bluuebunny/crossref_metadata_2025 huggingface dataset:
Mechanical Responses of 316L Stainless Steel Printed by Wire Arc Additive Manufacturing With Different Thermal Histories
Authors: Tang Wei , Giuliano Dominic , Martinez Oscar , Gussev Maxim , Nycz Andrzej , An Ke , Meyer Luke , Masuo Chris , Yu Dunji , Carter William , Walters Alex , Wallace Riley , Vaughan Derek
Published: November 2023

In this paper, 316L stainless steel walls were printed using single-bead pass and multiple-bead pass wire arc additive manufacturing (WAAM), which represent the internal basket wall and external wall of a spent nuclear fuel (SNF) canister, respectively. Scanning electron microscopy (SEM) microstructure characterization and tensile tests at room temperature (21 °C) and elevated temperature (250 °C, the maximum temperature at the center of a SNF canister.) were performed on specimens extracted along the length and height directions of the printed walls. Results showed that grain morphology, grain angles, and retained ferrite are different between the two printed walls, which received different heat input in WAAM. The single-bead pass printed wall exhibited higher yield strength than the multiple-bead pass printed wall because of more retained ferrite and larger portion of random-high angle boundaries (RHAB) grains.
Case Study on the Affect of Hydrogen on Ground Storage Tanks Designed to ASME Section VIII
Authors: Peters Daniel T. , Ritter Erick R.
Published: November 2023

The effect of hydrogen on the cyclic life of stainless-steel tanks is widely debated. Many ground storage tanks built for the hydrogen economy, and particularly for hydrogen fueling stations, are designed to ASME Section VIII, Division 3 [1] for pressures between 7,500 and 15,000 psi (517–1034 bar). ASME Section VIII, Division 3, Article KD-10 has rules for these hydrogen vessels regarding the assessment of life using fracture mechanics. This assessment leverages empirical testing for crack growth rate and determination of the threshold intensity factor for hydrogen assisted cracking. Additionally, Code Case 2938 [2], Hydrogen Crack Growth Rate Constants, Threshold Stress Intensity Factor, KIH, and Critical Crack Size Requirements for SA372 and SA-723 Steels in ASME Section VIII Division 3, has been developed.

While rules have been established for the ASME Section VIII, Division 3 design, there is controversy regarding what impact hydrogen has on pressure vessels designed to either ASME Section VIII, Division 2 [3] or ASME Section VIII, Division 1 [4]. This paper is a case study to provide a comparison of the life assessment of various vessels in hydrogen and dry air. This study will attempt to provide background in the discussion for the magnitude of impact that hydrogen has on the life of vessels operated at various pressure ratings when designed to each of the three (3) ASME Section VIII Divisions.
Effect of Pitch Spacing on Fluidelastic Forces in a Rotated Triangular Array
Authors: Darwish Sameh , Mureithi Njuki , Cho Minki
Published: November 2023

Time-averaged quasi-static forces are significant in the study of the fluidelastic instability of tube arrays. Furthermore, measuring the fluid force phase from the unsteady force measurements could be used to directly investigate the dynamic behaviour of an array and predict the array instability onset. Force measurements were previously performed for a rotated triangular array with spacing ratio P/D = 1.5. In this paper, a more compact rotated triangular array is studied following the same measurement approach. This rotated triangular array has a pitch ratio P/D = 1.33. Determining the relationship between the fluid force coefficients used in the quasi-steady model, and fluid force phase used to predict the fluid damping, is one of the main objectives of this work. This is in order to relate the fluid forces to the array pitch spacing. This should be a step toward generalizing the quasi-steady model for the rotated triangular array for various pitch ratios. In this paper, the quasi-static fluid forces are measured in single phase (water) and two-phase (air-water) cross flow in the streamwise direction. The quasi-steady model is then solved, using the forces, to predict the fluidelastic instability onset of the array. Model results are also directly compared with vibration experimental results.
Corrosion Assessment Models for Predicting Remaining Strength of Corroded Thick-Walled Pipelines
Authors: Zhu Xian-Kui , Wiersma Bruce , Johnson William R. , Sindelar Robert
Published: November 2023

Corrosion is a major threat to pipeline integrity. Over the past half century, many corrosion assessment models have been developed for determining the remaining strength of corroded pipelines, including the traditional industry codes of ASME B31.G, Modified B31.G and PRCI RSTRENG, and numerous newer corrosion criteria of LPC, PCORRC and their modified models. However, all available corrosion assessment models are applicable to large diameter, thin-walled line pipes with a diameter to wall thickness ratio D/t ≥ 20. In practice, there are many small-diameter, thick-walled pipelines with a D/t ratio < 20, and thus an adequate corrosion assessment model is needed for predicting remaining strength for corroded thick-walled pipelines.

This paper first reviews the burst pressure models for defect-free thin and thick-walled pipelines and a variety of corrosion assessment models for thin-walled pipelines. On this basis, three corrosion assessment models are developed for thick-walled pipelines in terms of the average shear stress yielding theory. A large set of burst pressure test data is employed to evaluate and validate the proposed corrosion assessment models for thick-walled pipelines in a wide range of pipeline steel grades. The comparison shows that the proposed thick-wall corrosion models can more accurately predict the remaining strength for both thin and thick-walled pipelines with corrosion defects.
Applicability Analysis of Thermoplastic Material As Liner Pipe for Trenchless Rehabilitation of Thermal Pipelines
Authors: Wang Zhongzhen , Shi Jianfeng , Zhang Liang
Published: November 2023

Thermal pipelines are an essential part between the heat source and the user. Thermal pipeline failure frequently occurs with expanding the systems’ scale and increasing elapsed service life. These faulty and damaged pipelines need to be repaired and replaced in time. Trenchless rehabilitation technology has the advantages of high construction efficiency and a small impact on traffic and the environment, so it is the current research focus of pipeline rehabilitation technology. The liner pipe made of thermoplastic materials such as Polyethylene (PE) has been used in drainage, oil, and other fields, and the relevant standards are gradually forming. Nevertheless, for the thermal pipeline, the transmission medium is hot water or hot steam, usually temperature above 80°C. The operating temperature is higher than the operating temperature of conventional thermoplastic pipes.

Therefore, in this paper the typical thermodynamic properties of 8 engineering plastics were tested, such as PE, Polyamide (PA), and Polyformaldehyde (POM). Combined with the test results and the operational characteristics of the thermal pipeline, the applicability of 8 kinds of engineering plastics as the lining materials of the thermal pipeline was analyzed. The analysis results can provide a reference for determining the operating temperature of the engineering plastics. This article preliminarily determined that Polyethylene of raised temperature resistance (PE-RT) is suitable as the material of the 80 °C thermal liner pipe.
Research on the Influence of the Liner Crack Size and Location on Fatigue Life of 70MPa Type III Cylinder
Authors: Wang Yulin , Li Qinan , Ha Wenlong , Zhao Yiming , Hua Zhengli , Wei Liqing , Gu Chaohua
Published: November 2023

At present, the researches on the factors affecting the fatigue life of type III hydrogen storage cylinder mainly focus on the structure and technological parameters of the cylinder, and there are few studies on the type III cylinder with initial liner cracks. In this paper, a finite element model of fatigue analysis for 70MPa Type III cylinder based on fracture mechanics method was established. The influences of the depth, length, and position of the axial semi-elliptical initial liner crack on the fatigue life of the cylinder were discussed, and the tolerance size of inner surface crack was calculated. The results show that the cylinder fatigue life increased significantly with the decrease of the crack size. The fatigue life of the cylinder is more sensitive to the change of crack depth than the change of crack length. According to GB/T 35544, the fatigue life requirement of the cylinder studied in this paper is 7500 cycles of filling and releasing hydrogen. For the inner surface axial crack, when the crack depth-length ratio is 1/3, the maximum allowable crack depth is 0.167 mm; when the crack depth is 0.2 mm, the maximum allowable crack length is 0.443 mm. Furthermore, under the same initial crack size, the fatigue life of the cylinder with a crack on the outer surface is longer than that on the inner surface.
Design of Torispherical and Ellipsoidal Heads in Pressure Vessel and Review of Restrictions for the Onset of Buckling-Internal Pressure in ASME Sec.VIII Div.1: A Comparative Study of Various Codes of Construction
Authors: Pathre Sujay S. , Mathkar Ameya , Gopalakrishnan Shyam
Published: November 2023

Pressure Vessels are made with various types of end closures. Commonly used end closures are torispherical dished ends, ellipsoidal dished ends, and hemispherical dished ends. For the design of these end closures the rules provided in ASME Sec. VIII Div. 1 [1] and ASME Sec. VIII Div. 2[2] differ significantly, and a similar phenomenon could be observed when a review is done against popular International Codes for pressure vessel design like PD 5500 [3], and EN 13445[4]. The difference in the design methodology is due to the design approach used in developing the equations in these Codes of Construction.

ASME Sec. VIII Div.1 in Para. UG-32(c) and (d) for the design of all ellipsoidal heads and torispherical heads subject to internal pressure having ts/L ratio less than 0.002 directs the user to Para. 1-4 (f) of Mandatory Appendix 1 in code [1]. The requirements in Para. 1-4 (f) are added to prevent the possibility of buckling of the heads as the thickness is reduced as compared to the spherical radius. Buckling as a mode of failure is only envisaged when the ts/L ratio is less than 0.002 and no check on buckling is required when the ts/L ratio is greater or equal to 0.002.

If we refer to other Codes like ASME Sec. VIII Div.2, PD 5500 and EN 13445, one can observe that the design of the dished head is based on plastic collapse and buckling failure approach and these Codes make it mandatory to check both the plastic collapse and buckling failure modes in all the circumstances.

The work reported in this paper is an attempt to reviews the requirements of ASME Section VIII Division 1 for thin-walled dished heads with large internal diameter whose ratio of ts/L lie near the vicinity of 0.002 and comparative study of requirements imposed by ASME Section VIII Division 1 is compared with other International Codes.

Also, FEA of the dished ends is carried out to study the stress pattern and to determine the stresses induced, buckling. Further comparison is made against various Codes’ classical formula requirements.
What’s New in ASME PCC-1—2022?
Authors: Rodery Clay D.
Published: November 2023

The latest edition of ASME PCC-1 was released in September 2022. This edition represents a shift in the document as it transitions from a set of guidelines to a standard. Additionally, the document adopts a change in writing style in accordance with the ASME Style Guide, with an objective of providing better clarity in presenting the technical content of the document. This paper has several purposes. The first is to outline the process in how the document was rewritten, to whom was the document targeting, and to categorize the technical content into choices or selections that needed to be made, and instructions that were recommended for inclusion into the assembly procedure. The insights gained during the rewrite may prove to be insightful to others who are considering similar types of clarity rewrites of their standards. The second purpose of this paper is to identify and summarize the primary changes that appear in the 2022 edition of ASME PCC-1, for the benefit of those bolted joint practitioners who will be using the document. Finally, the paper will identify some elements that are in the course of preparation that may be issued before the next edition in the form of an early implementation Case.
“Learn to Function in the System”: The Organizational Socialization of Urban Physical Educators
Authors: Pennington Colin G. , Werber-Zion Galila , Prewitt-White Tanya
Published: November 2023

Purpose: The purpose of this study was to explore how urban physical educators’ experiences influence their motivations toward vocational persistence emphasizing health and fitness. Methods: Participants included 16 urban physical educators who participated in semistructured interviews about their experiences teaching in urban settings. For minority youths, who predominantly attend urban public schools, fitness rates are lower than the national average. Physical education has been discussed as a potential solution to combating this public health trend; however, considering Common Core reforms in public education by which health and physical education has been de-emphasized as a curricular requirement, scholars are pursuing knowledge of how the experiences of urban physical educators are evolving. Using occupational socialization as the operating theoretical framework, this study seeks to explore how 16 urban physical educators’ experiences are evolving with the changes in public education, including administrative support and other indicators of marginalization and attrition. Results: Qualitative data analysis resulted in the construction of six themes which suggest that teaching students to develop and maintain a healthy lifestyle remains a powerful motivator for urban physical educators’ persistence despite feelings of marginalization and burnout. Conclusions: The authors provide practical suggestions for practitioners and scholars to overcome feelings of marginalization and lack of resources.
Enhanced
TP53
reactivation disrupts
MYC
transcriptional program and overcomes venetoclax resistance in acute myeloid leukemias
Authors: Nishida Yuki , Ishizawa Jo , Ayoub Edward , Montoya Rafael Heinz , Ostermann Lauren B. , Muftuoglu Muharrem , Ruvolo Vivian R , Patsilevas Tallie , Scruggs Darah A. , Khazaei Shayaun , Mak Po Yee , Tao Wenjing , Carter Bing Z. , Boettcher Steffen , Ebert Benjamin L. , Daver Naval G. , Konopleva Marina , Seki Takahiko , Kojima Kensuke , Andreeff Michael
Published: November 2023

The tumor suppressor
TP53
is frequently inactivated in a mutation-independent manner in cancers and is reactivated by inhibiting its negative regulators. We here cotarget MDM2 and the nuclear exporter XPO1 to maximize transcriptional activity of p53. MDM2/XPO1 inhibition accumulated nuclear p53 and elicited a 25- to 60-fold increase of its transcriptional targets.
TP53
regulates
MYC
, and MDM2/XPO1 inhibition disrupted the c-MYC–regulated transcriptome, resulting in the synergistic induction of apoptosis in acute myeloid leukemia (AML). Unexpectedly, venetoclax-resistant AMLs express high levels of c-MYC and are vulnerable to MDM2/XPO1 inhibition in vivo. However, AML cells persisting after MDM2/XPO1 inhibition exhibit a quiescence- and stress response–associated phenotype. Venetoclax overcomes that resistance, as shown by single-cell mass cytometry. The triple inhibition of MDM2, XPO1, and BCL2 was highly effective against venetoclax-resistant AML in vivo. Our results propose a novel, highly translatable therapeutic approach leveraging p53 reactivation to overcome nongenetic, stress-adapted venetoclax resistance.
GTF2I
dosage regulates neuronal differentiation and social behavior in 7q11.23 neurodevelopmental disorders
Authors: López-Tobón Alejandro , Shyti Reinald , Villa Carlo Emanuele , Cheroni Cristina , Fuentes-Bravo Patricio , Trattaro Sebastiano , Caporale Nicolò , Troglio Flavia , Tenderini Erika , Mihailovich Marija , Skaros Adrianos , Gibson William T. , Cuomo Alessandro , Bonaldi Tiziana , Mercurio Ciro , Varasi Mario , Osborne Lucy , Testa Giuseppe
Published: November 2023

Copy number variations at 7q11.23 cause neurodevelopmental disorders with shared and opposite manifestations. Deletion causes Williams-Beuren syndrome featuring hypersociability, while duplication causes 7q11.23 microduplication syndrome (7Dup), frequently exhibiting autism spectrum disorder (ASD). Converging evidence indicates
GTF2I
as key mediator of the cognitive-behavioral phenotypes, yet its role in cortical development and behavioral hallmarks remains largely unknown. We integrated proteomic and transcriptomic profiling of patient-derived cortical organoids, including longitudinally at single-cell resolution, to dissect 7q11.23 dosage–dependent and
GTF2I
-specific disease mechanisms. We observed dosage-dependent impaired dynamics of neural progenitor proliferation, transcriptional imbalances, and highly specific alterations in neuronal output, leading to precocious excitatory neuron production in 7Dup, which was rescued by restoring physiological
GTF2I
levels. Transgenic mice with
Gtf2i
duplication recapitulated progenitor proliferation and neuronal differentiation defects alongside ASD-like behaviors. Consistently, inhibition of lysine demethylase 1 (LSD1), a
GTF2I
effector, was sufficient to rescue ASD-like phenotypes in transgenic mice, establishing
GTF2I
-LSD1 axis as a molecular pathway amenable to therapeutic intervention in ASD.
Exponential history integration with diverse temporal scales in retrosplenial cortex supports hyperbolic behavior
Authors: Danskin Bethanny P. , Hattori Ryoma , Zhang Yu E. , Babic Zeljana , Aoi Mikio , Komiyama Takaki
Published: November 2023

Animals use past experience to guide future choices. The integration of experiences typically follows a hyperbolic, rather than exponential, decay pattern with a heavy tail for distant history. Hyperbolic integration affords sensitivity to both recent environmental dynamics and long-term trends. However, it is unknown how the brain implements hyperbolic integration. We found that mouse behavior in a foraging task showed hyperbolic decay of past experience, but the activity of cortical neurons showed exponential decay. We resolved this apparent mismatch by observing that cortical neurons encode history information with heterogeneous exponential time constants that vary across neurons. A model combining these diverse timescales recreated the heavy-tailed, hyperbolic history integration observed in behavior. In particular, the time constants of retrosplenial cortex (RSC) neurons best matched the behavior, and optogenetic inactivation of RSC uniquely reduced behavioral history dependence. These results indicate that behavior-relevant history information is maintained across multiple timescales in parallel and that RSC is a critical reservoir of information guiding decision-making.
Octopus-inspired sensorized soft arm for environmental interaction
Authors: Xie Zhexin , Yuan Feiyang , Liu Jiaqi , Tian Lufeng , Chen Bohan , Fu Zhongqiang , Mao Sizhe , Jin Tongtong , Wang Yun , He Xia , Wang Gang , Mo Yanru , Ding Xilun , Zhang Yihui , Laschi Cecilia , Wen Li
Published: November 2023

Octopuses can whip their soft arms with a characteristic “bend propagation” motion to capture prey with sensitive suckers. This relatively simple strategy provides models for robotic grasping, controllable with a small number of inputs, and a highly deformable arm with sensing capabilities. Here, we implemented an electronics-integrated soft octopus arm (E-SOAM) capable of reaching, sensing, grasping, and interacting in a large domain. On the basis of the biological bend propagation of octopuses, E-SOAM uses a bending-elongation propagation model to move, reach, and grasp in a simple but efficient way. E-SOAM’s distal part plays the role of a gripper and can process bending, suction, and temperature sensory information under highly deformed working states by integrating a stretchable, liquid-metal–based electronic circuit that can withstand uniaxial stretching of 710% and biaxial stretching of 270% to autonomously perform tasks in a confined environment. By combining this sensorized distal part with a soft arm, the E-SOAM can perform a reaching-grasping-withdrawing motion across a range up to 1.5 times its original arm length, similar to the biological counterpart. Through a wearable finger glove that produces suction sensations, a human can use just one finger to remotely and interactively control the robot’s in-plane and out-of-plane reaching and grasping both in air and underwater. E-SOAM’s results not only contribute to our understanding of the function of the motion of an octopus arm but also provide design insights into creating stretchable electronics-integrated bioinspired autonomous systems that can interact with humans and their environments.
T cell responses to SARS-CoV-2 infection and vaccination are elevated in B cell deficiency and reduce risk of severe COVID-19
Authors: Zonozi Reza , Walters Lucy C. , Shulkin Aaron , Naranbhai Vivek , Nithagon Pravarut , Sauvage Gabriel , Kaeske Clarety , Cosgrove Katherine , Nathan Anusha , Tano-Menka Rhoda , Gayton Alton C. , Getz Matthew A. , Senjobe Fernando , Worrall Daniel , Iafrate A. John , Fromson Caroline , Montesi Sydney B. , Rao Deepak A. , Sparks Jeffrey A. , Wallace Zachary S. , Farmer Jocelyn R. , Walker Bruce D. , Charles Richelle C. , Laliberte Karen , Niles John L. , Gaiha Gaurav D.
Published: November 2023

Individuals with primary and pharmacologic B cell deficiencies have high rates of severe disease and mortality from coronavirus disease 2019 (COVID-19), but the immune responses and clinical outcomes after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and vaccination have yet to be fully defined. Here, we evaluate the cellular immune responses after both SARS-CoV-2 infection and vaccination in patients receiving the anti-CD20 therapy rituximab (RTX) and those with low B cell counts due to common variable immune deficiency (CVID) disease. Assessment of effector and memory CD4
+
and CD8
+
T cell responses to SARS-CoV-2 revealed elevated reactivity and proliferative capacity after both infection and vaccination in B cell–deficient individuals, particularly within the CD8
+
T cell compartment, in comparison with healthy controls. Evaluation of clinical outcomes demonstrates that vaccination of RTX-treated individuals was associated with about 4.8-fold reduced odds of moderate or severe COVID-19 in the absence of vaccine-induced antibodies. Analysis of T cell differentiation demonstrates that RTX administration increases the relative frequency of naïve CD8
+
T cells, potentially by depletion of CD8
+
CD20
dim
T cells, which are primarily of an effector memory or terminal effector memory (TEMRA) phenotype. However, this also leads to a reduction in preexisting antiviral T cell immunity. Collectively, these data indicate that individuals with B cell deficiencies have enhanced T cell immunity after both SARS-CoV-2 infection and vaccination that potentially accounts for reduced hospitalization and severe disease from subsequent SARS-CoV-2 infection.
A T cell receptor β chain–directed antibody fusion molecule activates and expands subsets of T cells to promote antitumor activity
Authors: Hsu Jonathan , Donahue Renee N. , Katragadda Madan , Lowry Jessica , Huang Wei , Srinivasan Karunya , Guntas Gurkan , Tang Jian , Servattalab Roya , Moisan Jacques , Tsai Yo-Ting , Stoop Allart , Palakurthi Sangeetha , Chopra Raj , Liu Ke , Wherry E. John , Su Zhen , Gulley James L. , Bayliffe Andrew , Schlom Jeffrey
Published: November 2023

Despite the success of programmed cell death-1 (PD-1) and PD-1 ligand (PD-L1) inhibitors in treating solid tumors, only a proportion of patients respond. Here, we describe a first-in-class bifunctional therapeutic molecule, STAR0602, that comprises an antibody targeting germline Vβ6 and Vβ10 T cell receptors (TCRs) fused to human interleukin-2 (IL-2) and simultaneously engages a nonclonal mode of TCR activation with costimulation to promote activation and expansion of αβ T cell subsets expressing distinct variable β (Vβ) TCR chains. In solution, STAR0602 binds IL-2 receptors in cis with Vβ6/Vβ10 TCRs on the same T cell, promoting expansion of human Vβ6 and Vβ10 CD4
+
and CD8
+
T cells that acquire an atypical central memory phenotype. Monotherapy with a mouse surrogate molecule induced durable tumor regression across six murine solid tumor models, including several refractory to anti–PD-1. Analysis of murine tumor-infiltrating lymphocyte (TIL) transcriptomes revealed that expanded Vβ T cells acquired a distinct effector memory phenotype with suppression of genes associated with T cell exhaustion and TCR signaling repression. Sequencing of TIL TCRs also revealed an increased T cell repertoire diversity within targeted Vβ T cell subsets, suggesting clonal revival of tumor T cell responses. These immunological and antitumor effects in mice were recapitulated in studies of STAR0602 in nonhuman primates and human ex vivo models, wherein STAR0602 boosted human antigen-specific T cell responses and killing of tumor organoids. Thus, STAR0602 represents a distinct class of T cell–activating molecules with the potential to deliver enhanced antitumor activity in checkpoint inhibitor–refractory settings.
Repurposing a human acetyl-CoA carboxylase inhibitor firsocostat to treat fungal candidiasis alone and in combination
Authors: Chen Tianyu , Yao Jing , Quan Keao , Xu Jingchen , Hang Xudong , Tong Qian , Liu Genyan , Luo Peipei , Zeng Liping , Feng Ganzhu , Bi Hongkai
Published: November 2023

Opportunistic fungal infections, particularly caused by
Candida albicans
, remain a common cause of high morbidity and mortality in immunocompromised patients. The escalating prevalence of antifungal drug resistance necessitates the immediate exploration of alternative treatment strategies to combat these life-threatening fungal diseases. In this study, we investigated the antifungal efficacy of firsocostat, a human acetyl-CoA carboxylase (ACC) inhibitor, against
C. albicans
. Firsocostat alone displayed moderate antifungal activity, while combining it with voriconazole, itraconazole, or amphotericin B exhibited synergistic effects across almost all drug-sensitive and drug-resistant
C. albicans
strains tested. These observed synergies were further validated in two mouse models of oropharyngeal and systemic candidiasis, where the combination therapies demonstrated superior fungicidal effects compared to monotherapy. Moreover, firsocostat was shown to directly bind to
C. albicans
ACC and inhibit its enzymatic activity. Sequencing spontaneous firsocostat-resistant mutants revealed mutations mapping to
C. albicans
ACC, confirming that firsocostat has retained its target in
C. albicans
. Overall, our findings suggest that repurposing firsocostat, either alone or in combination with other antifungal agents, holds promising potential in the development of antifungal drugs and the treatment of candidiasis.
Closed genomes of four multidrug resistance
Salmonella enterica
serotype Infantis isolated in Costa Rica
Authors: Duarte Francisco , Cordero Estela , Calderon Melany , Godinez Adriana , Ross Bruce , Allard Marc , Gonzalez-Escalona Narjol
Published: November 2023

Here, we report the complete genome of four
S. enterica
Infantis isolated in Costa Rica from human, poultry rinse, and raw chicken meat from 2017 to 2019. All genomes belonged to ST32 and carried a 310-kb plasmid with many antimicrobial resistance genes including the
bla
CTX-M65
gene.
Complete genomes of
Limosilactobacillus portuensis
and
Limosilactobacillus vaginalis
isolated from the urine of postmenopausal women
Authors: Nguyen Vivian H. , Sharon Belle M. , Shipman Braden M. , Zimmern Philippe E. , De Nisco Nicole J.
Published: November 2023

There is frequent evidence that
Limosilactobacillus vaginalis
colonizes female genitourinary tracts but few reports of
Limosilactobacillus portuensis
. Their role in urinary tract infection (UTI) is unclear. We present the first complete genome of
L. portuensis
and a complete genome of
L. vaginalis
isolated from postmenopausal women with varying UTI histories.
Integrated multi-omics reveals the roles of cecal microbiota and its derived bacterial consortium in promoting chicken growth
Authors: Zhang Meihong , Li Depeng , Yang Xinyue , Wei Fuxiao , Wen Qiu , Feng Yuqing , Jin Xiaolu , Liu Dan , Guo Yuming , Hu Yongfei
Published: November 2023

Growing evidence has shown a close connection between gut microbiota and chicken growth performance; however, the crosstalk between microbes and chicken host remains elusive. Here, we integrated multi-omics approaches, fecal microbiota transplantation, and body weight-associated bacterial consortium to investigate the host-microbiota interactions in different body weight chickens. Microbial profiling analysis showed that uncultured
Barnesiellaceae
,
Lactobacillus
,
Bacillus
,
Ruminococcaceae UCG-004
, and
Ruminococcaceae UCG-014
were highly enriched in the high body weight (HBW) chickens. The combination of
Lactobacillus
and
Bacillus
had 95.1% accuracy in discriminating HBW from low body weight chickens. Lipids and lipid-like molecules were found to be more abundant in the HBW chickens, and the differentially expressed cecal genes were enriched in the peroxisome proliferator-activated receptor (PPAR) signaling pathway and calcium signaling pathway. Correlations among the weight-associated genera, gut content metabolites, and gut gene expression were established, and fecal microbiota transplantation from HBW microbiota to newly born chicks increased the chicken antioxidant status, gut sugar transport, and immunity. A total of 67 strains belonging to
Lactobacillus
and
Bacillus
were isolated from the HBW chickens by the targeted culturomics method. Among six pairwise combinations of four selected strains, the consortium consisting of
Limosilactobacillus reuteri
CML393 and
Bacillus velezensis
CML396 significantly improved the chicken growth performance and gut health and influenced the cecal microbiota, metabolites, and gene expression. Further
in vitro
and
in silico
analyses indicated that
L. reuteri
CML393 and
B. velezensis
CML396 were less competitive but more cooperative than other pairwise combinations tested.

IMPORTANCE

The improvement of chicken growth performance is one of the major concerns for the poultry industry. Gut microbes are increasingly evidenced to be associated with chicken physiology and metabolism, thereby influencing chicken growth and development. Here, through integrated multi-omics analyses, we showed that chickens from the same line differing in their body weight were very different in their gut microbiota structure and host-microbiota crosstalk; microbes in high body weight (HBW) chickens contributed to chicken growth by regulating the gut function and homeostasis. We also verified that a specific bacterial consortium consisting of isolates from the HBW chickens has the potential to be used as chicken growth promoters. These findings provide new insights into the potential links between gut microbiota and chicken phenotypes, shedding light on future manipulation of chicken gut microbiota to improve chicken growth performance.
Efficacy of the combination of amphotericin B and echinocandins against
Candida auris in vitro
and in the
Caenorhabditis elegans
host model
Authors: Hernando-Ortiz Ainara , Eraso Elena , Jauregizar Nerea , de Groot Piet W.J. , Quindós Guillermo , Mateo Estibaliz
Published: November 2023

The multidrug-resistant
Candida auris
is a global health emergency, being responsible for outbreaks of invasive candidiasis worldwide. Limited effective therapeutic options make it difficult to treat this emerging pathogen. In this context, combinations of different antifungal drugs are considered a promising therapeutic alternative. The aim of this work was to analyze the antifungal activity of combinations of amphotericin B and echinocandins against five clinical blood isolates of
C. auris
. One of these isolates showed an aggregative phenotype already described in
C. auris
species, forming large aggregates of cells that are very difficult to disintegrate. First, the
in vitro
activity of these drugs was evaluated both in monotherapy and in combination, and results showed synergistic interactions between amphotericin B and echinocandins in most cases, although higher minimum inhibitory concentration (MIC) values were observed against the aggregative isolate compared to non-aggregative counterparts. The most promising drug combinations were then selected for
in vivo
activity evaluation using a
Caenorhabditis elegans
model of candidiasis and by determination of survival rates. The combination of amphotericin B and caspofungin showed the strongest protective effect during
C. elegans
infection with
C. auris
blood isolates, achieving up to 99%
C
.
elegans
survival. Although the MIC values for micafungin were low
in vitro
, these drug concentrations had no effect
in vivo
, and the combination of amphotericin B and micafungin was the least effective. The results of this study showed that the combination amphotericin B and echinocandins might be a promising therapeutic approach for the treatment of invasive candidiasis caused by
C. auris
. Moreover, the nematode
C. elegans
is a suitable alternative model for screening of new therapeutic agents capable of overcoming multidrug-resistant
C. auris
infections.

IMPORTANCE

Multidrug resistance is a rising problem among non-
Candida albicans
species, such as
Candida auris
. This therapeutic problem has been very important during the COVID-19 pandemic. The World Health Organization has included
C. auris
in its global priority list of health-threatening fungi, to study this emerging multidrug-resistant species and to develop effective alternative therapies. In the present study, the synergistic effect of the combination of amphotericin B and echinocandins has been demonstrated against blood isolates of
C. auris
. Different susceptibility responses were also observed between aggregative and non-aggregative phenotypes. The antifungal activity of these drug combinations against
C. auris
was also demonstrated in the
Caenorhabditis elegans
host model of candidiasis, confirming the suitability and usefulness of this model in the search for solutions to antimicrobial resistance.
Detection and absolute quantification of
Lactiplantibacillus plantarum
ATCC 202195 by quantitative real-time PCR
Authors: Shawon Jakaria , Pell Lisa G. , Kabir Mamun , Evans Kara , Hasan Mehedi , Li Grace , Qamar Huma , Starke Cody W. E. , Kurukulasuriya Shakya , Al Mahmud Abdullah , Sherman Philip M. , Sarker Shafiqul Alam , Roth Daniel E. , Haque Rashidul
Published: November 2023

Lactiplantibacillus plantarum
ATCC 202195 has probiotic properties that may be beneficial in early infancy. Since the effects of probiotics are often strain and dose specific, tools are needed to identify and enumerate
L. plantarum
ATCC 202195 with high sensitivity and specificity. Herein, a probe-based real-time quantitative PCR (qPCR) assay was developed to detect and enumerate
L. plantarum
ATCC 202195. The probe sequence contained a single nucleotide polymorphism within gene FEE41_08190 that was unique to
L. plantarum
ATCC 202195 at the time of the assay’s design. The linear dynamic range of the assay spanned five orders of magnitude with an
R
2
that did not deviate from linearity and an amplification efficiency that ranged from 97% to 110% across six independent plates. At 95% confidence, the limit of detection in the assay was estimated at roughly 15 cells. No amplification was observed for reactions containing gDNA from seven other
Lactobacillus
species. This is the first report of a qPCR assay that detects and quantifies
L. plantarum
ATCC 202195. The assay is intended to be used as a resource for future clinical trials and commercial manufacturing settings.

IMPORTANCE

When administered for seven consecutive days shortly after birth, the probiotic bacterium
Lactiplantibacillus plantarum
ATCC 202195 plus fructooligosaccharide (FOS) was reported to reduce sepsis and lower respiratory tract infection events during early infancy in a randomized trial in India. Since probiotic effects are often strain specific, strain-level detection and quantification by routine molecular methods enables the monitoring of safety outcomes, such as probiotic-associated bacteremia, and allows for the quality of probiotic interventions to be assessed and monitored (i.e., verify strain identity and enumerate). Despite the potential clinical applications of
L. plantarum
ATCC 202195, an assay to detect and quantify this strain has not previously been described. Herein, we report the design of primer and probe sequences to detect
L. plantarum
ATCC 202195 and the development and optimization of a real-time PCR assay to detect and quantify the strain with high specificity and high sensitivity.
Co-PATHOgenex web application for assessing complex stress responses in pathogenic bacteria
Authors: Fernandez Leyden , Rosvall Martin , Normark Johan , Fällman Maria , Avican Kemal
Published: November 2023

Pathogenic bacteria encounter various stressors while residing in the host. They respond through intricate mechanisms of gene expression regulation, ensuring their survival and adaptation. Understanding how bacteria adapt to different stress conditions through regulatory processes of specific genes requires exploring complex transcriptional responses using gene co-expression networks. We employed a large transcriptome data set comprising 32 diverse human bacterial pathogens exposed to the same 11 host-mimicking stress conditions. Using the weighted gene co-expression network analysis algorithm, we generated bacterial gene co-expression networks. By associating modular eigengene expression with specific stress conditions, we identified gene co-expression modules and stress-specific stimulons, including genes with unique expression patterns under specific stress conditions. Suggesting a new potential role of the
frm
operon in responding to bile stress in enteropathogenic bacteria demonstrates the effectiveness of our approach. We also revealed the regulation of streptolysin S genes, involved in the production, processing, and export of streptolysin S, a toxin responsible for the β-hemolytic phenotype of group A
Streptococcus
. In a comparative analysis of stress responses in three
Escherichia coli
strains from the core transcriptome, we revealed shared and unique expression patterns across the strains, offering insights into convergent and divergent stress responses. To help researchers perform similar analyses, we created the user-friendly web application Co-PATHOgenex. This tool aids in deepening our understanding of bacterial adaptation to stress conditions and in deciphering complex transcriptional responses of bacterial pathogens.

IMPORTANCE

Unveiling gene co-expression networks in bacterial pathogens has the potential for gaining insights into their adaptive strategies within the host environment. Here, we developed Co-PATHOgenex, an interactive and user-friendly web application that enables users to construct networks from gene co-expressions using custom-defined thresholds (
https://avicanlab.shinyapps.io/copathogenex/)
. The incorporated search functions and visualizations within the tool simplify the usage and facilitate the interpretation of the analysis output. Co-PATHOgenex also includes stress stimulons for various bacterial species, which can help identify gene products not previously associated with a particular stress condition.
High-performance enrichment-based genome sequencing to support the investigation of hepatitis A virus outbreaks
Authors: Zufan Sara E. , Mercoulia Karolina , Kwong Jason C. , Judd Louise M. , Howden Benjamin P. , Seemann Torsten , Stinear Timothy P.
Published: November 2023

Hepatitis A virus (HAV) infections are an increasing public health concern in low-endemicity regions due to outbreaks from food-borne infections and sustained transmission among vulnerable groups, including persons experiencing homelessness, those who inject drugs, and men who have sex with men, which is further compounded by aging, unvaccinated populations. DNA sequence characterization of HAV for source tracking is performed by comparing small subgenomic regions of the virus. While this approach has been successful when robust epidemiological data are available, poor genetic resolution can lead to the conflation of outbreaks with sporadic cases. HAV outbreak investigations would greatly benefit from the additional phylogenetic resolution obtained by whole virus genome sequence comparisons. However, HAV genomic approaches can be difficult because of challenges in isolating the virus, low sensitivity of direct metagenomic sequencing in complex sample matrices like various foods, such as fruits, vegetables, and molluscs, and difficulty designing highly multiplexed PCR primers across diverse HAV genotypes. Here, we introduce a proof-of-concept pan-HAV oligonucleotide hybrid capture enrichment assay from serum and frozen berry specimens that yields complete and near-complete HAV genomes from as few as four input HAV genome copies. We used this method to recover HAV genomes from human serum specimens with high Cτ values (34.7–42.7), with high assay performance for all six human HAV subgenotypes, both contemporary and historical. Our approach provides a highly sensitive and streamlined workflow for HAV whole-genome sequencing from diverse sample types that can be the basis for harmonized and high-resolution molecular epidemiology during HAV outbreak surveillance.

IMPORTANCE

This proof-of-concept study introduces a hybrid capture oligo panel for whole-genome sequencing of all six human pathogenic hepatitis A virus (HAV) subgenotypes, exhibiting a higher sensitivity than some conventional genotyping assays. The ability of hybrid capture to enrich multiple targets allows for a single, streamlined workflow, thus facilitating the potential harmonization of molecular surveillance of HAV with other enteric viruses. Even challenging sample matrices can be accommodated, making them suitable for broad implementation in clinical and public health laboratories. This innovative approach has significant implications for enhancing multijurisdictional outbreak investigations as well as our understanding of the global diversity and transmission dynamics of HAV.
Transcriptome profiling of type VI secretion system core gene
tssM
mutant of
Xanthomonas perforans
highlights regulators controlling diverse functions ranging from virulence to metabolism
Authors: Ramamoorthy Sivakumar , Pena Michelle , Ghosh Palash , Liao Ying-Yu , Paret Mathews , Jones Jeffrey B. , Potnis Neha
Published: November 2023

Type VI secretion system (T6SS) is a versatile, contact-dependent contractile nano-weapon in Gram-negative bacteria that fires proteinaceous effector molecules directly into prokaryotic and eukaryotic cells aiding in manipulation of the host and killing of competitors in complex niches. In plant pathogenic xanthomonads, T6SS has been demonstrated to play these diverse roles in individual pathosystems. However, the molecular network underlying the regulation of T6SS is still elusive in
Xanthomonas
spp. To bridge this knowledge gap, we conducted an
in vitro
transcriptome screen using plant apoplast mimicking minimal medium, XVM2 medium, to decipher the effect of
tssM
deletion, a core gene belonging to T6SS-cluster i3*, on the regulation of gene expression in
Xanthomonas perforans
strain AL65. Transcriptomic data revealed that a total of 277 and 525 genes were upregulated, while 307 and 392 genes were downregulated in the mutant strain after 8 and 16 hours of growth in XVM2 medium. The transcript abundance of several genes associated with flagellum and pilus biogenesis as well as type III secretion system was downregulated in the mutant strain. Deletion of
tssM
of cluster-i3* resulted in upregulation of several T6SS genes belonging to cluster-i3*** and genes involved in biofilm and cell wall biogenesis. Similarly, transcription regulators like
rpoN
, Pho regulon,
rpoE
, and
csrA
were identified to be upregulated in the mutant strain. Our results suggest that T6SS modulates the expression of global regulators like
csrA
,
rpoN
, and
pho
regulons, triggering a signaling cascade, and co-ordinates the expression of suite of virulence factors, stress response genes, and metabolic genes.

IMPORTANCE

T6SS has received attention due to its significance in mediating interorganismal competition through contact-dependent release of effector molecules into prokaryotic and eukaryotic cells. Reverse-genetic studies have indicated the role of T6SS in virulence in a variety of plant pathogenic bacteria, including the one studied here,
Xanthomonas
. However, it is not clear whether such effect on virulence is merely due to a shift in the microbiome-mediated protection or if T6SS is involved in a complex virulence regulatory network. In this study, we conducted in vitro transcriptome profiling in minimal medium to decipher the signaling pathways regulated by tssM-i3* in
X. perforans
AL65. We show that TssM-i3* regulates the expression of a suite of genes associated with virulence and metabolism either directly or indirectly by altering the transcription of several regulators. These findings further expand our knowledge on the intricate molecular circuits regulated by T6SS in phytopathogenic bacteria.
miR-26a exerts broad-spectrum antiviral effects via the enhancement of RIG-I-mediated type I interferon response by targeting USP15
Authors: Zhang Jikai , Li Chunyang , Hou Yao , Liu Dan , Li Qiudi , Wang Zijie , Tang Renxian , Zheng Kuiyang , Guo Hongbo , Wang Wenshi
Published: November 2023

Host innate immunity is an important defense line against virus infection and is precisely regulated by various factors. Studying the mechanism of virus-host interaction is essential to developing novel antivirals. Being one of the key host natural antiviral responses, host small non-coding RNAs (miRNAs) possess promising antiviral potential worthy of study. Herein, we found that miR-26a exerted broad-spectrum antiviral effect against multiple viruses, e.g., Hepatitis E virus, Vesicular Stomatitis Virus, and Sendai Virus. Mechanistically, miR-26a specifically targets 3′UTR of mRNA to inhibit USP15 expression. USP15 interacted directly with RIG-I to deubiquitinate K63-linked RIG-I, thus negatively regulating type I interferon (IFN) signaling. Consequently, miR-26a, by downregulating USP15, promotes K63 ubiquitination of RIG-I to enhance type I IFN responses, resulting in an active antiviral state against virus infection. Intriguingly, the activation of type I IFN responses could suppress miR-26a expression, serving as an intrinsic negative feedback loop to avoid dysregulated signal activation. Hence, the broad-spectrum antiviral effects of miR-26a and its mode-of-action enriched the interaction networks between miRNAs and innate immunity, providing insights for the development of broad-spectrum antivirals against viral infection.

IMPORTANCE

miR-26a serves as a potent positive regulator of type I interferon (IFN) responses. By inhibiting USP15 expression, miR-26a promotes RIG-I K63-ubiquitination to enhance type I IFN responses, resulting in an active antiviral state against viruses. Being an intricate regulatory network, the activation of type I IFN responses could in turn suppress miR-26a expression to avoid the disordered activation that might result in the so-called “type I interferonopathy.” The knowledge gained would be essential for the development of novel antiviral strategies against viral infection.