bluuebunny/crossref_metadata_2025 huggingface dataset:
Constitutive IL-1RA production by modified immune cells protects against IL-1–mediated inflammatory disorders
Authors: Colantuoni Mariasilvia , Jofra Hernandez Raisa , Pettinato Emanuela , Basso-Ricci Luca , Magnani Laura , Andolfi Grazia , Rigamonti Chiara , Finardi Annamaria , Romeo Valentina , Soldi Monica , Sergi Sergi Lucia , Rocchi Martina , Scala Serena , Hoffman Hal M. , Gregori Silvia , Kajaste-Rudnitski Anna , Sanvito Francesca , Muzio Luca , Naldini Luigi , Aiuti Alessandro , Mortellaro Alessandra
Published: May 2023

Dysregulation of the interleukin-1 (IL-1) pathway leads to immune diseases that can result in chronic tissue and organ inflammation. Although IL-1 blockade has shown promise in ameliorating these symptoms and improving patients’ quality of life, there is an urgent need for more effective, long-lasting treatments. We developed a lentivirus (LV)–mediated gene transfer strategy using transplanted autologous hematopoietic stem/progenitor cells (HSPCs) as a source of IL-1 receptor antagonist (IL-1RA) for systemic delivery to tissues and organs. Transplantation of mouse and human HSPCs transduced with an IL-1RA–encoding LV ensured stable IL-1RA production while maintaining the clonogenic and differentiation capacities of HSPCs in vivo. We examined the efficacy of cell-mediated IL-1RA delivery in three models of IL-1–dependent inflammation, for which treatment hindered neutrophil recruitment in an inducible model of gout, prevented systemic and multi-tissue inflammation in a genetic model of cryopyrin-associated periodic syndromes, and reduced disease severity in an experimental autoimmune encephalomyelitis model of multiple sclerosis. Our findings demonstrate HSPC-mediated IL-1RA delivery as a potential therapeutic modality that can be exploited to suppress tissue and organ inflammation in diverse immune-related diseases involving IL-1–driven inflammation.
The Type IV Secretion System (T4SS) Mediates Symbiosis between
Bradyrhizobium
sp. SUTN9-2 and Legumes
Authors: Wangthaisong Praneet , Piromyou Pongdet , Songwattana Pongpan , Wongdee Jenjira , Teamtaisong Kamonluck , Tittabutr Panlada , Boonkerd Nantakorn , Teaumroong Neung
Published: May 2023

SUTN9-2 is a broad host range strain capable of symbiosis with several legumes. Two copies of T4SS clusters belonging to the
tra/trb
operon are observed on chromosomes with different gene arrangements.
Identification of Virulence Factors Involved in a Murine Model of Severe Achromobacter xylosoxidans Infection
Authors: Wills Brandon M. , Garai Preeti , Riegert Molly O. , Sanchez Felix T. , Pickrum Adam M. , Frank Dara W. , Brockman Kenneth L.
Published: May 2023

Achromobacter xylosoxidans
(Ax) is an opportunistic pathogen and causative agent of numerous infections particularly in immunocompromised individuals with increasing prevalence in cystic fibrosis (CF). To date, investigations have focused on the clinical epidemiology and genomic comparisons of Ax isolates, yet little is known about disease pathology or the role that specific virulence factors play in tissue invasion or damage.
Location, Location, Location: an Antidote That Both Activates and Neutralizes a Toxin Used in Bacterial Warfare
Authors: Ahmad Shehryar , Whitney John C.
Published: May 2023

S.J. Jensen, Z.C.
Critical Role of Viral Protein Hexon in Hypervirulent Fowl Adenovirus Serotype-4-Induced Autophagy by Interaction with BAG3 and Promotion of Viral Replication in LMH Cells
Authors: Li Wei , You Guangju , Haiyilati Areayi· , Wang Hongnuan , Jiao Huixuan , Wang Yongqiang , Gao Li , Cao Hong , Li Xiaoqi , Zheng Shijun J.
Published: May 2023

HHS, mainly caused by HPFAdV-4, has caused large economic losses to the stakeholders in recent years. Infection of leghorn male hepatocellular (LMH) cells by HPFAdV-4 induced complete autophagy that is essential for HPFAdV-4 replication.
Acquisition of a large virulence plasmid (pINV) promoted temperature-dependent virulence and global dispersal of O96:H19 enteroinvasive
Escherichia coli
Authors: Miles Sydney L. , Torraca Vincenzo , Dyson Zoe A. , López-Jiménez Ana Teresa , Foster-Nyarko Ebenezer , Lobato-Márquez Damián , Jenkins Claire , Holt Kathryn E. , Mostowy Serge
Published: May 2023

Enteroinvasive
Escherichia coli
(EIEC) and
Shigella
are closely related agents of bacillary dysentery. It is widely viewed that EIEC and
Shigella
species evolved from
E. coli
via independent acquisitions of a large virulence plasmid (pINV) encoding a type 3 secretion system (T3SS). Sequence Type (ST)99 O96:H19
E. coli
is a novel clone of EIEC responsible for recent outbreaks in Europe and South America. Here, we use 92 whole genome sequences to reconstruct a dated phylogeny of ST99
E. coli
, revealing distinct phylogenomic clusters of pINV-positive and -negative isolates. To study the impact of pINV acquisition on the virulence of this clone, we developed an EIEC-zebrafish infection model showing that virulence of ST99 EIEC is thermoregulated. Strikingly, zebrafish infection using a T3SS-deficient ST99 EIEC strain and the oldest available pINV-negative isolate reveals a separate, temperature
-
independent mechanism of virulence, indicating that ST99 non-EIEC strains were virulent before pINV acquisition. Taken together, these results suggest that an already pathogenic
E. coli
acquired pINV and that virulence of ST99 isolates became thermoregulated once pINV was acquired.

IMPORTANCE

Enteroinvasive
Escherichia coli
(EIEC) and
Shigella
are etiological agents of bacillary dysentery. Sequence Type (ST)99 is a clone of EIEC hypothesized to cause human disease by the recent acquisition of pINV, a large plasmid encoding a type 3 secretion system (T3SS) that confers the ability to invade human cells. Using Bayesian analysis and zebrafish larvae infection, we show that the virulence of ST99 EIEC isolates is highly dependent on temperature, while T3SS-deficient isolates encode a separate temperature-independent mechanism of virulence. These results indicate that ST99 non-EIEC isolates may have been virulent before pINV acquisition and highlight an important role of pINV acquisition in the dispersal of ST99 EIEC in humans, allowing wider dissemination across Europe and South America.
Complete Genome Sequences of Subcluster C1 Mycobacteriophages Blackbrain, Cactojaque, Kboogie, Trinitium, and YoungMoneyMata
Authors: Moore Madison M. , Ayuk Mary A. , Johnson Amber A. , Sims Triniti , Haamen Sanaa , Haidara Ramata , Allen Adrian D. , Dickson Leon A. , Ghosh Somiranjan , Gugssa Ayele , Ullah Hemayet , Bassey Glory B. , Fernando Lourds M. , London Laricca Y. , Irabor Esohe G. , Roy Swagota D. , Quagraine Benedict K. , Smith Michael ,   Howard University SEA-PHAGES Students, Anderson Winston A. , Robinson Courtney J. , Adegboye Comfort Y. , Adigun Alexandria , Adams Brianna , Adu Deborah , Akaya Sirri , Akhimien Colette , Anderson Akiria , Andrade Sydney , Archibald Ahlina C. , Black Amia , Breaux Denia L. , Charles Olivia R. , Cheung Laraine , Chinboot Jirachat , Dawson Maya , Denton Jielle , Frederick Kirk , Garner Jarius A. , Givens SeighViance , Henry Nazareth N. , Henry-Smith Charnae’ , Hernandez Imani M. , James Niaya , Kane Syntyche , Kerr Devante , King Camille A. , Lam Camryn , Louis Briana , Luellen Xavier , Malone Trinity S. , Morton-Lane Bria , Nwozo Esther , Odu Toluwani , Oduguwa Antonia , Richardson Kasyah , Robinson Delandra M. , Salters Dylan , Scott Rajon , Williams Lauren , Williams Jalen , Williams Marc , Wilson Maya
Published: May 2023

Five subcluster C1 mycobacteriophages, Blackbrain, Cactojaque, Kboogie, Trinitium, and YoungMoneyMata, were isolated from soil using the host
Mycobacterium smegmatis
mc
2
155. The genome sizes range from 154,512 to 156,223 bp. The largest genome encodes 237 predicted proteins, 34 tRNAs, and 1 transfer-messenger RNA (tmRNA).
Choreography of Lyme Disease Spirochete Adhesins To Promote Vascular Escape
Authors: Tan Xi , Castellanos Mildred , Chaconas George
Published: May 2023

Lyme disease is caused by the spirochete
Borrelia burgdorferi
, which is transmitted by a bite from an infected tick. Disease development involves a complex series of host-pathogen interactions as well as dissemination of the infecting organisms to sites distal to the original tick bite.
Clinicopathological analysis of extraneural sporadic haemangioblastoma occurring in the tongue
Authors: Chen Yacun , Chen Jie , Jiang Ye , Lin Xiang
Published: May 2023

Haemangioblastoma is a morphologically distinctive tumour with uncertain histogenesis, typically occurring in the cerebellum, brain stem or spinal cord and less commonly in extraneural locations. Here, we present a case of haemangioblastoma occurring in the tongue, which is the first reported case in terms of the pathogenic site. The tumour was morphologically indistinguishable from central nervous system haemangioblastoma, that is, neoplastic stromal cells with cytoplasmic vacuolisation and abundant small vessels. Immunohistochemical studies revealed that the tumour cells were positive for S100, NSE, CD56, Syn, EMA, vimentin and α-inhibin, while negative for CK, SMA, factor Ⅷ, D2-40 and GFAP. Immunostainings for CD34 and CD31 outlined the rich and delicate vascular channels. Ki-67 expression was presented in approximately 3% of tumour cells. Primary haemangioblastoma has not been previously described at this site, and this case emphasises the need to consider haemangioblastoma in the differential diagnoses of neoplasms occurring in the tongue.
Implementation of the injury prevention exercise programmeKnee Control+: a cross-sectional study after dissemination efforts within a football district
Authors: Lindblom Hanna , Sonesson Sofi , Forslind Josefin , Waldén Markus , Hägglund Martin
Published: May 2023

Background

The Reach, Effectiveness, Adoption, Implementation, and Maintenance (RE-AIM) framework can be used for evaluation of implementation initiatives in sports injury prevention. The aim was to evaluate the implementation of the injury prevention exercise programmeKnee Control+among amateur clubs and coaches in one regional football district using all five dimensions of the RE-AIM framework.

Methods

Dissemination ofKnee Control+during the 2021 season with information and webinars within one regional football district. This was followed by a cross-sectional study with questionnaires to club personnel and coaches after the season.

Results

The reach ofKnee Control+was fair to high, 83% of club personnel and 66% of coaches knew about the programme. 41% of club personnel and 51% of coaches had adopted it. Perceived programme effectiveness was high (6 on a 1–7 Likert scale) among coaches. Regarding implementation and maintenance, 27% of club personnel had informed coaches aboutKnee Control+and 57% planned to inform coaches. The coaches had implemented the programme mainly as recommended, but half used the programme once per week or less. Intention to maintain use of the programme was high (7 on a 1–7 Likert scale) among coaches.

Conclusion

The reach ofKnee Control+was fair to high, and adoption was fair in clubs, but there was a lack of policies for preventive training. Active strategies probably need to accompany dissemination of programme material. Reach, perceived effectiveness, adoption, implementation and planned maintenance were positive among coaches, but further studies are needed to analyse long-term maintenance.
Nitrous oxide-induced myeloneuropathy: a case series
Authors: Mair Devan , Paris Alvar , Zaloum Safiya A , White Laura M , Dodd Katherine C , Englezou Christina , Patel Farhin , Abualnaja Siraj , Lilleker James B , Gosal David , Hayton Tom , Liang Di , Allroggen Holger , Pucci Mark , Keddie Stephen , Noyce Alastair J
Published: May 2023

Background

Nitrous oxide (N2O) is the second most common recreational drug used by 16- to 24-year-olds in the UK. Neurological symptoms can occur in some people that use N2O recreationally, but most information comes from small case series.

Methods

We describe 119 patients with N2O-myeloneuropathy seen at NHS teaching hospitals in three of the UK’s largest cities: London, Birmingham and Manchester. This work summarises the clinical and investigative findings in the largest case series to date.

Results

Paraesthesia was the presenting complaint in 85% of cases, with the lower limbs more commonly affected than the upper limbs. Gait ataxia was common, and bladder and bowel disturbance were frequent additional symptoms. The mid-cervical region of the spinal cord (C3–C5) was most often affected on MRI T2-weighted imaging. The number of N2O canisters consumed per week correlated with methylmalonic acid levels in the blood as a measure of functional B12deficiency (rho (ρ)=0.44, p=0.04).

Conclusions

Preventable neurological harm from N2O abuse is increasingly seen worldwide. Ease of access to canisters and larger cylinders of N2O has led to an apparent rise in cases of N2O-myeloneuropathy in several areas of the UK. Our results highlight the range of clinical manifestations in a large group of patients to improve awareness of risk, aid early recognition, and promote timely treatment.
Investigating the impact of condomless vaginal intercourse and lubricant use on the vaginal metabolome: a pre-post observational study
Authors: Borgogna Joanna-Lynn C , Grace Savannah G , Holm Johanna B , Aviles Zuniga Tadeo , Kadriu Herlin , He Xin , McCoski Sarah R , Ravel Jacques , Brotman Rebecca M , Yeoman Carl J
Published: May 2023

Objective

The vaginal metabolome is a significant factor in the vaginal microenvironment, and data are emerging on its independent role in urogenital health. Condomless vaginal intercourse and personal lubricant use are common practices that may affect the vaginal metabolome. The aim of the present study is to describe the associations between condomless intercourse and lubricant use on the vaginal metabolome.

Methods

This study used archived mid-vaginal swabs from a 10-week observational cohort of reproductive age women who self-collected samples and recorded behavioural diaries daily. Cases and controls were defined as participants who self-reported condomless vaginal intercourse with or without lubricant use, respectively. Samples were drawn prior to and following condomless vaginal intercourse. Twenty-two case participants were race/ethnicity matched to 22 control participants. Mid-vaginal swabs were subjected to 16S rRNA gene amplicon sequencing and untargeted ultrahigh performance liquid chromatography tandem mass spectroscopy metabolomics. Bayesian mixed-effects regression (unadjusted and adjusted for the vaginal microbiota) was used to evaluate differences in metabolite concentration associated with vaginal intercourse and lubricant use.

Results

Both condomless penile–vaginal intercourse and lubricant use were independently associated with higher (up to 8.3-fold) concentrations of metabolites indicative of epithelial damage (eg, sarcosine) and many host-produced antioxidants. Lubricant use was significantly associated with increases in lipids related to cellular damage, host-produced sphingolipids (antimicrobials), antioxidants and salicylate, a cooling agent common to lubricants, in a study design which controls for the independent effect of intercourse. Metabolites involved in oxidative stress and salicylate were strongly correlated with several molecular bacterial vaginosis-associated bacteria.

Conclusions

This study provides important foundational data on how condomless vaginal–penile intercourse and lubricant use affect the vaginal metabolome and may affect the protective mechanisms in the vaginal microenvironment.
What Quality Aspects Influence the Adoption of Docker Images?
Authors: Rosa Giovanni , Scalabrino Simone , Bavota Gabriele , Oliveto Rocco
Published: May 2023

Docker is a containerization technology that allows developers to ship software applications along with their dependencies in Docker images. Developers can extend existing images using them as base images when writing Dockerfiles. However, a lot of alternative functionally equivalent base images are available. Although many studies define and evaluate quality features that can be extracted from Docker artifacts, the criteria on which developers choose a base image over another remain unclear.

In this article, we aim to fill this gap. First, we conduct a literature review through which we define a taxonomy of quality features, identifying two main groups:
configuration-related features
(i.e., mainly related to the Dockerfile and image build process), and
externally observable features
(i.e., what the Docker image users can observe). Second, we ran an empirical study considering the developers’ preference for 2,441 Docker images in 1,911 open source software projects. We want to understand how the externally observable features influence the developers’ preferences, and how they are related to the configuration-related features. Our results pave the way to the definition of a reliable quality measure for Docker artifacts, along with tools that support developers for a quality-aware development of them.
DiRaC-I: Identifying Diverse and Rare Training Classes for Zero-Shot Learning
Authors: Sarma Sandipan , Sur Arijit
Published: May 2023

Zero-Shot Learning (ZSL)
is an extreme form of transfer learning that aims at learning from a few “seen classes” to have an understanding about the “unseen classes” in the wild. Given a dataset in ZSL research, most existing works use a predetermined, disjoint set of seen-unseen classes to evaluate their methods. These seen (training) classes might be sub-optimal for ZSL methods to appreciate the diversity and rarity of an object domain. Inspired by strategies like active learning, it is intuitive that intelligently selecting the training classes can improve ZSL performance. In this work, we propose a framework called
Diverse and Rare Class Identifier (DiRaC-I)
which, given an attribute-based dataset, can intelligently yield the most suitable “seen classes” for training ZSL models. DiRaC-I has two main goals – constructing a diversified set of seed classes, and using them to initialize a visual-semantic mining algorithm for acquiring the classes capturing both diversity and rarity in the object domain adequately. These classes can then be used as “seen classes” to train ZSL models for image classification. We simulate a real-world scenario where visual samples of novel object classes in the wild are available to neither DiRaC-I nor the ZSL models during training and conducted extensive experiments on two benchmark data sets for zero-shot image classification — CUB and SUN. Our results demonstrate DiRaC-I helps ZSL models to achieve significant classification accuracy improvements – specifically, up to 8% for CUB and up to 5% for SUN dataset. Additionally, while recognizing classes exhibiting rare attributes we also observe a performance boost for ZSL models, which is up to 10% and 7% for CUB and SUN datasets, respectively.
Mimas: Frozen Fragment, Ring Relic, or Emerging Ocean World?
Authors: Rhoden Alyssa Rose
Published: May 2023

Mimas, the smallest and innermost of Saturn's mid-sized moons, has a heavily cratered surface devoid of the intricate fracture systems of its neighbor, Enceladus. However, Cassini measurements identified a signature of an ocean under Mimas’ ice shell, although a frozen ice shell over a rocky interior could not be ruled out. The Mimas ocean hypothesis has stimulated inquiry into Mimas’ geologic history and orbital evolution. Here, we summarize the results of these investigations, which (perhaps surprisingly) are consistent with an ocean-bearing Mimas as long as it is geologically young. In that case, a ring origin for Mimas is favored over primordial accretion. An independently developed model for the formation of a gap in Saturn's rings provides a potential mechanism for generating a late-stage ocean within Mimas and may have assisted in the development of Enceladus’ ocean and associated geologic activity. Rather than a battered relic, Mimas may be the youngest ocean moon in the Saturn system, destined to join Enceladus as an active world in the future. The presence of oceans within Saturn's mid-sized moons also has implications for the habitability of Uranus’ moons; the Uranus system was chosen as the highest priority target for the next NASA Flagship-class mission.▪Models of Mimas’ tides and rotation state support a present-day internal ocean.▪Mimas’ craters, impact basin, and lack of widespread tectonism are compatible with a stable/warming ocean.▪The formation of the Cassini Division within Saturn's rings provides a potential pathway to a present-day ocean within Mimas.▪If Mimas has an ocean today, it is geologically young.
The Reemergence of Phycopathology: When Algal Biology Meets Ecology and Biosecurity
Authors: Murúa Pedro , Garvetto Andrea , Egan Suhelen , Gachon Claire M.M.
Published: May 2023

Viruses, bacteria, and eukaryotic symbionts interact with algae in a variety of ways to cause disease complexes, often shaping marine and freshwater ecosystems. The advent of phyconomy (a.k.a. seaweed agronomy) represents a need for a greater understanding of algal disease interactions, where underestimated cryptic diversity and lack of phycopathological basis are prospective constraints for algal domestication. Here, we highlight the limited yet increasing knowledge of algal pathogen biodiversity and the ecological interaction with their algal hosts. Finally, we discuss how ecology and cultivation experience contribute to and reinforce aquaculture practice, with the potential to reshape biosecurity policies of seaweed cultivation worldwide.
International Trade and Local Effects of Viral and Bacterial Diseases in Ornamental Plants
Authors: Hammond John , Huang Qi , Jordan Ramon , Meekes Ellis , Fox Adrian , Vazquez-Iglesias Ines , Vaira Anna Maria , Copetta Andrea , Delmiglio Catia
Published: May 2023

Since the 1950s, there have been major changes in the scope, value, and organization of the ornamental plant industry. With fewer individual producers and a strong trend toward consolidation and globalization, increasing quantities of diverse plant genera and species are being shipped internationally. Many more ornamentals are propagated vegetatively instead of by seed, further contributing to disease spread. These factors have led to global movement of pathogens to countries where they were not formerly known. The emergence of some previously undescribed pathogens has been facilitated by high-throughput sequencing, but biological studies are often lacking, so their roles in economic diseases are not yet known. Case studies of diseases in selected ornamentals discuss the factors involved in their spread, control measures to reduce their economic impact, and some potential effects on agronomic crops. Advances in diagnostic techniques are discussed, and parallels are drawn to the international movement of human diseases.
Breaking Boundaries: The Perpetual Interplay Between Tobamoviruses and Plant Immunity
Authors: Spiegelman Ziv , Dinesh-Kumar Savithramma P.
Published: May 2023

Plant viruses of the genus Tobamovirus cause significant economic losses in various crops. The emergence of new tobamoviruses such as the tomato brown rugose fruit virus (ToBRFV) poses a major threat to global agriculture. Upon infection, plants mount a complex immune response to restrict virus replication and spread, involving a multilayered defense system that includes defense hormones, RNA silencing, and immune receptors. To counter these defenses, tobamoviruses have evolved various strategies to evade or suppress the different immune pathways. Understanding the interactions between tobamoviruses and the plant immune pathways is crucial for the development of effective control measures and genetic resistance to these viruses. In this review, we discuss past and current knowledge of the intricate relationship between tobamoviruses and host immunity. We use this knowledge to understand the emergence of ToBRFV and discuss potential approaches for the development of new resistance strategies to cope with emerging tobamoviruses.
Visual accuracy dominates over haptic speed for state estimation of a partner during collaborative sensorimotor interactions
Authors: Lokesh Rakshith , Sullivan Seth R. , St. Germain Laura , Roth Adam M. , Calalo Jan A. , Buggeln John , Ngo Truc , Marchhart Vanessa R. F. , Carter Michael J. , Cashaback Joshua G. A.
Published: May 2023

Physical collaboration between two or more individuals involves both visual and haptic feedback. Here, we investigated how visual and haptic feedback is used to estimate the movements of a partner during a collaboration task. Our experimental and computational modeling results parsimoniously support the notion that greater visual accuracy is more important than faster yet noisier haptic feedback when estimating the state of a partner.
NSF (Nylon Synthetic Fiber) Effectiveness in Stabilizing Weak Subgrade Soil: An Experimental Investigation
Authors: Demsie Tarekegn Shumetie , Beyene Markos Tsegaye , Lemma Abuye Boja , Alemayehu Esayas
Published: May 2023

Improvement in subgrade soil has always been an area of concern for highway and geotechnical engineers. Weak subgrade soil results in a greater thickness of the pavement layer, which increases the cost of pavement construction. It further leads to large deformations, which in turn cause continuous deterioration of the paved surface. To solve this problem, various engineering solutions and soil improvement mechanisms were previously proposed. This study was designed to investigate the stabilization of weak subgrade soil with nylon synthetic fiber (NSF) in a compromising combination. Previously, some investigations used a lower fiber content with a higher fiber length, whereas others used a lower fiber length with a higher fiber content. However, this investigation was uniquely designed to stabilize weak subgrade soil with the consideration of appropriate fiber length (10 mm and 20 mm) and content (0.5%, 1%, 1.5%, and 2.5%). The engineering properties of the soil, the effect of NSF on weak subgrade soil, various fiber content and aspect ratios, and the optimum content and critical fiber aspect ratio were investigated in a laboratory. The effect of fibers on compaction, CBR values, and CBR swell values has also been studied. Laboratory results on the modified compaction tests showed that maximum dry density (MDD) was increased with the increment of fiber content, whereas optimum moisture content (OMC) remained constant. The soaked CBR and CBR swell values of natural soil were 1.80% and 8.95%, respectively. Due to reinforcement, the percentage increase in soaked CBR value at the optimum NSF content is 265.3, 310.0, 282.8, and 342.2 for aspect ratios of 33.33, 66.67, 25, and 50, respectively, with reference to natural soil. Also, the percentage decrease in swelling is 34.7, 52.75, 43.55, and 36.9, respectively. Moreover, the CBR value increases with the increase in aspect ratio by keeping the diameter constant and decreases with the increase in aspect ratio by keeping the length constant. It was also observed that increasing the length and diameter of NSF further increased the CBR value of reinforced soil. This increment was substantial at a fiber content of 1.5% for an aspect ratio of 50 (length = 20 mm, diameter = 0.4 mm). There was also a decrease in the CBR swelling value with an increase in fiber content. Finally, this investigation concluded that the use of NSF is a solution to weak soils with regard to moisture and performance problems.
Authorization Recycling in Attribute-Based Access Control
Authors: An Yan , Helil Nurmamat
Published: May 2023

In most access control scenarios, the communication between the PDP (policy decision point) and the PEP (policy enforcement point) can cause high authorization overhead. Authorization recycling enables PEP to use the previous access control decisions fetched from the PDP to handle some upcoming access control requests, reduce authorization costs, and increase the efficiency of access control decision-making. Inspired by the RBAC (role-based access control) authorization recycling mechanism, this article first presents an ABAC (attribute-based access control) model based on Boolean expressions of subject and object attributes. It then proposes an authorization recycling approach for this model. In this approach, we provide construction and update methods for authorization data caches and access control decision-making rules for SDP (secondary decision point) by using the caches. The proposed approach can deduce precise and approximate access control decisions from the cache of authorization data, reducing communication between the PEP and the PDP. Finally, the feasibility of the proposed method is verified by conducting a small-scale test. ABAC, SDP, authorization recycling, and authorization caching.
LINC01614 Promotes Colorectal Cancer Cell Growth and Migration by Regulating miR‐217‐5p/HMGA1 Axis
Authors: Jia Jiwei , Guo Pei , Zhang Li , Kong Wenqing , Wang Fangfang
Published: May 2023

Colorectal cancer (CRC) substantially contributes to cancer‐related deaths worldwide. Recently, a long non‐coding RNA (lncRNA), LINC01614, has emerged as a vital gene regulator in cancer progression. Yet, how LINC01614 affects CRC progression remains enigmatic. Here, we defined LINC01614 expression in CRC, investigated the performance of CRC cells lacking LINC01614, and elucidated the underpinning mechanism. We observed that LINC01614 was upregulated in both CRC tissues and cell lines. LINC01614 knockdown repressed the proliferation and metastasis capacity of CRC cell lines. Consistently, an in vivo LINC01614 deficiency model exhibited slow tumor growth rate. Moreover, luciferase reporter assay, RNA pull‐down, and immunoprecipitation confirmed that LINC01614 targeted miR‐217‐5p. LINC01614 knockdown reduced the expression of HMGA1 and N‐cadherin, while increasing that of E‐cadherin, resulting in decreased viability, proliferation, migration, and invasion capacity of CRC cells. Our results demonstrate that LINC01614 regulates CRC progression by modulating the miR‐217‐5p/HMGA1 axis, thus holding great potential as a prognostic biomarker for CRC diagnosis and treatment.
An Anomaly Detection Approach Based on Integrated LSTM for IoT Big Data
Authors: Li Chao , Fu Yuhan , Zhang Rui , Liang Hai , Wang Chonghua , Li Junjian
Published: May 2023

Due to the expanding scope of Industry 4.0, the Internet of Things has become an important element of the information age. Cyber security relies heavily on intrusion detection systems for Internet of Things (IoT) devices. In the face of complex network data and diverse intrusion methods, today’s network security environment requires more suitable machine learning methods to meet its security needs, and the current machine learning methods are hardly competent. In part because of network attacks by intruders using cutting-edge techniques and the constrained environment of IoT devices themselves, the most widely used algorithms in recent years include CNN and LSTM, with the former being particularly good at extracting features from the original data space and the latter concentrating more on temporal features of the data. We aim to address the issue of merging spatial and temporal variables in intrusion detection models by introducing a fusion model CNN and C-LSTM in this paper. Fusion features enhanced parallelism in the training process and better results without a very deep network, giving the model a shorter training time, fast convergence, and computational speed for emerging resource-limited network entities. This model is more suitable for anomaly detection tasks in the resource-constrained and time-sensitive big data environment of the Internet of Things. KDDCup-99, a publicly available IBD dataset, was applied in our experiments to demonstrate the model’s validity. In comparison to existing deep learning implementations, our proposed multiclass classification model delivers higher accuracy, precision, and recall.
Synthesis of Green Cerium Oxide Nanoparticles Using Plant Waste from Colocasia esculenta for Seed Germination of Mung Bean (Vigna radiata)
Authors: Monica Ahmad Nor , Aishah Hasan Nor’
Published: May 2023

Synthesis of cerium oxide (CeO2) nanoparticles (NPs) via biological approach has received a lot of interest to reduce the harmful effects of chemical synthesis. In the present study, Colocasia esculenta leaf extract facilitated the preparation of CeO2-NPs by using the sol-gel technique. The crystal structural of CeO2-NPs was proven by X-ray powder diffraction (XRD) investigation to be cubic with size of 2.94 nm according to Debye–Scherrer equation. As demonstrated in the transmission electron microscopy (TEM) image, CeO2-NPs have a spherical form with an average size of 2.04 nm which is almost consistent with a finding from XRD analysis. Energy dispersive X-ray (EDX) measurements exhibited high-intensity peaks attributed to Ce and oxygen and further proved the creation of CeO2-NPs. The Fourier transform infrared spectroscopy (FTIR) analysis revealed the presence of Ce-O stretching, indicating the formation of CeO2-NPs. Functional groups of O-H, C-O, and C=O peaks were found in a spectrum due to the phytochemical components that were responsible for reducing and stabilizing during the synthesis process of CeO2-NPs. The examined UV-visible spectra exhibited the absorbance peak at 213 nm. The synthesized NPs produced in this study were further investigated for mung bean seed germination, whereby the influence of grain germination and growth rate demonstrated the significant finding.
Supplementary Table S3 from Associations of Race and Ethnicity with Hepatocellular Carcinoma, Decompensation, and Mortality in US Veterans with Cirrhosis
Authors: VoPham Trang , Cravero Anne , Feld Lauren D. , Green Pamela , Feng Ziding , Berry Kristin , Kim Nicole J. , Vutien Philip , Mendoza Jason A. , Ioannou George N.
Published: May 2023

Supplementary Table S3. Association between race/ethnicity and risk of HCC in patients with cirrhosis overall and by cirrhosis etiology: follow-up from cirrhosis diagnosis (2001-2014) to 2020
Supplementary Figure S7 from Overlaid Transcriptional and Proteome Analyses Identify Mitotic Kinesins as Important Targets of Arylsulfonamide-Mediated RBM39 Degradation
Authors: Coomar Seemon , Mota Pedro , Penson Alexander , Schwaller Jürg , Abdel-Wahab Omar , Gillingham Dennis
Published: May 2023

Supplementary Figure S7
Supplementary Table 5 from ZEB1 is Regulated by K811 Acetylation to Promote Stability, NuRD Complex Interactions, EMT, and NSCLC Metastasis
Authors: Perez-Oquendo Mabel , Manshouri Roxsan , Tian Yanhua , Fradette Jared J. , Rodriguez B. Leticia , Kundu Samrat T. , Gibbons Don L.
Published: May 2023

ChIP Primer Sequences
Supplementary Table 3 from ZEB1 is Regulated by K811 Acetylation to Promote Stability, NuRD Complex Interactions, EMT, and NSCLC Metastasis
Authors: Perez-Oquendo Mabel , Manshouri Roxsan , Tian Yanhua , Fradette Jared J. , Rodriguez B. Leticia , Kundu Samrat T. , Gibbons Don L.
Published: May 2023

Antibody information
Figure S4 from A Comparative Study of Neuroendocrine Heterogeneity in Small Cell Lung Cancer and Neuroblastoma
Authors: Cai Ling , DeBerardinis Ralph J. , Xie Yang , Minna John D. , Xiao Guanghua
Published: May 2023

SCLC vs. NBL concordance of NE score association with omics, drug sensitivity, and dependency data.
Supplementary Data Table 1 from Overlaid Transcriptional and Proteome Analyses Identify Mitotic Kinesins as Important Targets of Arylsulfonamide-Mediated RBM39 Degradation
Authors: Coomar Seemon , Mota Pedro , Penson Alexander , Schwaller Jürg , Abdel-Wahab Omar , Gillingham Dennis
Published: May 2023

Supplementary Data Table 1
Data from ZEB1 Is Regulated by K811 Acetylation to Promote Stability, NuRD Complex Interactions, EMT, and NSCLC Metastasis
Authors: Perez-Oquendo Mabel , Manshouri Roxsan , Tian Yanhua , Fradette Jared J. , Rodriguez B. Leticia , Kundu Samrat T. , Gibbons Don L.
Published: May 2023

Abstract
Epithelial-to-mesenchymal transition results in loss of specialized epithelial cell contacts and acquisition of mesenchymal invasive capacity. The transcription repressor zinc finger E-box-binding homeobox 1 (ZEB1) binds to E-boxes of gene promoter regions to suppress the expression of epithelial genes. ZEB1 has inconsistent molecular weights, which have been attributed to posttranslational modifications (PTM). We performed mass spectrometry and identified K811 acetylation as a novel PTM in ZEB1. To define the role of ZEB1 acetylation in regulating function, we generated ZEB1 acetyl-mimetic (K811Q) and acetyl-deficient (K811R) mutant-expressing non–small cell lung cancer cell lines (NSCLC). We demonstrate that the K811R ZEB1 (125 kDa) has a shorter protein half-life than wild-type (WT) ZEB1 and K811Q ZEB1 (∼225 kDa), suggesting that lack of ZEB1 acetylation in the lower molecular weight form affects protein stability. Further, the acetylated form of ZEB1 recruits the nucleosome remodeling and deacetylase (NuRD) complex to bind the promoter of its target genes mir200c-141 and SEMA3F. RNA-sequencing revealed that WT ZEB1 and K811Q ZEB1 downregulate the expression of epithelial genes to promote lung adenocarcinoma invasion and metastasis, whereas the K811R ZEB1 does not. Our findings establish that the K811 acetylation promotes ZEB1 protein stability, interaction with other protein complexes, and subsequent invasion/metastasis of lung adenocarcinoma via epithelial-to-mesenchymal transition.
Implications:
The molecular mechanisms by which ZEB1 is regulated by K811 acetylation to promote protein stability, NuRD complex and promoter interactions, and function are relevant to the development of treatment strategies to prevent and treat metastasis in patients with NSCLC.
FIGURE 4 from Targeting CHAF1B Enhances IFN Activity against Myeloproliferative Neoplasm Cells
Authors: Saleiro Diana , Kosciuczuk Ewa M. , Fischietti Mariafausta , Perez Ricardo E. , Yang G. Sohae , Eckerdt Frank , Beauchamp Elspeth M. , Hou Ye , Wang Qixuan , Weinberg Rona Singer , Fish Eleanor N. , Yue Feng , Hoffman Ronald , Platanias Leonidas C.
Published: May 2023

Inhibition of CHAF1B increases IFNα-induced anticlonogenic effects in MPN. HEL cells (A) and SET-2 cells (B) were transfected with either control (Ctrl) siRNA or CHAF1B siRNA, and leukemic CFU-L colony formation was assessed in clonogenic assays in the presence or absence of IFNα, as indicated. Data are expressed as percentage of colony formation over control siRNA-transfected untreated cells (control), and the scatter dot plots represent means ± SEM of four independent experiments for each cell line. C, Clonogenic capability of primary malignant erythroid progenitors isolated from PV patients transfected with either control (Ctrl) siRNA or CHAF1B siRNA and either left untreated or treated with IFNα, as indicated. Data are expressed as percentage of colony formation over control siRNA-transfected untreated cells (control) and shown are means ± SEM of six independent experiments using cells from six different patients with PV. Percentages for the same patient are represented by the same symbol and different patients have different symbols. A–C, Statistical analyses were performed using one-way ANOVA followed by Tukey multiple comparisons test. *, P < 0.05; **, P < 0.01; ****, P < 0.0001.
Supplementary Table S8 from Desmoplastic reaction associates with prognosis and adjuvant chemotherapy response in colorectal cancer: a multicenter retrospective study
Authors: Hu Qingru , Wang Yiting , Yao Su , Mao Yun , Liu Liu , Li Zhenhui , Chen Yonghe , Zhang Shenyan , Li Qian , Zhao Yingnan , Fan Xinjuan , Cui Yanfen , Zhao Ke , Liu Zaiyi
Published: May 2023

Correlation between DR and Stroma AReactive Invasion Front Areas
Supplementary Figure S2 from Maternal embryonic leucine zipper kinase is associated with metastasis in triple-negative breast cancer
Authors: Xie Xuemei , Chauhan Gaurav B , Edupuganti Ramakrishna , Kogawa Takahiro , Park Jihyun , Tacam Moises J , Tan Alex W , Mughees Mohd , Vidhu Fnu , Liu Diane D , Taliaferro Juliana M. , Pitner Mary K , Browning Luke Samuel , Lee Ju-Hyeon , Shen Yu , Wang Jian , Ueno Naoto T. , Krishnamurthy Savitri , Hortobagyi Gabriel N. , Tripathy Debu , Van Laere Steven , Bartholomeusz Geoffrey , Dalby Kevin N. , Bartholomeusz Chandra
Published: May 2023

Supplementary Figure S2. Volcano plots show differences in gene expression in parental and Cas9-p15 control or MELK knockout (KO) MDA-MB-231 cells.
Supplementary Table S5 from Desmoplastic reaction associates with prognosis and adjuvant chemotherapy response in colorectal cancer: a multicenter retrospective study
Authors: Hu Qingru , Wang Yiting , Yao Su , Mao Yun , Liu Liu , Li Zhenhui , Chen Yonghe , Zhang Shenyan , Li Qian , Zhao Yingnan , Fan Xinjuan , Cui Yanfen , Zhao Ke , Liu Zaiyi
Published: May 2023

Correlation between DR and TB
Supplementary Figure S1 from Maternal embryonic leucine zipper kinase is associated with metastasis in triple-negative breast cancer
Authors: Xie Xuemei , Chauhan Gaurav B , Edupuganti Ramakrishna , Kogawa Takahiro , Park Jihyun , Tacam Moises J , Tan Alex W , Mughees Mohd , Vidhu Fnu , Liu Diane D , Taliaferro Juliana M. , Pitner Mary K , Browning Luke Samuel , Lee Ju-Hyeon , Shen Yu , Wang Jian , Ueno Naoto T. , Krishnamurthy Savitri , Hortobagyi Gabriel N. , Tripathy Debu , Van Laere Steven , Bartholomeusz Geoffrey , Dalby Kevin N. , Bartholomeusz Chandra
Published: May 2023

Figure S1. Inhibitory effect of treatment with MELK-In-17 on the expression of epithelial-to-mesenchymal transition markers in murine 4T1 triple-negative breast cancer cells.
Figure S4 from Targeting fatty acid reprogramming suppresses CARM1-expressing ovarian cancer
Authors: Lombardi Simona , Goldman Aaron R , Tang Hsin-Yao , Kossenkov Andrew V , Liu Heng , Zhou Wei , Herlyn Meenhard , Lin Jianhuang , Zhang Rugang
Published: May 2023

CARM1 expression confers the sensitivity to SCD1 inhibition.
Figure S2 from Targeting fatty acid reprogramming suppresses CARM1-expressing ovarian cancer
Authors: Lombardi Simona , Goldman Aaron R , Tang Hsin-Yao , Kossenkov Andrew V , Liu Heng , Zhou Wei , Herlyn Meenhard , Lin Jianhuang , Zhang Rugang
Published: May 2023

CARM1 regulates FASN and ACC1 expression by recruiting XBP1s to their promoters.
Supplementary Figure S6 from Desmoplastic reaction associates with prognosis and adjuvant chemotherapy response in colorectal cancer: a multicenter retrospective study
Authors: Hu Qingru , Wang Yiting , Yao Su , Mao Yun , Liu Liu , Li Zhenhui , Chen Yonghe , Zhang Shenyan , Li Qian , Zhao Yingnan , Fan Xinjuan , Cui Yanfen , Zhao Ke , Liu Zaiyi
Published: May 2023

Predictive significance of other clinical risk factors on the ACT of stage II CRC
Supplementary Figure S3 from Desmoplastic reaction associates with prognosis and adjuvant chemotherapy response in colorectal cancer: a multicenter retrospective study
Authors: Hu Qingru , Wang Yiting , Yao Su , Mao Yun , Liu Liu , Li Zhenhui , Chen Yonghe , Zhang Shenyan , Li Qian , Zhao Yingnan , Fan Xinjuan , Cui Yanfen , Zhao Ke , Liu Zaiyi
Published: May 2023

Correlation between DR and DFS
Supplementary Figure S1 from Desmoplastic reaction associates with prognosis and adjuvant chemotherapy response in colorectal cancer: a multicenter retrospective study
Authors: Hu Qingru , Wang Yiting , Yao Su , Mao Yun , Liu Liu , Li Zhenhui , Chen Yonghe , Zhang Shenyan , Li Qian , Zhao Yingnan , Fan Xinjuan , Cui Yanfen , Zhao Ke , Liu Zaiyi
Published: May 2023

Correlation between DR and T status, N status
Data from Targeting CHAF1B Enhances IFN Activity against Myeloproliferative Neoplasm Cells
Authors: Saleiro Diana , Kosciuczuk Ewa M. , Fischietti Mariafausta , Perez Ricardo E. , Yang G. Sohae , Eckerdt Frank , Beauchamp Elspeth M. , Hou Ye , Wang Qixuan , Weinberg Rona Singer , Fish Eleanor N. , Yue Feng , Hoffman Ronald , Platanias Leonidas C.
Published: May 2023

Interferons (IFNs) are cytokines with potent antineoplastic and antiviral properties. IFNα has significant clinical activity in the treatment of myeloproliferative neoplasms (MPN), but the precise mechanisms by which it acts are not well understood. Here, we demonstrate that chromatin assembly factor 1 subunit B (CHAF1B), an Unc-51-like kinase 1 (ULK1)-interactive protein in the nuclear compartment of malignant cells, is overexpressed in patients with MPN. Remarkably, targeted silencing of CHAF1B enhances transcription of IFNα-stimulated genes and promotes IFNα-dependent antineoplastic responses in primary MPN progenitor cells. Taken together, our findings indicate that CHAF1B is a promising newly identified therapeutic target in MPN and that CHAF1B inhibition in combination with IFNα therapy might offer a novel strategy for treating patients with MPN.
Significance:
Our findings raise the potential for clinical development of drugs targeting CHAF1B to enhance IFN antitumor responses in the treatment of patients with MPN and should have important clinical translational implications for the treatment of MPN and possibly in other malignancies.
Notch3/Hes5 Induces Vascular Dysfunction in Hypoxia-Induced Pulmonary Hypertension Through ER Stress and Redox-Sensitive Pathways
Authors: Morris Hannah E. , Neves Karla B. , Nilsen Margaret , Montezano Augusto C. , MacLean Margaret R. , Touyz Rhian M.
Published: May 2023

BACKGROUND:

Notch3 (neurogenic locus notch homolog protein 3) is implicated in vascular diseases, including pulmonary hypertension (PH)/pulmonary arterial hypertension. However, molecular mechanisms remain elusive. We hypothesized increased Notch3 activation induces oxidative and endoplasmic reticulum (ER) stress and downstream redox signaling, associated with procontractile pulmonary artery state, pulmonary vascular dysfunction, and PH development.

METHODS:

Studies were performed in TgNotch3
R169C
mice (harboring gain-of-function [GOF] Notch3 mutation) exposed to chronic hypoxia to induce PH, and examined by hemodynamics. Molecular and cellular studies were performed in pulmonary artery smooth muscle cells from pulmonary arterial hypertension patients and in mouse lung. Notch3-regulated genes/proteins, ER stress, ROCK (Rho-associated kinase) expression/activity, Ca
2+
transients and generation of reactive oxygen species, and nitric oxide were measured. Pulmonary vascular reactivity was assessed in the presence of fasudil (ROCK inhibitor) and 4-phenylbutyric acid (ER stress inhibitor).

RESULTS:

Hypoxia induced a more severe PH phenotype in TgNotch3
R169C
mice versus controls. TgNotch3
R169C
mice exhibited enhanced Notch3 activation and expression of Notch3 targets Hes Family BHLH Transcription Factor 5 (Hes5), with increased vascular contraction and impaired vasorelaxation that improved with fasudil/4-phenylbutyric acid. Notch3 mutation was associated with increased pulmonary vessel Ca
2+
transients, ROCK activation, ER stress, and increased reactive oxygen species generation, with reduced NO generation and blunted sGC (soluble guanylyl cyclase)/cGMP signaling. These effects were ameliorated by N-acetylcysteine. pulmonary artery smooth muscle cells from patients with pulmonary arterial hypertension recapitulated Notch3/Hes5 signaling, ER stress and redox changes observed in PH mice.

CONCLUSIONS:

Notch3 GOF amplifies vascular dysfunction in hypoxic PH. This involves oxidative and ER stress, and ROCK. We highlight a novel role for Notch3/Hes5-redox signaling and important interplay between ER and oxidative stress in PH.