bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protocol on Mutation Induction in Coffee Using In Vitro Tissue Cultures
Authors: Laimer Margit , Boro Rashmi , Hanzer Veronika , Ogwok Emmanuel , Borroto Fernandez Eduviges G. 
Published: September 2023

AbstractPathogens are the major limiting factors in coffee production. Approximately 26% of the global annual coffee production is lost to diseases, threatening the income of approx. 125 million people worldwide. Therefore, reducing coffee yield losses by improving coffee resistance to diseases and insect attacks through breeding can make a major contribution to agricultural sustainability. Mutation breeding in vegetatively propagated and perennial crops is hampered in large part due to bottlenecks in the induction of variation (lack of recombination) and challenges in screening. Tissue culture approaches using alternative types of material were developed. This offers a clear advantage of providing the required sample size for mutation induction and subsequent screening within a reasonable time frame. The protocols developed compare different tissue culture systems for mutation induction involving unicellular and multicellular explants requiring different numbers of subsequent subcultures to reduce the impact of chimerism: (a) axillary shoot culture for the provision of donor material for mutation induction and regeneration; (b) leaf disc cultures for the induction of calli; (c) direct and indirect somatic embryogenesis for the production of somatic embryos; (d) the irradiation of somatic embryos at the globular and cotyledonary stage. Mutagenesis was induced by irradiation with a Cobalt-60 Gamma-source at the FAO/IAEA Laboratories in Seibersdorf, Austria. A comparison of the time required for the regeneration of high numbers (hundreds) of plantlets from irradiated in vitro shoots versus irradiated embryogenic calli is clearly in favor of embryogenic calli, since the plantlets regenerate from individual cells and can be used for genotypic and phenotypic analyses directly. This chapter describes the general methods for mutation induction using gamma irradiation and the procedures that can be used to generate large numbers of induced mutants in different tissues of coffee under in vitro conditions.
Mutation Induction Using Gamma-Ray Irradiation and High Frequency Embryogenic Callus from Coffee (Coffea arabica L.)
Authors: Barquero-Miranda Miguel , Céspedes Reina 
Published: September 2023

AbstractMutation induction through chemical or physical mutagenesis has been widely used for crop improvement for more than 70 years. Coffee is one of the most important crops in Latin-America, and, as any other crop, it can be affected by pests and diseases. Coffee leaf rust (CLR), caused by the biotrophic fungus Hemileia vastatrix, is the most important disease affecting Arabica coffee leading to significant losses for growers. As a perennial crop, conventional breeding of Arabica coffee is time-consuming. Plant tissue culture in combination with mutation induction techniques can provide an alternative approach to increase genetic variability of Arabica coffee for breeding applications. The present chapter describes protocols to establish embryogenic callus suspensions from Arabica coffee cv Venecia and for gamma ray irradiation of callus suspension cultures to achieve genetic improvement in the crop.
Chemical Mutagenesis of Embryogenic Cell Suspensions of Coffea arabica L. var. Catuaí Using EMS and NaN3
Authors: Gatica-Arias Andrés , Bolívar-González Alejandro 
Published: September 2023

AbstractChemical mutagens, such as ethyl methanesulfonate (EMS) and sodium azide (NaN3), interact with DNA and can primarily induce single base modifications along the genome. Populations derived from chemical mutagenesis experiments are presumed to harbor high density of point mutations in the genome. Therefore, this technique, along with in vitro culture methods such as somatic embryogenesis (SE), can introduce genetic variation in otherwise genetically homogeneous populations. In vitro mutagenesis of embryogenic cell suspension cultures represents an efficient method to quickly develop mutant plantlets of unicellular origin. The development of mutant populations in this important crop represents a fundamental steppingstone in the development of novel varieties and the characterization of candidate genes involved in traits such as disease resistance, grain metabolite content and flowering induction. This chapter describes the protocol for establishment of embryogenic cell suspension cultures as well as methods of mutation induction using EMS and NaN3 on embryogenic cell suspensions of C. arabica, variety Catuaí. Furthermore, this chapter includes a protocol for mutant plant regeneration in in vitro conditions.
Vorbemerkungen zum politischen, institutionellen und historischen Hintergrund
Authors: Möller Ellen Franziska 
Published: September 2023

ZusammenfassungDas Philosophische Seminar der Universität zu Köln unterhält seit 2013 eine forschungsfähige Einheit, die empirisch zu Fragen des Philosophierens mit Kindern forscht. Das Forschungsprojekt Philosophie in der Primarstufe wird zusätzlich auch von zivilgesellschaftlicher Seite, namentlich durch den Kölner Gymnasial- undStiftungsfonds, finanziell unterstützt. Im Rahmen dieses Forschungsprojekts ist auch die vorliegende Studie entstanden. Dieses einleitende Kapitel verschafft einen kurzen Überblick darüber, vor welchem politischen, institutionellen und historischen Hintergrund die vorliegende Studie entwickelt wurde.
Offene Auswertung: Was geschieht…
Authors: Möller Ellen Franziska 
Published: September 2023

ZusammenfassungDie fokussierte Auswertung, die auf dem Analyseinstrument nach Daniel und Gagnon beruht (vgl. Kap. 10), legt insbesondere dar, welcher Stufe des Abstrakten die kindlichen Äußerungen nach Einsatz eines Kürzesttexts zuzuordnen sind. Einen detaillierten Einblick in das tatsächliche Unterrichtsgeschehen liefert diese Auswertung allerdings nicht: Was genau in den Lerngruppen nach Einsatz eines Kürzesttexts geschieht, bildet die fokussierte Auswertung unzureichend ab. Denn durch die Fokussierung auf die Stufen des Abstrakten gehen bedeutsame Informationen verloren, die durch das Analyseinstrument nicht erfasst werden.
Zentrale Herausforderung
Authors: Möller Ellen Franziska 
Published: September 2023

ZusammenfassungAn dieser Stelle ist eine Gegenüberstellung des bisher Erörterten angezeigt. Das Philosophieren mit Kindern wird aus zwei Richtungen betrachtet: Es werden Besonderheiten des Philosophierens mit Kindern herausgestellt, indem der Begriff Philosophieren definiert wird als ein Prozess, der ein abstraktes Element enthält (vgl. Kap. 3). Es werden Besonderheiten herausgestellt, die insbesondere für das Philosophieren mit Kindern gelten, indem Kinder dazu neigen, im Anschaulichen zu verharren (vgl. Kap. 4).
Transverse momentum distributions of heavy hadrons and polarized heavy quarks
Authors: von Kuk Rebecca , Michel Johannes K. L. , Sun Zhiquan 
Published: September 2023

Abstract
We initiate the study of transverse momentum-dependent (TMD) fragmentation functions for heavy quarks, demonstrate their factorization in terms of novel nonperturbative matrix elements in heavy-quark effective theory (HQET), and prove new TMD sum rules that arise from heavy-quark spin symmetry. We discuss the phenomenology of heavy-quark TMD FFs at B factories and find that the Collins effect, in contrast to claims in the literature, is not parametrically suppressed by the heavy-quark mass. We further calculate all TMD parton distribution functions for the production of heavy quarks from polarized gluons within the nucleon and use our results to demonstrate the potential of the future EIC to resolve TMD heavy-quark fragmentation in semi-inclusive DIS, complementing the planned EIC program to use heavy quarks as probes of gluon distributions.
The osteogenic and mineralogenic potential of the microalgae Skeletonema costatum and Tetraselmis striata CTP4 in fish models
Authors: Carletti Alessio , Rosa Joana T. , Pes Katia , Borges Inês , Santos Tamára , Barreira Luísa , Varela João , Pereira Hugo , Cancela M. Leonor , Gavaia Paulo J. , Laizé Vincent 
Published: September 2023

AbstractSkeletal disorders are problematic aspects for the aquaculture industry as skeletal deformities, which affect most species of farmed fish, increase production costs and affect fish welfare. Following recent findings that show the presence of osteoactive compounds in marine organisms, we evaluated the osteogenic and mineralogenic potential of commercially available microalgae strains Skeletonema costatum and Tetraselmis striata CTP4 in several fish systems. Ethanolic extracts increased extracellular matrix mineralization in gilthead seabream (Sparus aurata) bone-derived cell cultures and promoted osteoblastic differentiation in zebrafish (Danio rerio) larvae. Long-term dietary exposure to both extracts increased bone mineralization in zebrafish and upregulated the expression of genes involved in bone formation (sp7, col1a1a, oc1, and oc2), bone remodeling (acp5a), and antioxidant defenses (cat, sod1). Extracts also improved the skeletal status of zebrafish juveniles by reducing the incidence of skeletal anomalies. Our results indicate that both strains of microalgae contain osteogenic and mineralogenic compounds, and that ethanolic extracts have the potential for an application in the aquaculture sector as dietary supplements to support fish bone health. Future studies should also identify osteoactive compounds and establish whether they can be used in human health to broaden the therapeutic options for bone erosive disorders such as osteoporosis.
Elevated remnant cholesterol and atherosclerotic cardiovascular disease in diabetes: a population-based prospective cohort study
Authors: Wadström Benjamin N. , Pedersen Kasper M. , Wulff Anders B. , Nordestgaard Børge G. 
Published: September 2023

Abstract
Aims/hypothesis
Elevated remnant cholesterol is observationally and causally associated with increased risk of atherosclerotic cardiovascular disease (ASCVD) in the general population. This association is not well studied in individuals with diabetes, who are often included in clinical trials of remnant cholesterol-lowering therapy. We tested the hypothesis that elevated remnant cholesterol is associated with increased risk of ASCVD in individuals with diabetes. We also explored the fraction of excess risk conferred by diabetes which can be explained by elevated remnant cholesterol.

Methods
We included 4569 white Danish individuals with diabetes (58% statin users) nested within the Copenhagen General Population Study (2003–2015). The ASCVDs peripheral artery disease, myocardial infarction and ischaemic stroke were extracted from national Danish health registries without losses to follow-up. Remnant cholesterol was calculated from a standard lipid profile.

Results
During up to 15 years of follow-up, 236 individuals were diagnosed with peripheral artery disease, 234 with myocardial infarction, 226 with ischaemic stroke and 498 with any ASCVD. Multivariable adjusted HR (95% CI) per doubling of remnant cholesterol was 1.6 (1.1, 2.3; p=0.01) for peripheral artery disease, 1.8 (1.2, 2.5; p=0.002) for myocardial infarction, 1.5 (1.0, 2.1; p=0.04) for ischaemic stroke, and 1.6 (1.2, 2.0; p=0.0003) for any ASCVD. Excess risk conferred by diabetes was 2.5-fold for peripheral artery disease, 1.6-fold for myocardial infarction, 1.4-fold for ischaemic stroke and 1.6-fold for any ASCVD. Excess risk explained by elevated remnant cholesterol and low-grade inflammation was 14% and 8% for peripheral artery disease, 26% and 16% for myocardial infarction, 34% and 34% for ischaemic stroke, and 24% and 18% for any ASCVD, respectively. LDL-cholesterol did not explain excess risk, as it was not higher in individuals with diabetes. We also explored the fraction of excess risk conferred by diabetes which can be explained by elevated remnant cholesterol.

Conclusions/interpretation
Elevated remnant cholesterol was associated with increased risk of ASCVD in individuals with diabetes. Remnant cholesterol and low-grade inflammation explained substantial excess risk of ASCVD conferred by diabetes. Whether remnant cholesterol should be used as a treatment target remains to be determined in randomised controlled trials.

Graphical Abstract
How do German pharmacologists publish in the non-peer-reviewed science magazine Biospektrum?
Authors: Zöllner Helena , Seifert Roland 
Published: September 2023

AbstractPublications in peer-reviewed journals are the most important currency in science. But what about publications in non-peer-reviewed magazines? The objective of this study was to analyze the publications of scientists, with a focus on pharmacologists, in the non-peer-reviewed German science magazine Biospektrum from 1999 to 2021. Biospektrum is edited by five scientific societies in Germany including the Society for Experimental and Clinical Society Pharmacology and Toxicology (DGPT) and provides opportunities to researchers to showcase their research to a broad audience. We analyzed 3197 authors of 1326 articles. Compared to the fields of biochemistry, microbiology, and genetics, pharmacology was largely underrepresented. Just three institutions in Germany contributed most papers to Biospektrum. Researchers with a doctoral degree were the largest author group, followed by researchers with a habilitation degree. Among all major fields, women were underrepresented as authors, particularly as senior authors. The Covid pandemic leads to a drop of publications of female first authors but not last authors. Compared to publications in the peer-reviewed journal Naunyn–Schmiedeberg’s Archives of Pharmacology (Zehetbauer et al., Naunyn-Schmiedebergs Arch Pharmacol 395:39–50 (2022)), female pharmacologists were underrepresented in the Biospektrum. Thus, German pharmacologists as a group do not value investing in “social impact” gained by publications in Biospektrum, and this attitude is even more prominent among female pharmacologists. Investing less in “social impact” by female pharmacologists may result in reduced visibility on the academic job market and may contribute to reduced opportunities to achieve high academic positions.
Carbon ion radiotherapy combined with immunotherapy: synergistic anti-tumor efficacy and preliminary investigation of ferroptosis
Authors: Huang Qingting , Hu Jiyi , Chen Li , Lin Wanzun , Yang Jing , Hu Weixu , Gao Jing , Zhang Haojiong , Lu Jiade Jay , Kong Lin 
Published: September 2023

AbstractCarbon ion radiotherapy (CIRT) may yield satisfactory clinical outcomes for patients who are resistant to radiotherapy. However, the therapeutic impact of carbon ions is still limited in certain recurring or refractory tumors. Therefore, we aimed to evaluate the synergistic anti-tumor effects of immune checkpoint inhibitors (ICIs) in combination with CIRT. We then explored the involvement of ferroptosis in a preliminary investigation. A tumor-bearing mouse model was established, and mice were inoculated subcutaneously with B16-OVA cells into the flanks of both hind legs. Mice were assigned to four groups to receive CIRT, ICIs, or combined treatment. Thereafter, we conducted transcriptome sequencing (RNA-seq), bioinformatics analysis, and various immune-related experiments on the available tumor tissues to investigate differences in the synergistic anticancer effects and potential mechanisms across the groups. The combination therapies significantly improved the survival of mice and inhibited tumor growth, both at local and distant sites. Based on bioinformatics and RNA-seq data, immune-related pathways and genes, immune cell infiltration, and the production of cytokines and chemokines were the most enhanced in the combined treatment group compared to other groups. Finally, we identified a potential role for ferroptosis in the development of local anti-tumor synergy during CIRT combination treatment. In conclusion, this study showed that CIRT and ICIs can enhance the anti-tumor immune effects. We also proposed that ferroptosis may induce anti-tumor effects in CIRT combination therapy, offering a unique perspective on its ability to enhance immunotherapy responses.
Evaluation of simultaneous multi-slice acquisition with advanced processing for free-breathing diffusion-weighted imaging in patients with liver metastasis
Authors: Rata Mihaela , De Paepe Katja N. , Orton Matthew R. , Castagnoli Francesca , d’Arcy James , Winfield Jessica M. , Hughes Julie , Stemmer Alto , Nickel Marcel Dominik , Koh Dow-Mu 
Published: September 2023

Abstract
Objectives
Diffusion-weighted imaging (DWI) with simultaneous multi-slice (SMS) acquisition and advanced processing can accelerate acquisition time and improve MR image quality. This study evaluated the image quality and apparent diffusion coefficient (ADC) measurements of free-breathing DWI acquired from patients with liver metastases using a prototype SMS-DWI acquisition (with/without an advanced processing option) and conventional DWI.

Methods
Four DWI schemes were compared in a pilot 5-patient cohort; three DWI schemes were further assessed in a 24-patient cohort. Two readers scored image quality of all b-value images and ADC maps across the three methods. ADC measurements were performed, for all three methods, in left and right liver parenchyma, spleen, and liver metastases. The Friedman non-parametric test (post-hoc Wilcoxon test with Bonferroni correction) was used to compare image quality scoring; t-test was used for ADC comparisons.

Results
SMS-DWI was faster (by 24%) than conventional DWI. Both readers scored the SMS-DWI with advanced processing as having the best image quality for highest b-value images (b750) and ADC maps; Cohen’s kappa inter-reader agreement was 0.6 for b750 image and 0.56 for ADC maps. The prototype SMS-DWI sequence with advanced processing allowed a better visualization of the left lobe of the liver. ADC measured in liver parenchyma, spleen, and liver metastases using the SMS-DWI with advanced processing option showed lower values than those derived from the SMS-DWI method alone (t-test, p < 0.0001; p < 0.0001; p = 0.002).

Conclusions
Free-breathing SMS-DWI with advanced processing was faster and demonstrated better image quality versus a conventional DWI protocol in liver patients.

Clinical relevance statement
Free-breathing simultaneous multi-slice- diffusion-weighted imaging (DWI) with advanced processing was faster and demonstrated better image quality versus a conventional DWI protocol in liver patients.

Key Points
• Diffusion-weighted imaging (DWI) with simultaneous multi-slice (SMS) can accelerate acquisition time and improve image quality.
• Apparent diffusion coefficients (ADC) measured in liver parenchyma, spleen, and liver metastases using the simultaneous multi-slice DWI with advanced processing were significantly lower than those derived from the simultaneous multi-slice DWI method alone.
• Simultaneous multi-slice DWI sequence with inline advanced processing was faster and demonstrated better image quality in liver patients.
Intraoperative neurophysiology in pediatric neurosurgery: a historical perspective
Authors: Sala Francesco 
Published: September 2023

Abstract
Introduction
Intraoperative neurophysiology (ION) has been established over the past three decades as a valuable discipline to improve the safety of neurosurgical procedures with the main goal of reducing neurological morbidity. Neurosurgeons have substantially contributed to the development of this field not only by implementing the use and refinement of ION in the operating room but also by introducing novel techniques for both mapping and monitoring of neural pathways.

Methods
This review provides a personal perspective on the evolution of ION in a variety of pediatric neurosurgical procedures: from brain tumor to brainstem surgery, from spinal cord tumor to tethered cord surgery.

Results and discussion
The contribution of pediatric neurosurgeons is highlighted showing how our discipline has played a crucial role in promoting ION at the turn of the century. Finally, a view on novel ION techniques and their potential implications for pediatric neurosurgery will provide insights into the future of ION, further supporting the view of a functional, rather than merely anatomical, approach to pediatric neurosurgery.
Comparison of the optimal and suboptimal quantity of mitotype libraries using next-generation sequencing
Authors: Obal Marcel , Zupanc Tomaž , Zupanič Pajnič Irena 
Published: September 2023

AbstractOptimizing analysis parameters and sample input is crucial in forensic genetics methods to generate reliable results, and even more so when working with muti-copy mitochondrial DNA (mtDNA) and low-quality samples. This study compared mitotypes based on next-generation sequencing (NGS) results derived from the same samples at two different sequencing library concentrations—30 pM and 0.3 pM. Thirty femur samples from the Second World War were used as a model for poorly preserved DNA. Quantitative PCR (qPCR) method targeting 113 bp long fragment was employed to assess the quantity of mitogenomes. HID Ion Chef™ Instrument with Precision ID mtDNA Control Region Panel was used for library preparation and templating. Sequencing was performed with Ion GeneStudio™ S5 System. Reference haplotypes were determined from sequencing samples at 30 pM library input. Haplotypes were compared between optimal (30 pM) and suboptimal (0.3 pM) library inputs. Often the difference in haplotypes was length heteroplasmy, which in line with other studies shows that this type of variant is not reliable for interpretation in forensics. Excluding length variants at positions 573, 309, and 16,193, 56.7% of the samples matched, and in two samples, no sequence was obtained at suboptimal library input. The rest of the samples differed between optimal and suboptimal library input. To conclude, genotyping and analyzing low-quantity libraries derived from low-quality aged skeletonized human remains therefore must be done with caution in forensic genetics casework.
A nonlocal free boundary problem with Wasserstein distance
Authors: Karakhanyan Aram L. 
Published: September 2023

AbstractWe study the probability measures $$\rho \in \mathcal M(\mathbb R^{2})$$

ρ
∈
M
(

R
2

)

minimizing the functional $$\begin{aligned} J[\rho ]=\iint \log \frac{1}{|x-y|}d\rho (x)d\rho (y)+d^2(\rho , \rho _0), \end{aligned}$$

J

[
ρ
]

=
∬
log

1

|
x
-
y
|

d
ρ

(
x
)

d
ρ

(
y
)

+

d
2

(
ρ
,

ρ
0

)

,

where $$\rho _0$$

ρ
0

is a given probability measure and $$d(\rho , \rho _0)$$

d
(
ρ
,

ρ
0

)

is the 2-Wasserstein distance of $$\rho $$
ρ
and $$\rho _0$$

ρ
0

. $$J[\rho ]$$

J
[
ρ
]

appears in aggregation models when the movement of particles is advanced by the potential $$-\log |x|*\rho $$

-
log
|
x
|

∗
ρ

. We prove the existence of minimizers $$\rho $$
ρ
and show that the potential $$U^\rho =-\log |x|*\rho $$

U
ρ

=
-
log

|
x
|

∗
ρ

solves a degenerate obstacle problem, the obstacle being the transport potential. Every minimizer $$\rho $$
ρ
is absolutely continuous with respect to the Lebesgue measure. The singular set of the free boundary of the obstacle problem is contained in a rectifiable set, and its Hausdorff dimension is $$< n-1$$

<
n
-
1

.Moreover, $$U^\rho $$

U
ρ

solves a nonlocal Monge–Ampère equation, which after linearization leads to the equation $$\rho _t={\text {div}}(\rho \nabla U^\rho )$$

ρ
t

=
div

(
ρ
∇

U
ρ

)

. The methods we develop use Fourier transform techniques. They work equally well in high dimensions $$n\ge 2$$

n
≥
2

for the energy $$\begin{aligned} J[\rho ]=\iint |x-y|^{2-n}d\rho (x)d\rho (y)+d^2(\rho , \rho _0). \end{aligned}$$

J

[
ρ
]

=

∬
|
x
-
y
|

2
-
n

d
ρ

(
x
)

d
ρ

(
y
)

+

d
2

(
ρ
,

ρ
0

)

.