , Sarkar Mriganka Shekhar , Mishra Arun Pratap , Singh Ajit Pratap , Costache Romulus , Abdulqadim Tuhami Jamil , Pande Chaitanya Baliram , Tolche Abebe Debele , Khan Mohd Yawar Ali
Published: May 2024

The snowline exhibits significant seasonal shifts upward and downward, reflecting the ever-changing dynamics of the seasons and being influenced by climate variations, which can vary annually. These fluctuations profoundly impact the cryosphere, biota, and ecosystem processes in high mountain regions. Despite the critical role of snowline variations, comprehensive information on how actual climate variability affects snow cover trends in the central mountain range of the western Himalayas is scarce. In the 'Pindari' region of the Uttarakhand district, India, which is part of the Himalayas, these challenges are exacerbated by the unchecked growth of anthropogenic activities and the broader impacts of climate change. This study analyses snowline variations in the Pindari glacial region from 1972 to 2018. The findings revealed that the snowline elevation significantly shifted upward between 1972 and 2018. Notably, this research revealed a decrease in snow-covered areas of approximately 5.01 km2 over the course of 46 years. This decrease is attributed to a direct response to the increasing number of high-temperature events that occurred during this extended period. This study emphasizes the urgent need for conservation measures in the study region and similar high mountains to combat global warming and safeguard the snowline, which serves as a visible proxy indicator to safeguard high-altitude Himalayan glaciers.
Transcriptome analysis of sexual dimorphism in dorsal down coloration in goslings
Authors: Liu Yi , Li Guangquan , Guo Zhanbao , Zhang Huiling , Wei Baozhi , He Daqian
Published: May 2024

Background

In day-old Hungarian white goose goslings, there is a noticeable difference in dorsal down coloration between males and females, with females having darker dorsal plumage and males having lighter plumage. The ability to autosex day-old goslings based on their dorsal down coloration is important for managing them efficiently and planning their nutrition in the poultry industry. The aim of this study was to determine the biological and genetic factors underlying this difference in dorsal down colorationthrough histological analysis, biochemical assays, transcriptomic profiling, and q‒PCR analysis.

Results

Tissue analysis and biochemical assays revealed that compared with males, 17-day-old embryos and day-old goslings of female geese exhibited a greater density of melanin-containing feather follicles and a greater melanin concentration in these follicles during development. Both female and male goslings had lower melanin concentrations in their dorsal skin compared to 17-day-old embryos. Transcriptome analysis identified a set of differentially expressed genes (DEGs) (MC1R, TYR, TYRP1, DCT and MITF) associated with melanogenesis pathways that were downregulated or silenced specifically in the dorsal skin of day-old goslings compared to 17-day-old embryos, affecting melanin synthesis in feather follicles. Additionally, two key genes (MC1R and MITF) associated with feather coloration showed differences between males and females, with females having higher expression levels correlated with increased melanin synthesis and darker plumage.

Conclusion

The expression of multiple melanogenesis genes determines melanin synthesis in goose feather follicles. The dorsal down coloration of day-old Hungarian white goose goslings shows sexual dimorphism, likely due to differences in the expression of the MC1R and MITF genes between males and females. These results could help us better understand why male and female goslings exhibit different plumage patterns.
Potential involvement of beta-lactamase homologous proteins in resistance to beta-lactam antibiotics in gram-negative bacteria of the ESKAPEE group
Authors: de Souza Joyce , Vieira Alexandre Zanatta , dos Santos Hellen Geremias , Faoro Helisson
Published: May 2024

Background

Enzymatic degradation mediated by beta-lactamases constitutes one of the primary mechanisms of resistance to beta-lactam antibiotics in gram-negative bacteria. This enzyme family comprises four molecular classes, categorized into serine beta-lactamases (Classes A, C, and D) and zinc-dependent metallo-beta-lactamases (Class B). Gram-negative bacteria producing beta-lactamase are of significant concern, particularly due to their prevalence in nosocomial infections. A comprehensive understanding of the evolution and dissemination of this enzyme family is essential for effective control of these pathogens.

In this study, we conducted the prospecting, phylogenetic analysis, and in silico analysis of beta-lactamases and homologous proteins identified in 1827 bacterial genomes with phenotypic data on beta-lactam resistance. These genomes were distributed among Klebsiella pneumoniae (45%), Acinetobacter baumannii (31%), Pseudomonas aeruginosa (14%), Escherichia coli (6%), and Enterobacter spp. (4%). Using an HMM profile and searching for conserved domains, we mined 2514, 8733, 5424, and 2957 proteins for molecular classes A, B, C, and D, respectively. This set of proteins encompasses canonical subfamilies of beta-lactamases as well as hypothetical proteins and other functional groups. Canonical beta-lactamases were found to be phylogenetically distant from hypothetical proteins, which, in turn, are closer to other representatives of the penicillin-binding-protein (PBP-like) and metallo-beta-lactamase (MBL) families. The catalytic amino acid residues characteristic of beta-lactamases were identified from the sequence alignment and revealed that motifs are less conserved in homologous groups than in beta-lactamases. After comparing the frequency of protein groups in genomes of resistant strains with those of sensitive ones applying Fisher’s exact test and relative risk, it was observed that some groups of homologous proteins to classes B and C are more common in the genomes of resistant strains, particularly to carbapenems.

We identified the beta-lactamase-like domain widely distributed in gram-negative species of the ESKAPEE group, which highlights its importance in the context of beta-lactam resistance. Some hypothetical homologous proteins have been shown to potentially possess promiscuous activity against beta-lactam antibiotics, however, they do not appear to expressly determine the resistance phenotype. The selective pressure due to the widespread use of antibiotics may favor the optimization of these functions for specialized resistance enzymes.
Genome-wide characterization and expression profiling of E2F/DP gene family members in response to abiotic stress in tomato (Solanum lycopersicum L.)
Authors: Divya Dhanasekar , Robin Arif Hasan Khan , Cho Lae-Hyeon , Kim Dohyeon , Lee Do-jin , Kim Chang-Kil , Chung Mi-Young
Published: May 2024

Background

E2F/DP (Eukaryotic 2 transcription factor/dimerization partner) family proteins play an essential function in the cell cycle development of higher organisms. E2F/DP family genes have been reported only in a few plant species. However, comprehensive genome-wide characterization analysis of the E2F/DP gene family of Solanum lycopersicum has not been reported so far.

Results

This study identified eight nonredundant SlE2F/DP genes that were classified into seven groups in the phylogenetic analysis. All eight genes had a single E2F-TDP domain and few genes had additional domains. Two segmental duplication gene pairs were observed within tomato, in addition to cis-regulatory elements, miRNA target sites and phosphorylation sites which play an important role in plant development and stress response in tomato. To explore the three-dimensional (3D) models and gene ontology (GO) annotations of SlE2F/DP proteins, we pointed to their putative transporter activity and their interaction with several putative ligands. The localization of SlE2F/DP-GFP fused proteins in the nucleus and endoplasmic reticulum suggested that they may act in other biological functions. Expression studies revealed the differential expression pattern of most of the SlE2F/DP genes in various organs. Moreover, the expression of E2F/DP genes against abiotic stress, particularly SlE2F/DP2 and/or SlE2F/DP7, was upregulated in response to heat, salt, cold and ABA treatment. Furthermore, the co-expression analysis of SlE2F/DP genes with multiple metabolic pathways was co-expressed with defence genes, transcription factors and so on, suggested their crucial role in various biological processes.

Conclusions

Overall, our findings provide a way to understand the structure and function of SlE2F/DP genes; it might be helpful to improve fruit development and tolerance against abiotic stress through marker-assisted selection or transgenic approaches.
Transcriptional changes during crown-root development and emergence in barley (Hordeum vulgare L.)
Authors: Nguyen Dieu Thu , Zavadil Kokáš Filip , Gonin Mathieu , Lavarenne Jérémy , Colin Myriam , Gantet Pascal , Bergougnoux Véronique
Published: May 2024

Background

Roots play an important role during plant growth and development, ensuring water and nutrient uptake. Understanding the mechanisms regulating their initiation and development opens doors towards root system architecture engineering.

Results

Here, we investigated by RNA-seq analysis the changes in gene expression in the barley stem base of 1 day-after-germination (DAG) and 10DAG seedlings when crown roots are formed. We identified 2,333 genes whose expression was lower in the stem base of 10DAG seedlings compared to 1DAG seedlings. Those genes were mostly related to basal cellular activity such as cell cycle organization, protein biosynthesis, chromatin organization, cytoskeleton organization or nucleotide metabolism. In opposite, 2,932 genes showed up-regulation in the stem base of 10DAG seedlings compared to 1DAG seedlings, and their function was related to phytohormone action, solute transport, redox homeostasis, protein modification, secondary metabolism. Our results highlighted genes that are likely involved in the different steps of crown root formation from initiation to primordia differentiation and emergence, and revealed the activation of different hormonal pathways during this process.

Conclusions

This whole transcriptomic study is the first study aiming at understanding the molecular mechanisms controlling crown root development in barley. The results shed light on crown root emergence that is likely associated with a strong cell wall modification, death of the cells covering the crown root primordium, and the production of defense molecules that might prevent pathogen infection at the site of root emergence.