bluuebunny/crossref_metadata_2025_split huggingface dataset:
Double diffraction imaging of x-ray induced structural dynamics in single free nanoparticles
Authors: Sauppe M , Bischoff T , Bomme C , Bostedt C , Colombo A , Erk B , Feigl T , Flückiger L , Gorkhover T , Heilrath A , Kolatzki K , Kumagai Y , Langbehn B , Müller J P , Passow C , Ramm D , Rolles D , Rompotis D , Schäfer-Zimmermann J , Senfftleben B , Treusch R , Ulmer A , Zimbalski J , Möller T , Rupp D 
Published: July 2024

Abstract
Because of their high photon flux, x-ray free-electron lasers (FEL) allow to resolve the structure of individual nanoparticles via coherent diffractive imaging (CDI) within a single x-ray pulse. Since the inevitable rapid destruction of the sample limits the achievable resolution, a thorough understanding of the spatiotemporal evolution of matter on the nanoscale following the irradiation is crucial. We present a technique to track x-ray induced structural changes in time and space by recording two consecutive diffraction patterns of the same single, free-flying nanoparticle, acquired separately on two large-area detectors opposite to each other, thus examining both the initial and evolved particle structure. We demonstrate the method at the extreme ultraviolet (XUV) and soft x-ray Free-electron LASer in Hamburg (FLASH), investigating xenon clusters as model systems. By splitting a single XUV pulse, two diffraction patterns from the same particle can be obtained. For focus intensities of about

2
×

10

12

W cm−2 we observe still largely intact clusters even at the longest delays of up to 650 picoseconds of the second pulse, indicating that in the highly absorbing systems the damage remains confined to one side of the cluster. Instead, in case of five times higher flux, the diffraction patterns show clear signatures of disintegration, namely increased diameters and density fluctuations in the fragmenting clusters. Future improvements to the accessible range of dynamics and time resolution of the approach are discussed.
The Rosenzweig–Porter model revisited for the three Wigner–Dyson symmetry classes
Authors: Čadež Tilen , Kumar Nandy Dillip , Rosa Dario , Andreanov Alexei , Dietz Barbara 
Published: July 2024

Abstract
Interest in the Rosenzweig–Porter model, a parameter-dependent random-matrix model which interpolates between Poisson and Wigner–Dyson (WD) statistics describing the fluctuation properties of the eigenstates of typical quantum systems with regular and chaotic classical dynamics, respectively, has come up again in recent years in the field of many-body quantum chaos. The reason is that the model exhibits parameter ranges in which the eigenvectors are Anderson-localized, non-ergodic (fractal) and ergodic extended, respectively. The central question is how these phases and their transitions can be distinguished through properties of the eigenvalues and eigenvectors. We present numerical results for all symmetry classes of Dyson’s threefold way. We analyzed the fluctuation properties in the eigenvalue spectra, and compared them with existing and new analytical results. Based on these results we propose characteristics of the short- and long-range correlations as measures to explore the transition from Poisson to WD statistics. Furthermore, we performed in-depth studies of the properties of the eigenvectors in terms of the fractal dimensions, the Kullback–Leibler (KL) divergences and the fidelity susceptibility. The ergodic and Anderson transitions take place at the same parameter values and a finite size scaling analysis of the KL divergences at the transitions yields the same critical exponents for all three WD classes, thus indicating superuniversality of these transitions.
Secant loci of scrolls over curves
Authors: Hitching George 
Published: July 2024

Given a curve

C
C

and a linear series

ℓ
\ell

on

C
C

, the secant locus

V
e

e
−
f

(
ℓ
)

V^{e-f}_e( \ell )

parametrises effective divisors of degree

e
e

which impose at most

e
−
f

e-f

conditions on

ℓ
\ell

. For

E
→
C

E \to C

a vector bundle of rank

r
r

, we define determinantal subschemes

H
e

e
−
f

(
ℓ
)
⊆

H
i
l
b

e

(

P

E
)

H^{e-f}_e ( \ell )\subseteq \mathrm {Hilb}^e ( \mathbb {P}E )

and

Q
e

e
−
f

(
V
)
⊆

Q
u
o
t

0
,
e

(

E
∗

)

Q^{e-f}_e(V)\subseteq \mathrm {Quot}^{0, e} ( E^* )

which generalise

V
e

e
−
f

(
ℓ
)

V^{e-f}_e( \ell )

, giving several examples. We describe the Zariski tangent spaces of

Q
e

e
−
f

(
V
)

Q^{e-f}_e(V)

, and give examples showing that smoothness of

Q
e

e
−
f

(
V
)

Q^{e-f}_e(V)

is not necessarily controlled by injectiveness of a Petri map. We generalise the Abel–Jacobi map and the notion of linear series to the context of Quot schemes.

We give some sufficient conditions for nonemptiness of generalised secant loci, and a criterion in the complete case when

f
=
1

f = 1

in terms of the Segre invariant

s
1

(
E
)

s_1 (E)

. This leads to a geometric characterisation of semistability similar to that in [Quot schemes, Segre invariants, and inflectional loci of scrolls over curves, Geom. Dedicata 205 (2020), 1–19]. Using these ideas, we also give a partial answer to a question of Lange on very ampleness of

O

P

E

(
1
)

\mathcal {O}_{\mathbb {P}E}(1)

, and show that for any curve,

Q
e

e
−
1

(
V
)

Q^{e-1}_e(V)

is either empty or of the expected dimension for sufficiently general

E
E

and

V
V

. When

Q
e

e
−
1

(
V
)

Q^{e-1}_e(V)

has and attains expected dimension zero, we use formulas of Oprea–Pandharipande and Stark to enumerate

Q
e

e
−
1

(
V
)

Q^{e-1}_e(V)

.

We mention several possible avenues of further investigation.
A multi-bin rarefying method for evaluating alpha diversities in TCR sequencing data
Authors: Li Mo , Hua Xing , Li Shuai , Wu Michael C , Zhao Ni 
Published: July 2024

Abstract

Motivation
T cell receptors (TCRs) constitute a major component of our adaptive immune system, governing the recognition and response to internal and external antigens. Studying the TCR diversity via sequencing technology is critical for a deeper understanding of immune dynamics. However, library sizes differ substantially across samples, hindering the accurate estimation/comparisons of alpha diversities. To address this, researchers frequently use an overall rarefying approach in which all samples are sub-sampled to an even depth. Despite its pervasive application, its efficacy has never been rigorously assessed.

Results
In this paper, we develop an innovative “multi-bin” rarefying approach that partitions samples into multiple bins according to their library sizes, conducts rarefying within each bin for alpha diversity calculations, and performs meta-analysis across bins. Extensive simulations using real-world data highlight the inadequacy of the overall rarefying approach in controlling the confounding effect of library size. Our method proves robust in addressing library size confounding, outperforming competing normalization strategies by achieving better-controlled type-I error rates and enhanced statistical power in association tests.

Availability and implementation
The code is available at https://github.com/mli171/MultibinAlpha. The datasets are freely available at https://doi.org/10.21417/B7001Z and https://doi.org/10.21417/AR2019NC.
Bromodomain-containing 4 is a Positive Regulator of the Inflammatory Cytokine Response in the Gut
Authors: Franzè Eleonora , Laudisi Federica , Maresca Claudia , Di Grazia Antonio , Iannucci Andrea , Pacifico Teresa , Ortenzi Angela , Sica Giuseppe , Lolli Elisabetta , Stolfi Carmine , Monteleone Ivan , Monteleone Giovanni 
Published: July 2024

Abstract

Background and Aim
Bromodomain-containing protein 4 [BRD4], one of the components of the bromodomain and extraterminal domain [BET] family, is a transcriptional and epigenetic regulator of cellular proliferation and cytokine production. In this study, we assessed whether BRD4 regulates the cytokine response in inflammatory bowel diseases [IBD].

Materials and Methods
BRD4 expression was analysed in intestinal mucosal samples of patients with ulcerative colitis [UC], patients with Crohn’s disease [CD], normal controls [CTRs], and mice with chemically-induced colitis, by real-time polymerase chain reaction [PCR], western blotting, and confocal microscopy. Cytokine production was evaluated in lamina propria mononuclear cells [LPMCs] of IBD patients and mucosal tissues of colitic mice treated with BRD4 inhibitors. Finally, we evaluated the effect of JQ1, an inhibitor of the BRD4 signalling pathway, on the course of murine colitis.

Results
BRD4 RNA and protein expression was up-regulated in the inflamed mucosa of patients with UC and patients with CD as compared with the uninvolved areas of the same patients and CTRs, and in the inflamed colon of colitic mice. Knockdown of BRD4 with a specific antisense oligonucleotide in IBD LPMCs led to reduced expression of TNF-α, IL-6, IFN-γ, and IL-17A. Administration of JQ1 to colitic mice inhibited the inflammatory cytokine response and attenuated the ongoing colitis.

Conclusions
This is the first study showing the up-regulation of BRD4 in IBD and suggesting the role of such a protein in the positive control of the inflammatory cytokine response in the gut.
Development and Investigation of a Non-invasive Disease Severity Index for Inflammatory Bowel Disease
Authors: Swaminathan Akhilesh , Borichevsky Grace Mary , Frampton Chris , Kettle Anthony James , Peyrin-Biroulet Laurent , Siegel Corey Allan , Day Andrew Stewart , Gearry Richard Blair 
Published: July 2024

Abstract

Introduction
The disease severity index [DSI] encapsulates the inflammatory bowel disease [IBD] burden but requires endoscopic investigations. This study developed a non-invasive DSI using faecal calprotectin [DSI-fCal] and faecal myeloperoxidase [DSI-fMPO] instead of colonoscopy.

Methods
Adults with IBD were recruited prospectively. Baseline biomarker concentrations were used to develop DSI-fCal and DSI-fMPO, and these were correlated with the original DSI, IBD symptoms, endoscopic activity, and quality of life [QoL]. Areas under the receiver operating characteristic curves [AUROC] assessed DSI-fCal and DSI-fMPO as predictors of clinical and biochemical remission at 6 months [symptom remission and fCal &lt; 150 μg/g, respectively], and a complicated IBD-course at 24 months [disease relapse needing escalation of biologics or immunomodulators, recurrent corticosteroids, IBD hospitalisations, and/or surgeries]. Multivariable logistic regression assessed the utility of DSI-fCal and DSI-fMPO in predicting a complicated IBD course at 24 months.

Results
In total, 171 patients were included (Crohn’s disease = 99, female = 90, median age = 46 years, interquartile range [IQR] 36–59]). DSI-fCal and DSI-fMPO correlated with the original DSI [r &gt; 0.9, p &lt; 0.001], endoscopic indices [r = 0.45–0.49, p &lt; 0.001], IBD symptoms [r = 0.53–0.58, p &lt; 0.001] and QoL [r = -0.57–0.58, p &lt; 0.001]. Baseline DSI-fCal [AUROC = 0.79, 95% CI 0.65–0.92] and DSI-fMPO [AUROC = 0.80, 95% CI 0.67–0.93] were associated with 6-month clinical and biochemical remission. DSI-fCal [AUROC = 0.83, 95% CI 0.77–0.89] and DSI-fMPO [AUROC = 0.80, 95% CI 0.73–0.87] performed similarly in predicting a complicated IBD course to the original DSI [pdifference &gt; 0.05]. The non-invasive DSI was independently associated with a complicated IBD course on multivariable analyses [DSI-fCal28, aOR = 6.04, 95% CI 2.42–15.08; DSI-fMPO25, aOR = 7.84, 95% CI 2.96–20.73].

Conclusions
The DSI-fCal and DSI-fMPO perform similarly in prognosticating the longitudinal disease course as the original DSI, whilst avoiding a need for an endoscopic assessment.
Microbial anabolic and catabolic utilization of hydrocarbons in deep subseafloor sediments of Guaymas Basin
Authors: Nagakura Toshiki , Morono Yuki , Ito Motoo , Mangelsdorf Kai , Pötz Stefanie , Schnabel Ellen , Kallmeyer Jens 
Published: July 2024

Abstract
Guaymas Basin, located in the Gulf of California, is a hydrothermally active marginal basin. Due to steep geothermal gradients and localized heating by sill intrusions, microbial substrates like short-chain fatty acids and hydrocarbons are abiotically produced from sedimentary organic matter at comparatively shallow depths. We analyzed the effect of hydrocarbons on uptake of hydrocarbons by microorganisms via nano-scale secondary ion mass spectrometry (NanoSIMS) and microbial sulfate reduction rates (SRR), using samples from two drill sites sampled by IODP Expedition 385 (U1545C and U1546D). These sites are in close proximity of each other (ca. 1 km) and have very similar sedimentology. Site U1546D experienced the intrusion of a sill that has since then thermally equilibrated with the surrounding sediment. Both sites currently have an identical geothermal gradient, despite their different thermal history. The localized heating by the sill led to thermal cracking of sedimentary organic matter and formation of potentially bioavailable organic substrates. There were low levels of hydrocarbon and nitrogen uptake in some samples from both sites, mostly in surficial samples. Hydrocarbon and methane additions stimulated SRR in near-seafloor samples from Site U1545C, while samples from Site U1546D reacted positively only on methane. Our data indicate the potential of microorganisms to metabolize hydrocarbons even in the deep subsurface of Guaymas Basin.
Natural forests support higher mycological diversity and more edible mushroom species than plantation forests in Ethiopia
Authors: Megersa Shasho , Yohannes Yonas , Dejene Tatek , Martín-Pinto Pablo 
Published: July 2024

Abstract
To identify measures to protect and conserve macrofungal communities in Ethiopian forests, we need a more comprehensive understanding of macrofungal diversity, functions, and fruiting body production. In this study, we assessed macrofungal communities in three forest types in Gambo Forest District, South-Central Ethiopia. We surveyed 18 plots (each 1000 m2) located in a clear-cut and replanted plantation forest, an old plantation forest, and a natural forest. We identified a total of 132 macrofungal species, of which 75% were saprotrophic, 16% were ectomycorrhizal, and 9% were plant pathogens. We identified 40 edible species, including economically important species, such as those from the genus of Agaricus, Morchella, Cantharellus, Suillus, and Termitomyces. The three forests were significantly different (P &lt; .001) in terms of their macrofungal community composition, with natural forest having the highest species richness and unique community assemblages. In total, 86 macrofungal species were collected from natural forest, of which 28 species were edible. The macrofungal diversity of clear-cut and old plantation forests did not differ significantly. Our findings suggest that prioritizing the restoration or preservation of fragmented natural forests rather than the expansion of exotic tree plantations would be a more effective strategy for conserving and enhancing macrofungal species diversity and the production of economically valuable edible species.
Chromosome-Scale Genome Assembly for Soft-Stem Bulrush (Schoenoplectus tabernaemontani) Confirms a Clade-Specific Whole-Genome Duplication in Cyperaceae
Authors: Li Yang , Ning Yu , Zheng Yan Chao , Lou Xuan Yu , Pan Zhe , Dong Shu Bin 
Published: July 2024

Abstract
Schoenoplectus tabernaemontani (C. C. Gmelin) Palla is a typical macrophyte in diverse wetland ecosystems. This species holds great potential in decontamination applications and carbon sequestration. Previous studies have shown that this species may have experienced recent polyploidization. This would make S. tabernaemontani a unique model to study the processes and consequences of whole-genome duplications in the context of the well-documented holocentric chromosomes and dysploidy events in Cyperaceae. However, the inference was not completely solid because it lacked homology information that is essential to ascertain polyploidy. We present here the first chromosome-level genome assembly for S. tabernaemontani. By combining Oxford Nanopore Technologies (ONT) long reads and Illumina short reads, plus chromatin conformation via the Hi-C method, we assembled a genome spanning 507.96 Mb, with 99.43% of Hi-C data accurately mapped to the assembly. The assembly contig N50 value was 3.62 Mb. The overall BUSCO score was 94.40%. About 68.94% of the genome was comprised of repetitive elements. A total of 36,994 protein-coding genes were predicted and annotated. Long terminal repeat retrotransposons accounted for ∼26.99% of the genome, surpassing the content observed in most sequenced Cyperid genomes. Our well-supported haploid assembly comprised 21 pseudochromosomes, each harboring putative holocentric centromeres. Our findings corroborated a karyotype of 2n = 2X = 42. We also confirmed a recent whole-genome duplication occurring after the divergence between Schoenoplecteae and Bolboschoeneae. Our genome assembly expands the scope of sequenced genomes within the Cyperaceae family, encompassing the fifth genus. It also provides research resources on Cyperid evolution and wetland conservation.
A Chromosome-Level Genome Assembly and Annotation for theOecanthus rufescens(Orthoptera: Oecanthidae)
Authors: Jing Xuan , Zhao Hui-Yao , Zheng Yan-Na , Nie Yi-Meng , Ma Li-Bin , Huang Yuan 
Published: July 2024

AbstractOecanthus is a genus of cricket known for its distinctive chirping and distributed across major zoogeographical regions worldwide. This study focuses on Oecanthus rufescens, and conducts a comprehensive examination of its genome through genome sequencing technologies and bioinformatic analysis. A high-quality chromosome-level genome of O. rufescens was successfully obtained, revealing significant features of its genome structure. The genome size is 877.9 Mb, comprising ten pseudo-chromosomes and 70 other sequences, with a GC content of 41.38% and an N50 value of 157,110,771 bp, indicating a high level of continuity. BUSCO assessment results demonstrate that the genome's integrity and quality are high (of which 96.8% are single-copy and 1.6% are duplicated). Comprehensive genome annotation was also performed, identifying approximately 310 Mb of repetitive sequences, accounting for 35.3% of the total genome sequence, and discovering 15,481 tRNA genes, 4,082 rRNA genes, and 1,212 other noncoding genes. Furthermore, 15,031 protein-coding genes were identified, with BUSCO assessment results showing that 98.4% (of which 96.3% are single-copy and 1.6% are duplicated) of the genes were annotated.
Carbapenem combination therapy versus standard of care for persistent methicillin-susceptible Staphylococcus aureus bacteraemia
Authors: Shah Sunish , Clarke Lloyd G , Ludwig Justin , Burgdorf Sarah , Arbulu Guerra Ricardo D , Shields Ryan K 
Published: July 2024

Abstract

Background
Successful use of carbapenems in combination with cefazolin or oxacillin for treatment of MSSA bacteraemia has been described; however, comparative data to standard treatment approaches are lacking.

Methods
This was a multicentre, retrospective study of adult patients with MSSA bacteraemia for &gt;48 h. Standard treatment was considered monotherapy with cefazolin, oxacillin or nafcillin. Combination therapy was defined as the addition of ertapenem or meropenem to standard treatment for at least 24 h. The primary outcome was duration of bacteraemia defined as time from administration of an antibiotic with in vitro activity to first negative blood culture. Time to blood culture sterilization was compared through risk-set matching with aid of a propensity score.

Results
Overall, 238 patients were included; 66% (157/238) received standard treatment and 34% (81/238) received combination therapy. The median (IQR) time to carbapenem initiation was 4.7 (3.63–6.5) days. Patients who received combination therapy were younger (P = 0.012), more likely to have endocarditis (P = 0.034) and had longer median duration of bacteraemia (P &lt; 0.001). After applying risk-set matching, patients who received combination therapy experienced faster time to blood culture sterilization compared with control patients [HR = 1.618 (95% CI; 1.119–2.339) P = 0.011]. Using a paired hazard model, 90 day mortality rates were not statistically different among patients who received combination therapy versus matched controls [HR = 1.267 (95% CI; 0.610–2.678), P = 0.608].

Discussion
Carbapenem combination therapy resulted in faster time to blood culture sterilization, but no differences in overall mortality rates. Randomized trials are critical to determine the utility of carbapenem combination therapy.
The interactive effects of medicinal dyes with conventional antimicrobials against skin pathogens
Authors: Ramfol Rhea , van Vuuren Sandy 
Published: July 2024

Abstract

Aims
This study aimed to explore potential synergistic effects of medicinal dyes with antimicrobials against pathogens responsible for skin infections.

Methods and results
Antimicrobial testing was conducted using minimum inhibitory concentrations and minimum bactericidal/fungicidal concentration assays. The fractional inhibitory index (ΣFIC) of combinations was calculated, and isobolograms were constructed on selected combinations. Toxicity studies were conducted using the brine-shrimp lethality assay. Combination (1:1 ratio) studies noted that 26% of dye-antibiotic combinations were synergistic against the Gram-positive strains, 15% against the Gram-negative strains, and 14% against the yeasts. The Mercurochrome: Betadine® combination noted synergy at ratios against all the Staphylococcus aureus strains with ΣFIC values ranging from 0.05 to 0.48. The combination of Gentian violet with Gentamycin noted a 15-fold decrease in toxicity, and a selectivity index of 977.50 against the Escherichia coli (DSM 22314) strain. Time-kill studies were conducted on the combinations with the highest safe selectivity index (SI) value and lowest safe SI value i.e. Gentian violet with Gentamycin and Malachite green with Neomycin. Both combinations demonstrated better antimicrobial activity in comparison to the independent values and the controls.

Conclusion
This study highlights the potential for medicinal dye combinations as a treatment for skin infections.
A Quantitative Review of Certified Burn Therapist’s Involvement in the JBCR Publications and ABA Leadership
Authors: Warthman Renée , O’Neil Audrey M , Murray Derek , Nedelec Bernadette , Islas Claudia , Foster Kevin N 
Published: July 2024

Abstract
The Burn Therapist Certification (BT-C) was introduced in 2018 to acknowledge occupational therapists (OT) and physical therapists (PT) with specialized knowledge, skill, and experience in the promotion of quality burn rehabilitation. Currently, BT-Cs make up 11.7% of therapists working in burn rehabilitation (n = 39/333). The purpose of this review is to report on the contributions of BT-Cs to organizational leadership of the American Burn Association (ABA) and in the generation of new knowledge through peer-reviewed publications. Despite the small percentage of burn therapists who are certified, they have a disproportionately large involvement in leadership within the ABA and burn research in the Journal of Burn Care and Rehabilitation (JBCR). From 2018 to 2023, BT-Cs have contributed to nearly one-half (n = 26/56) of therapy authored publications in the JBCR and almost one-third (n = 65/202) of accepted abstracts at the ABA annual meeting. Certified burn therapists demonstrate substantial involvement throughout the ABA, including maintaining an 85% membership rate and, on average, serve in 53% (n = 31/59) of the therapy allotted committee positions. Therapist pursuit of certification can have a profound impact on the burn community through publication, leadership, and development of care standards. Although therapists have indicated a desire to pursue certification, barriers related to a lack of association and center support have been identified. The burn community has endorsed certification as a mark of excellence for nurses and physicians. Maximizing the value of a transdisciplinary approach to burn care is also dependent on the excellence of therapies. If the burn community desires improved engagement and contribution from therapies, it should support therapist certification.