bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flagellar point mutation causes social aggregation in laboratory-adapted
Bacillus subtilis
under conditions that promote swimming
Authors: Alvi Safiya , Mondelo V. Denise , Boyle Jacqueline , Buck Amanda , Gejo Justin , Mason Molly , Matta Shriya , Sheridan Abigail , Kreutzberger Mark A. B. , Egelman Edward H. , McLoon Anna 
Published: September 2024

ABSTRACT

Motility allows microbes to explore and maximize success in their environment; however, many laboratory bacterial strains have a reduced or altered capacity for motility. Swimming motility in
Bacillus subtilis
depends on peritrichous flagella and is carried out individually as cells move by biased random walks toward attractants. Previously, we adapted
Bacillus subtilis
strain 3610 to the laboratory for 300 generations in lysogeny broth (LB) batch culture and isolated lab-adapted strains. Strain SH2 is motility-defective and in broth culture forms large, frequently spherical aggregates of cells. A single point mutation in the flagellin gene
hag
that causes amino acid 259 to switch from A to T is necessary and sufficient to cause these social cell aggregates, and aggregation occurs between flagellated cells bearing this point mutation regardless of the strain background. Cells associate when bearing this mutation, but flagellar rotation is needed to pull associating cells into spherical aggregates. Using electron microscopy, we are able to show that the SH2 flagellar filament has limited polymorphism when compared to other flagellar structures. This limited polymorphism hinders the flagellum’s ability to function as a motility apparatus but appears to alter its function to that of cell aggregation/adhesion. We speculate that the genotype-specific aggregation of cells producing Hag
A259T
flagella could have increased representation in a batch-culture experiment by allowing similar cells to go through a transfer together and also that this mutation could serve as an early step to evolve sociality in the natural world.

IMPORTANCE
The first life forms on this planet were prokaryotic, and the earliest environments were aquatic, and from these relatively simple starting conditions, complex communities of microbes and ultimately multicellular organisms were able to evolve. Usually, motile cells in aqueous environments swim as individuals but become social by giving up motility and secreting extracellular substances to become a biofilm. Here, we identify a single point mutation in the flagellum that is sufficient to allow cells containing this mutation to specifically form large, suspended groups of cells. The specific change in the flagellar filament protein subunits causes a unique change in the flagellar structure. This could represent a distinct way for closely related cells to associate as an early precursor to sociality.
The combination of three CD4-induced antibodies targeting highly conserved Env regions with a small CD4-mimetic achieves potent ADCC activity
Authors: Marchitto Lorie , Richard Jonathan , Prévost Jérémie , Tauzin Alexandra , Yang Derek , Chiu Ta-Jung , Chen Hung-Ching , Díaz-Salinas Marco A. , Nayrac Manon , Benlarbi Mehdi , Beaudoin-Bussières Guillaume , Anand Sai Priya , Dionne Katrina , Bélanger Étienne , Chatterjee Debashree , Medjahed Halima , Bourassa Catherine , Tolbert William D. , Hahn Beatrice H. , Munro James B. , Pazgier Marzena , Smith Amos B. , Finzi Andrés 
Published: September 2024

ABSTRACT

The majority of naturally elicited antibodies against the HIV-1 envelope glycoproteins (Env) are non-neutralizing (nnAbs) because they are unable to recognize the Env trimer in its native “closed” conformation. Nevertheless, it has been shown that nnAbs have the potential to eliminate HIV-1-infected cells by antibody-dependent cellular cytotoxicity (ADCC) provided that Env is present on the cell surface in its “open” conformation. This is because most nnAbs recognize epitopes that become accessible only after Env interaction with CD4 and the exposure of epitopes that are normally occluded in the closed trimer. HIV-1 limits this vulnerability by downregulating CD4 from the surface of infected cells, thus preventing a premature encounter of Env with CD4. Small CD4-mimetics (CD4mc) sensitize HIV-1-infected cells to ADCC by opening the Env glycoprotein and exposing CD4-induced (CD4i) epitopes. There are two families of CD4i nnAbs, termed anti-cluster A and anti-CoRBS Abs, which are known to mediate ADCC in the presence of CD4mc. Here, we performed Fab competition experiments and found that anti-gp41 cluster I antibodies comprise a major fraction of the plasma ADCC activity in people living with HIV (PLWH). Moreover, addition of gp41 cluster I antibodies to cluster A and CoRBS antibodies greatly enhanced ADCC-mediated cell killing in the presence of a potent indoline CD4mc, CJF-III-288. This cocktail outperformed broadly neutralizing antibodies and even showed activity against HIV-1-infected monocyte-derived macrophages. Thus, combining CD4i antibodies with different specificities achieves maximal ADCC activity, which may be of utility in HIV cure strategies.

IMPORTANCE
The elimination of HIV-1-infected cells remains an important medical goal. Although current antiretroviral therapy decreases viral loads below detection levels, it does not eliminate latently infected cells that form the viral reservoir. Here, we developed a cocktail of non-neutralizing antibodies targeting highly conserved Env regions and combined it with a potent indoline CD4mc. This combination exhibited potent ADCC activity against HIV-1-infected primary CD4 + T cells as well as monocyte-derived macrophages, suggesting its potential utility in decreasing the size of the viral reservoir.
The complete mitochondrial genome of the banana pathogen
Fusarium oxysporum
f. sp.
cubense
M5
Authors: Maldonado-Bonilla Luis David , Caballero-Pérez Juan , Ángeles-Argáiz Rodolfo Enrique 
Published: September 2024

ABSTRACT

We report the complete mitochondrial genome of a causal agent of banana fusarium wilt isolated in Mexico. The whole set of genes encoding proteins related to respiration and ATP synthesis, rRNAs, tRNAs are enlisted. Two open reading frames of unknown function conserved in
Fusarium oxysporum
were also identified.
Complete genome sequence of
Synechocystis
sp. LKSZ1 isolated from a pond in the Suzukakedai campus of Tokyo Institute of Technology
Authors: Okumura Leonardo Ken , Masuda Shinji 
Published: September 2024

ABSTRACT

Cyanobacteria belonging to the
Synechocystis
genus have been isolated from diverse aquatic environments. This announcement reports the complete genome sequence of
Synechocystis
sp. LKSZ1 newly isolated from a pond in a university campus in Yokohama, Japan. The genome sequencing was performed using the PacBio Revio HiFi long-read technology.
Complete genome sequence of
E. coli
lytic bacteriophage BAU.Micro_ELP-22, isolated from sewage water, Bangladesh
Authors: Kallol Md. Arefin , Nazir K.H.M. Nazmul Hussain , Alam Jahangir , Rahman Md. Bahanur , Rahman Marzia 
Published: September 2024

ABSTRACT

Escherichia coli
lytic bacteriophage BAU.Micro_ELP-22 was isolated from sewage wastewater as a therapeutic agent alternative to antibiotics. The phage genome is 373,488 bp in length, encoding 744 protein-coding sequences and 7 tRNAs, and contains no antibiotic resistance, virulence, or temperate marker genes, which specifies its potentiality as a compatible phage therapy candidate.
Complete genome sequences of four lytic bacteriophages against multidrug-resistant
Enterococcus faecium
Authors: Soro Oumarou , Kigen Collins , Nyerere Andrew , Gachoya Moses , Wachira James , Onyonyi Vanessa , Georges Martin , Wataka Allan , Ondolo Stephen , Cherono Karen , Odoyo Erick , Musila Lillian 
Published: September 2024

ABSTRACT

We report the genome sequences of four
Enterococcus faecium
phages isolated from environmental wastewater in Kenya. They are double-stranded DNA phages with genomes varying in length from 42,231 to 43,348 bp, with G+C contents ranging from 34.96% to 35.2%. The genomes contain 78–82 coding sequences.
First draft genome sequence of a
Pectobacterium polaris
strain isolated in South Africa from potato tuber affected by soft rot
Authors: Dapuliga Christiana C. , Claussen Maike , Schmidt Stefan 
Published: September 2024

ABSTRACT

A phytopathogenic strain of
Pectobacterium polaris
(designated SRB2) was isolated for the first time in South Africa from a potato tuber affected by soft rot. The draft genome of strain SRB2 encodes various plant cell wall-degrading enzymes and genes associated with biofilm formation and virulence. Antibiotic resistance genes were not detected.
Risk of hepatic events associated with use of sodium-glucose cotransporter-2 inhibitors versus glucagon-like peptide-1 receptor agonists, and thiazolidinediones among patients with metabolic dysfunction-associated steatotic liver disease
Authors: Bea Sungho , Ko Hwa Yeon , Bae Jae Hyun , Cho Young Min , Chang Yoosoo , Ryu Seungho , Byrne Christopher D , Shin Ju-Young 
Published: September 2024

Objective
To examine the hepatic effectiveness of sodium-glucose cotransporter-2 inhibitors (SGLT-2i) through a head-to-head comparison with glucagon-like peptide-1 receptor agonists (GLP-1RA) or thiazolidinediones (TZD) in patients with metabolic dysfunction-associated steatotic liver disease (MASLD).

Design
This population-based cohort study was conducted using a nationwide healthcare claims database (2014–2022) of Korea. We included individuals with MASLD (aged ≥40 years) who initiated SGLT-2i or comparator drugs (GLP-1RA or TZD). Primary outcome was a composite of hepatic decompensation events, including ascites, oesophageal varices with bleeding, hepatic failure or liver transplant. Liver-cause death and all-cause death were also assessed as secondary outcomes. Cox proportional hazards models were used to estimated HRs with 95% CIs.

Results
After 1:1 propensity score matching, we included 22 550 patients who initiated SGLT-2i and GLP-1RA (median age=57 years, 60% male), and 191 628 patients who initiated SGLT-2i and TZD (median age=57 years, 72% male). Compared with GLP-1RA, SGLT-2i showed a similar risk of hepatic decompensation events (HR 0.93, 95% CI 0.76 to 1.14). Compared with TZD, SGLT-2i demonstrated a reduced risk of hepatic decompensation events (HR 0.77, 95% CI 0.72 to 0.82). As compared with TZD, the results of secondary analyses showed significantly lower hepatic decompensation event risks with SGLT-2i when stratified by sex (male: HR 0.87 (95% CI 0.80–0.94); female: HR 0.62 (95% CI 0.55–0.69)).

Conclusions
In this nationwide cohort study, SGLT-2i was associated with a lower risk of hepatic decompensation events in patients with MASLD compared with TZD, while demonstrating similar effectiveness to GLP-1RA.
Whether mTICI 3 or mTICI 2b is better in patients with vertebrobasilar artery occlusion undergoing endovascular treatment depends on pc-ASPECTS
Authors: Zhang Pan , Chen Ping , Xu Yingjie , Hu Miaomiao , Wang Ruyue , Li Zhanglin , Alexandre Andrea M , Pedicelli Alessandro , Broccolini Aldobrando , Scarcia Luca , Liu Xinfeng , Sun Wen 
Published: September 2024

BackgroundThe clinical relevance of differentiating between mTICI (modified Thrombolysis In Cerebral Infarction) 2b and mTICI 3 in patients with vertebrobasilar artery occlusion (VBAO) remains unclear. This study aimed to investigate whether mTICI 3 improves functional outcomes compared with mTICI 2b in patients with VBAO and whether this improvement differs according to extent of ischemic damage.MethodsThis retrospective study enrolled patients with VBAO within 24 hours of the estimated occlusion time at 65 stroke centers in a nationwide registration in China. The primary outcome was favorable functional outcome (modified Rankin scale score 0–3) at 90 days. Patients were matched by final mTICI grade using propensity score matching (PSM) and inverse probability of treatment weighting (IPTW). Logistic regression and ordinal regression models were used to assess the impact of mTICI 2b versus mTICI 3 grading on prognosis, based on different extent of ischemia damage (posterior circulation Alberta Stroke Program Early CT Score—pc-ASPECTS of 9–10, 7–8, and 3–6) and treatment strategies (bridging therapy and direct endovascular therapy (EVT)).ResultsA total of 2075 patients with VBAO and successful reperfusion were included, 652 patients (31.4%) achieved mTICI 2b and 1423 patients (68.6%) achieved mTICI 3. After adjustment for confounders, achieving mTICI 3 following EVT in patients with VBAO and pc-ASPECTS 9–10 (OR 1.54, 95% CI 1.16 to 2.03) and pc-ASPECTS 7–8 (OR 1.80, 95% CI (1.26 to 2.56) were associated with favorable functional outcome compared with mTICI 2b, especially in those receiving direct EVT. However, in patients with pc-ASPECTS≤6, functional outcomes at 90 days did not differ between mTICI 3 and mTICI 2b (OR 1.12, 95% CI 0.67 to 1.88), irrespective of using bridging therapy or direct EVT.ConclusionIn patients with VBAO undergoing EVT with pc-ASPECTS>6, achieving mTICI 3 favors better outcomes compared with mTICI 2b, especially in those receiving direct EVT. However, in patients with pc-ASPECTS≤6, mTICI 3 did not improve functional outcomes compared with mTICI 2b. Interventionalists should carefully assess the risk-benefit of additional maneuvers once mTICI 2b reperfusion is restored in EVT for patients with VBAO and pc-ASPECTS≤6. Further studies are needed to guide treatment decisions in these cases.
Associations between work-related factors and sickness presenteeism: a prospective study using the national French working conditions survey
Authors: Niedhammer Isabelle , Pineau Elodie , Bertrais Sandrine 
Published: September 2024

ObjectivesThe objectives were to assess the prospective associations between work-related factors, including psychosocial and physical work factors and working time/hours factors, and sickness presenteeism alone or combined with sickness absence.MethodsThe study relied on prospective data of a national representative sample of 16 129 employees followed up from 2013 to 2016 in France. Work-related factors were assessed in 2013 and included 20 psychosocial work factors, 4 working time/hours factors and 4 physical work factors. Sickness presenteeism was studied using two items in 2016: the presence and duration of sickness presenteeism within the last 12 months. Weighted Hurdle and multinomial logistic regression models were performed to study the prospective associations between work-related factors at baseline and sickness presenteeism (both presence and duration) and sickness absence at follow-up. Models were adjusted for covariates.ResultsAlmost all psychosocial and physical work factors were predictive of sickness presenteeism (ORs ranging from 1.30 to 2.07 for men, and from 1.16 to 2.30 for women) but only some of them predicted its duration. Dose–response associations were observed between multiple exposures to these factors and sickness presenteeism. These factors predicted more sickness presenteeism alone or combined with sickness absence than sickness absence alone. Gender differences were observed in these associations, as some associations were found to be stronger among women than among men.ConclusionsThere is a need to study sickness presenteeism and sickness absence combined. Prevention oriented towards the psychosocial and physical work environment may contribute to reduce sickness presenteeism and sickness absence.
Systematic evaluation of generative machine learning capability to simulate distributions of observables at the large hadron collider
Authors: Gavranovič Jan , Kerševan Borut Paul 
Published: September 2024

AbstractMonte Carlo simulations are a crucial component when analysing the Standard Model and New physics processes at the Large Hadron Collider. This paper aims to explore the performance of generative models for complementing the statistics of classical Monte Carlo simulations in the final stage of data analysis by generating additional synthetic data that follows the same kinematic distributions for a limited set of analysis-specific observables to a high precision. Several deep generative models are adapted for this task and their performance is systematically evaluated using a well-known benchmark sample containing the Higgs boson production beyond the Standard Model and the corresponding irreducible background. The paper evaluates the autoregressive models and normalizing flows and the applicability of these models using different model configurations is investigated. The best performing model is chosen for a further evaluation using a set of statistical procedures and a simplified physics analysis. By implementing and performing a series of statistical tests and evaluations we show that a machine-learning-based generative procedure can be used to generate synthetic data that matches the original samples closely enough and that it can therefore be incorporated in the final stage of a physics analysis with some given systematic uncertainty.
A quantitative approach to reflectance transformation imaging in profilometric applications
Authors: Verni Eleonora , Fiocco Giacomo , Grifoni Emanuela , Lippolis Giulia , Ludwig Nicola , Malagodi Marco , Pisani Marco , Rovetta Tommaso , Zucco Massimo , Gargano Marco 
Published: September 2024

AbstractReflectance transformation imaging (RTI) is a technique employed to assess both the intensity and directional properties of light reflected from an object, aiming to visualize an object under different incident light directions. This technique has quickly become a commonly used approach for the documentation, acquisition and deciphering for cultural heritage objects, because it enables to enhance and highlight image details. The output of this mathematical synthesis technique, which elaborates illumination information, is contained in a pseudocolour image called normal map. Starting from this image, this technique allows to obtain the reconstruction of the outline of semi-flat objects by integrating the normal map given by the RTI, i.e. normal integration. The technique of normal integration has been known for many years, being widely used in graphical modelling across various fields of 3D imaging. In the context of cultural heritage, this particular form of 3D modelling has already found application in the reconstruction of semi-flat objects, albeit with some limitations in the accurate portraying of low spatial frequencies. However, quantitative and systematic studies on the efficiency of 3D rendering of objects using RTI and normal integration have not yet been conducted. In the context of this research, the quantitative evaluation of the accuracy of the RTI technique with normal integration for profilometric applications on semi-flat objects is proposed and a study on its fidelity in reproducing the considered artefact is conducted. For this purpose, ad hoc profilometric targets were designed, realized and analysed to quantitatively compare the results of RTI and normal integration with different standardized techniques: micro-photogrammetry, laser scanning and optical profilometry.
Graphical abstract
Online Fast Assessment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Proliferation Through Replication
Authors: Ansari Mohammad Zaheer 
Published: September 2024

Purpose. A virus, when it infects a host organism, multiplies its ribonucleic acid (RNA) to make it more harmful. We analyze if a view-based temporal template method, the motion history image (MHI) algorithm, may be of use to extract information on the progression of viral interactions over time. Methods. We employ an alternative online processing modality to comprehend and analyze the replication dynamics of severe acute respiratory syndrome coronavirus 2 (SARS CoV 2). The data are evaluated using the computation of a quantitative algorithm, the absolute value of differences (AVD), followed by the generation of temporal template map, the MHI of viral contact. Results. We show that the MHI identifies various stages to examine cultural characteristics and information on the progression of viral interactions over time. The results are more easily obtained compared to a visual inspection of the frames constituting the recordings. MHI also has the advantage of relying on a simple algorithm. The AVD index further provides deeper insights into the dynamics of the viral interaction over time, and its measurement suggests that SARS CoV-2 virus is becoming more widespread. This study shows that the replication process damages the host cell over time, in addition to causing SARS CoV-2 to proliferate. Conclusions. The MHI provides a framework for automated feature extraction from time series data. The combined approach results in decreased computational complexity and enables online assessment of the assay. Clinical and research studies can be conducted to evaluate MHI and AVD and their utility in aiding diagnostic analysis.
Beyond "Taming Electric Scooters": Disentangling Understandings of Micromobility Naturalistic Riding
Authors: Tabatabaie Mahan , He Suining , Wang Hao , Shin Kang G. 
Published: September 2024

Electric(e)-scooters have emerged as a popular, ubiquitous, and first/last-mile micromobility transportation option within and across many cities worldwide. With the increasing situation-awareness and on-board computational capability, such intelligent micromobility has become a critical means of understanding the rider's interactions with other traffic constituents (called Rider-to-X Interactions, RXIs), such as pedestrians, cars, and other micromobility vehicles, as well as road environments, including curbs, road infrastructures, and traffic signs. How to interpret these complex, dynamic, and context-dependent RXIs, particularly for the rider-centric understandings across different data modalities --- such as visual, behavioral, and textual data --- is essential for enabling safer and more comfortable micromobility riding experience and the greater good of urban transportation networks.
Under a naturalistic riding setting (i.e., without any unnatural constraint on rider's decision-making and maneuvering), we have designed, implemented, and evaluated a pilot Cross-modality E-scooter Naturalistic Riding Understanding System, namely CENRUS, from a human-centered AI perspective. We have conducted an extensive study with CENRUS in sensing, analyzing, and understanding the behavioral, visual, and textual annotation data of RXIs during naturalistic riding. We have also designed a novel, efficient, and usable disentanglement mechanism to conceptualize and understand the e-scooter naturalistic riding processes, and conducted extensive human-centered AI model studies. We have performed multiple downstream tasks enabled by the core model within CENRUS to derive the human-centered AI understandings and insights of complex RXIs, showcasing such downstream tasks as efficient information retrieval and scene understanding. CENRUS can serve as a foundational system for safe and easy-to-use micromobility rider assistance as well as accountable use of micromobility vehicles.
KLF3 impacts insulin sensitivity and glucose uptake in skeletal muscle
Authors: Fu Shuying , Gong Xiaocheng , Liang Keying , Ding Ke , Qiu Li , Cen Huice , Du Hongli 
Published: September 2024

The knockdown of Klf3 increased glucose uptake and improved insulin sensitivity in L6 myotubes, whereas its overexpression had the opposite effect. To explore the underlying mechanisms, we evaluated the transcriptional profiles of L6 myotubes after Klf3 knockdown and overexpression and revealed that metabolism and insulin-related pathways were significantly impacted. Klf3 also influenced the expression or modification of glucose transporter 4 (GLUT4), protein kinase B (AKT), TBC1 domain family member 1 (TBC1D1), and TBC1 domain family member 4 (TBC1D4) in the insulin signaling pathway, affecting insulin sensitivity and glucose uptake.