bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient markerless genetic manipulation of
Pasteurella multocida
using
lacZ
and
pheS
m as selection markers
Authors: Jiang Jinfei , Zhao Yishan , Chen Aihua , Sun Juan , Zhou Mengruo , Hu Jialian , Cao Xuewei , Dai Ning , Liang Zhaoping , Feng Saixiang 
Published: March 2024

ABSTRACT

Pasteurella multocida
is a zoonotic conditional pathogen that infects multiple livestock species, causing substantial economic losses in the animal husbandry industry. An efficient markerless method for gene manipulation may facilitate the investigations of
P. multocida
gene function and pathogenesis of
P. multocida
. Herein, a temperature-sensitive shuttle vector was constructed using
lacZ
as a selection marker, and markerless
glgB
,
opa
, and
hyaE
mutants of
P. multocida
were subsequently constructed through blue–white colony screening. The screening efficiency of markerless deletion strains was improved by the
lacZ
system, and the method could be used for multiple gene deletions. However, the
fur
mutant was unavailable via this method. Therefore, we constructed a
pheS
m screening system based on mutated phenylalanine tRNA synthetase as a counterselection marker to achieve
fur
deletion mutant. The transformed strain was sensitive to 20 mM
p
-chloro-phenylalanine, demonstrating the feasibility of
pheS
m as a counter-selective marker. The
pheS
m system was used for markerless deletions of
glgB
,
opa
, and
hyaE
as well as
fur
that could not be screened by the
lacZ
system. A comparison of screening efficiencies of the system showed that the
pheS
m counterselection system was more efficient than the
lacZ
system and broadly applicable for mutant screening. The methods developed herein may provide valuable tools for genetic manipulation of
P. multocida
.

IMPORTANCE

Pasteurella multocida
is a highly contagious zoonotic pathogen. An understanding of its underlying pathogenic mechanisms is of considerable importance and requires efficient species-specific genetic tools. Herein, we propose a screening system for
P. multocida
mutants using
lacZ
or
pheS
m screening markers. We evaluated the efficiencies of both systems, which were used to achieve markerless deletion of multiple genes. The results of this study support the use of
lacZ
or
pheS
m as counterselection markers to improve counterselection efficiency in
P. multocida
. This study provides an effective genetic tool for investigations of the virulence gene functions and pathogenic mechanisms of
P. multocida
.
Assessment of Perfusion Volumes by a New Automated Software for Computed Tomography Perfusion
Authors: Cao Zhixin , Wang David , Feng Xueyan , Yang Pengfei , Wang Hao , Xu Ziqi , Hao Yahui , Ye Wanxing , Chen Fengwei , Wang Liyuan , Hao Manjun , Wu Na , Yang Kai-Xuan , Xiong Yunyun , Wang Yongjun 
Published: March 2024

IntroductionTo compare the perfusion volumes assessed by a new automated CT perfusion (CTP) software iStroke with the circular singular value decomposition software RAPID and determine its predictive value for functional outcome in patients with acute ischaemic stroke (AIS) who underwent endovascular treatment (EVT).MethodsData on patients with AIS were collected from four hospitals in China. All patients received CTP followed by EVT with complete recanalisation within 24 hours of symptom onset. We evaluated the agreement of CTP measures between the two softwares by Spearman’s rank correlation tests and kappa tests. Bland-Altman plots were used to evaluate the agreement of infarct core volume (ICV) on CTP and ground truth on diffusion-weighted imaging (DWI). Logistic regression models were used to test the association between ICV on these two softwares and functional outcomes.ResultsAmong 326 patients, 228 had DWI examinations and 40 of them had infarct volume >70 mL. In all patients, the infarct core and hypoperfusion volumes on iStroke had a strong correlation with those on RAPID (ρ=0.68 and 0.66, respectively). The agreement of large infarct core (volume >70 mL) was substantial (kappa=0.73, p<0.001) between these two softwares. The ICV measured by iStroke and RAPID was significantly correlated with independent functional outcome at 90 days (p=0.009 and p<0.001, respectively). In patients with DWI examinations and those with an ICV >70 mL, the ICV of iStroke and RAPID was comparable on individual agreement with ground truth.ConclusionThe automatic CTP software iStroke is a reliable tool for assessing infarct core and mismatch volumes, making it clinically useful for selecting patients with AIS for acute reperfusion therapy in the extended time window.
Thermodynamic properties of disordered quantum spin ladders
Authors: Vatansever Erol , Grahovski Georgi G. , Fytas Nikolaos G. 
Published: March 2024

Abstract
In this paper, we study the thermodynamic properties of spin-1/2 antiferromagnetic Heisenberg ladders by means of the stochastic series expansion quantum Monte Carlo technique. This includes the thermal properties of the specific heat, uniform and staggered susceptibilities, spin gap, and structure factor. Our numerical simulations are probed over a large ensemble of random realizations in a wide range of disorder strengths r, from the clean ($$r=0$$

r
=
0

) case up to the diluted ($$r \rightarrow 1$$

r
→
1

) limit, and for selected choices of number of legs $$L_y$$

L
y

per site. Our results show some interesting phenomena, like the presence of crossing points in the temperature plane for both the specific heat and uniform susceptibility curves which appear to be universal in r, as well as a variable dependence of the spin gap in the amount of disorder upon increasing $$L_y$$

L
y

.

Graphical Abstract
Correlation function for the $$a_0(980)$$
Authors: Molina R. , Liu Zhi-Wei , Geng Li-Sheng , Oset E. 
Published: March 2024

AbstractWe have conducted a model independent analysis of the $$K^+ \bar{K}^0$$

K
+

K

¯

0

pair correlation function obtained from ultra high energy pp collisions, with the aim of extracting the information encoded in it related to the $$K\bar{K}$$

K

K

¯

interaction and the coupled channel $$\pi ^+ \eta $$

π
+

η

. With the present large errors at small relative $$K^+\bar{K}^0$$

K
+

K

¯

0

momenta, we find that the information obtained about the scattering matrix suffers from large uncertainties. Even then, we are able to show that the data imply the existence of the $$a_0$$

a
0

resonance, $$a_0(980)$$

a
0

(
980
)

, showing as a strong cusp close to the $$K\bar{K}$$

K

K

¯

threshold. We also mention that the measurement of the $$\pi ^+ \eta $$

π
+

η

correlation function will be essential in order to constrain more the information on $$K\bar{K}$$

K

K

¯

dynamics that can be obtained from correlation functions.
Some Lp norm involving the polar derivative of a polynomial
Authors: Wani Irfan Ahmad , Mir Mohammad Ibrahim , Nazir Ishfaq 
Published: March 2024

Let [Formula: see text], [Formula: see text], is a polynomial of degree [Formula: see text] having all zeros in [Formula: see text], [Formula: see text], then for [Formula: see text] with [Formula: see text], [Formula: see text] and for each [Formula: see text] with [Formula: see text]; it was proved by (N. A. Rather et al., Some [Formula: see text] inequalities involving the polar derivative of a polynomial, Appl. Math. E-Notes 14 (2014) 116–122) [Formula: see text] [Formula: see text] In this paper, we establish some refinements and generalizations of above and some known polynomial inequalities concerning the polar derivative of a polynomial.
Hepatitis B Virus–Mediated m6A Demethylation Increases Hepatocellular Carcinoma Stemness and Immune Escape
Authors: Meng Yuting , Shu Zheyue , Wang Xueyao , Hong Liang , Wang Baohua , Jiang Jingjing , He Kangxin , Cao Qingyi , Shi Fan , Wang Hai , Gong Lan , Diao Hongyan 
Published: March 2024

Abstract

Hepatitis B viral (HBV) persistent infection plays a significant role in hepatocellular carcinoma (HCC) tumorigenesis. Many studies have revealed the pivotal roles of N6-methyladenosine (m6A) in multiple cancers, while the regulatory mechanism in stemness maintenance of HBV persistent infection-related HCC remains elusive. Here, we demonstrated that the level of m6A modification was downregulated by HBV in HBV-positive HCC, through enhanced stability of ALKBH5 mRNA. More specifically, we also identified that ALKBH5 mRNA was functionally required for the stemness maintenance and self-renewal in the HBV-positive HCC, but dispensable in HBV-negative HCC. Mechanistically, ALKBH5 demethylated the m6A modification in the 3′ untranslated region of the oncogenic gene SNAI2 to prevent the recognition of YTHDF2 therewith stabilize SNAI2 transcripts, contributing to cancer stem cell traits in HBV-positive HCC. Moreover, the expression of SNAI2 reversed the suppression of stemness properties by knocking down ALKBH5. In addition, ALKBH5/SNAI2 axis accelerates tumor immune evasion through activated ligand of immune checkpoint CD155. Our study unveiled that the ALKBH5 induces m6A demethylation of the SNAI2 as a key regulator in HBV-related HCC, and identifies the function of ALKBH5/SNAI2/YTHDF2 axis in promoting the stem-like cells phenotype and immune escape during HBV infection.

Implications:
HBV promotes HCC stemness maintenance through elevate m6A modification of SNAI2 in an ALKBH5-YTHDF2–dependent manner and increases the expression of the ligand of immune checkpoint CD155.
Gut Microbiota and Blood Metabolites Related to Fiber Intake and Type 2 Diabetes
Authors: Wang Zheng , Peters Brandilyn A. , Yu Bing , Grove Megan L. , Wang Tao , Xue Xiaonan , Thyagarajan Bharat , Daviglus Martha L. , Boerwinkle Eric , Hu Gang , Mossavar-Rahmani Yasmin , Isasi Carmen R. , Knight Rob , Burk Robert D. , Kaplan Robert C. , Qi Qibin 
Published: March 2024

BACKGROUND:
Consistent evidence suggests diabetes-protective effects of dietary fiber intake. However, the underlying mechanisms, particularly the role of gut microbiota and host circulating metabolites, are not fully understood. We aimed to investigate gut microbiota and circulating metabolites associated with dietary fiber intake and their relationships with type 2 diabetes (T2D).

METHODS:
This study included up to 11 394 participants from the HCHS/SOL (Hispanic Community Health Study/Study of Latinos). Diet was assessed with two 24-hour dietary recalls at baseline. We examined associations of dietary fiber intake with gut microbiome measured by shotgun metagenomics (350 species/85 genera and 1958 enzymes; n=2992 at visit 2), serum metabolome measured by untargeted metabolomics (624 metabolites; n=6198 at baseline), and associations between fiber-related gut bacteria and metabolites (n=804 at visit 2). We examined prospective associations of serum microbial-associated metabolites (n=3579 at baseline) with incident T2D over 6 years.

RESULTS:

We identified multiple bacterial genera, species, and related enzymes associated with fiber intake. Several bacteria (eg,
Butyrivibrio
,
Faecalibacterium
) and enzymes involved in fiber degradation (eg, xylanase EC3.2.1.156) were positively associated with fiber intake, inversely associated with prevalent T2D, and favorably associated with T2D-related metabolic traits. We identified 159 metabolites associated with fiber intake, 47 of which were associated with incident T2D. We identified 18 of these 47 metabolites associated with the identified fiber-related bacteria, including several microbial metabolites (eg, indolepropionate and 3-phenylpropionate) inversely associated with the risk of T2D. Both
Butyrivibrio
and
Faecalibacterium
were associated with these favorable metabolites. The associations of fiber-related bacteria, especially
Faecalibacterium
and
Butyrivibrio
, with T2D were attenuated after further adjustment for these microbial metabolites.

CONCLUSIONS:
Among United States Hispanics/Latinos, dietary fiber intake was associated with favorable profiles of gut microbiota and circulating metabolites for T2D. These findings advance our understanding of the role of gut microbiota and microbial metabolites in the relationship between diet and T2D.
PRERISK: A Personalized, Artificial Intelligence–Based and Statistically–Based Stroke Recurrence Predictor for Recurrent Stroke
Authors: Colangelo Giorgio , Ribo Marc , Montiel Estefanía , Dominguez Didier , Olivé-Gadea Marta , Muchada Marian , Garcia-Tornel Álvaro , Requena Manuel , Pagola Jorge , Juega Jesús , Rodriguez-Luna David , Rodriguez-Villatoro Noelia , Rizzo Federica , Taborda Belén , Molina Carlos A. , Rubiera Marta 
Published: March 2024

BACKGROUND:
Predicting stroke recurrence for individual patients is difficult, but individualized prediction may improve stroke survivors’ engagement in self-care. We developed PRERISK: a statistical and machine learning classifier to predict individual risk of stroke recurrence.

METHODS:
We analyzed clinical and socioeconomic data from a prospectively collected public health care–based data set of 41 975 patients admitted with stroke diagnosis in 88 public health centers over 6 years (2014–2020) in Catalonia-Spain. A new stroke diagnosis at least 24 hours after the index event was considered as a recurrent stroke, which was considered as our outcome of interest. We trained several supervised machine learning models to provide individualized risk over time and compared them with a Cox regression model. Models were trained to predict early, late, and long-term recurrence risk, within 90, 91 to 365, and >365 days, respectively. C statistics and area under the receiver operating characteristic curve were used to assess the accuracy of the models.

RESULTS:

Overall, 16.21% (5932 of 36 114) of patients had stroke recurrence during a median follow-up of 2.69 years. The most powerful predictors of stroke recurrence were time from previous stroke, Barthel Index, atrial fibrillation, dyslipidemia, age, diabetes, and sex, which were used to create a simplified model with similar performance, together with modifiable vascular risk factors (glycemia, body mass index, high blood pressure, cholesterol, tobacco dependence, and alcohol abuse). The areas under the receiver operating characteristic curve were 0.76 (95% CI, 0.74–0.77), 0.60 (95% CI, 0.58–0.61), and 0.71 (95% CI, 0.69–0.72) for early, late, and long-term recurrence risk, respectively. The areas under the receiver operating characteristic curve of the Cox risk class probability were 0.73 (95% CI, 0.72–0.75), 0.59 (95% CI, 0.57–0.61), and 0.67 (95% CI, 0.66–0.70); machine learning approaches (random forest and AdaBoost) showed statistically significant improvement (
P
<0.05) over the Cox model for the 3 recurrence time periods. Stroke recurrence curves can be simulated for each patient under different degrees of control of modifiable factors.

CONCLUSIONS:
PRERISK is a novel approach that provides a personalized and fairly accurate risk prediction of stroke recurrence over time. The model has the potential to incorporate dynamic control of risk factors.
Creolization as Decolonial Theory
Authors: Drabinski John E. 
Published: March 2024

Abstract
What does Édouard Glissant have to contribute to theorizing decolonization and a philosophy of difference? And how is this contribution tied to rethinking place (from Caribbean to Caribbeanness) and world (comprised of creolized culture and identity)? This essay takes up Glissant’s work in the context of questions of history and memory, with particular focus on how historical experience grounds philosophical work on place and world through articulations of identity, language, cultural production, and thinking after catastrophe. Drawing from a contrast with Martin Heidegger and Walter Benjamin, this essay shows how Glissant’s critical concept “creolization” works as an expression of what I call “the afropostmodern,” and also as an important contribution to decolonial theories of world, culture, memory, language, and subjectivity after the Middle Passage.
The International Maritime Organization’s Revised Greenhouse Gas Strategy: A Political Signal of Shipping’s Regulatory Future
Authors: Friedman Andrew 
Published: March 2024

Abstract
The International Maritime Organization (IMO) 2023 Strategy on Reduction of GHG Emission from Ships offers few specifics from a legal perspective, but is an important political signal. IMO Member States have committed to adopt binding rules to incentivise greenhouse gas emission reductions in 2025 which will enter into force by 2027. Moreover, the Strategy calls for the elimination of shipping emissions by or around 2050 and sets checkpoints to track progress. IMO now faces key decisions to implement the Strategy, including how to structure a goal-based fuel standard, how to integrate an economic element (e.g., an emission levy) into its regulatory framework, its methods for assessing upstream emissions and effects of fuel production, and specific reduction pathways. These measures will likely be effectuated as amendments to Annex VI of the International Convention for the Prevention of Pollution from Ships, leveraging its existing compliance and enforcement tools, including port State controls.
The Turbulence of Postcolonial Displacement, Exclusion and Racism in Tahar Ben Jelloun’s Les Yeux Baissés
Authors: Baba Nouzha 
Published: March 2024

Abstract
This article examines the Moroccan-French author, Tahar Ben Jelloun’s novel Les Yeux Baissés, translated as With Downcast Eyes. A winner of the Prix Goncourt, the author narrates the challenges of postcolonial displacement, exclusion and racism in a French multicultural neighbourhood. The novel explores the theme of displacement as one that is two-fold: firstly, it refers to the migration process, while secondly, it foregrounds the socio-cultural dimension of being “out of place” in the diaspora. I delve into the way migrants’ children experience the turbulence of displacement, exclusion, and racism. While engaging with postcolonial theoretical debates, this study considers the representation of migrants’ alienation in the narrative resulting from a lack of French hospitality and acute hostility. As such, this article demonstrates that postcolonial displacement does not enable the homogenization of cultures, but rather reinforces boundaries, at the social and cultural level, in the diaspora.
Toward Building a Virtual Laboratory to Investigate Rainfall Microphysics at Process Scales
Authors: Ji Lihui , Barros Ana P. 
Published: March 2024

Abstract
A 3D numerical model was built to serve as a virtual microphysics laboratory (VML) to investigate rainfall microphysical processes. One key goal for the VML is to elucidate the physical basis of warm precipitation processes toward improving existing parameterizations beyond the constraints of past physical experiments. This manuscript presents results from VML simulations of classical tower experiments of raindrop collisional collection and breakup. The simulations capture large raindrop oscillations in shape and velocity in both horizontal and vertical planes and reveal that drop instability increases with diameter due to the weakening of the surface tension compared with the body force. A detailed evaluation against reference experimental datasets of binary collisions over a wide range of drop sizes shows that the VML reproduces collision outcomes well including coalescence, and disk, sheet, and filament breakups. Furthermore, the VML simulations captured spontaneous breakup, and secondary coalescence and breakup. The breakup type, fragment number, and size distribution are analyzed in the context of collision kinetic energy, diameter ratio, and relative position, with a view to capture the dynamic evolution of the vertical microstructure of rainfall in models and to interpret remote sensing measurements.

Significance Statement
Presently, uncertainty in precipitation estimation and prediction remains one of the grand challenges in water cycle studies. This work presents a detailed 3D simulator to characterize the evolution of drop size distributions (DSDs), without the space and functional constraints of laboratory experiments. The virtual microphysics laboratory (VML) is applied to replicate classical tower experiments from which parameterizations of precipitation processes used presently in weather and climate models and remote sensing algorithms were derived. The results presented demonstrate that the VML is a robust tool to capture DSD dynamics at the scale of individual raindrops (precipitation microphysics). VML will be used to characterize DSD dynamics across scales for environmental conditions and weather regimes for which no measurements are available.
Clinical and treatment characteristics of infants and toddlers less than 2 years of age with hemophilia
Authors: Han Jennifer H. , Dupervil Brandi , Mahajerin Arash , Kulkarni Roshni , Manco-Johnson Marilyn , Thornburg Courtney 
Published: March 2024

Abstract
Infants and toddlers (ITs) with hemophilia have unique bleeding features. Factor prophylaxis has been shown to decrease the risk of intracranial hemorrhage (ICH), which supports recommendations to begin at a young age. Clinical and demographic characteristics were analyzed for 883 ITs ≤2 years old with hemophilia A and B, seen at US Hemophilia Treatment Centers and enrolled in the Community Counts Registry, a surveillance program of the Centers for Disease Control and Prevention. ICH in the first 2 years of life was seen in 68 of 883 (7.7%) ITs, of whom 8 of 68 (11.8%) were on continuous prophylaxis at the time of ICH. ITs in this study usually started prophylaxis within the first year of life (mean, 10.3 months), with earlier ages of prophylaxis initiation in later birth cohorts in ITs with hemophilia A. Compared with those without a family history (FH) of hemophilia, known positive FH of hemophilia was associated with earlier age of diagnosis (P ≤ .0001) and decreased rates of vaginal delivery (P = .0006). The use of factor VIII mimetics and extended half-life clotting factor prophylaxis increased with later birth cohorts for ITs with hemophilia A and B. The study highlights that ICH rates in ITs with hemophilia remains substantial and underscores the need for further research to identify modifiable risk factors to prevent ICH by earlier diagnosis and initiating prophylaxis early, even within the first month of life.