bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced bacterial cancer therapy delivering therapeutic RNA interference of c-Myc
Authors: Williams Jason S. , Higgins Adam T. , Stott Katie J. , Thomas Carly , Farrell Lydia , Bonnet Cleo S. , Peneva Severina , Derrick Anna V. , Hay Trevor , Wang Tianqi , Morgan Claire , Dwyer Sarah , D’Ambrogio Joshua , Hogan Catherine , Smalley Matthew J. , Parry Lee , Dyson Paul 
Published: March 2024

Abstract
Background
Bacterial cancer therapy was first trialled in patients at the end of the nineteenth century. More recently, tumour-targeting bacteria have been harnessed to deliver plasmid-expressed therapeutic interfering RNA to a range of solid tumours. A major limitation to clinical translation of this is the short-term nature of RNA interference in vivo due to plasmid instability. To overcome this, we sought to develop tumour-targeting attenuated bacteria that stably express shRNA by virtue of integration of an expression cassette within the bacterial chromosome and demonstrate therapeutic efficacy in vitro and in vivo.

Results
The attenuated tumour targeting Salmonella typhimurium SL7207 strain was modified to carry chromosomally integrated shRNA expression cassettes at the xylA locus. The colorectal cancer cell lines SW480, HCT116 and breast cancer cell line MCF7 were used to demonstrate the ability of these modified strains to perform intracellular infection and deliver effective RNA and protein knockdown of the target gene c-Myc. In vivo therapeutic efficacy was demonstrated using the Lgr5creERT2Apcflx/flx and BlgCreBrca2flx/flp53flx/flx orthotopic immunocompetent mouse models of colorectal and breast cancer, respectively. In vitro co-cultures of breast and colorectal cancer cell lines with modified SL7207 demonstrated a significant 50–95% (P < 0.01) reduction in RNA and protein expression with SL7207/c-Myc targeted strains. In vivo, following establishment of tumour tissue, a single intra-peritoneal administration of 1 × 106 CFU of SL7207/c-Myc was sufficient to permit tumour colonisation and significantly extend survival with no overt toxicity in control animals.

Conclusions
In summary we have demonstrated that tumour tropic bacteria can be modified to safely deliver therapeutic levels of gene knockdown. This technology has the potential to specifically target primary and secondary solid tumours with personalised therapeutic payloads, providing new multi-cancer detection and treatment options with minimal off-target effects. Further understanding of the tropism mechanisms and impact on host immunity and microbiome is required to progress to clinical translation.
The role of long noncoding RNAs in ocular angiogenesis and vascular oculopathy
Authors: Gandhi Pranali , Wang Yuzhi , Li Guigang , Wang Shusheng 
Published: March 2024

Abstract
Background
Long noncoding RNAs (lncRNAs) are RNA transcripts over 200 nucleotides in length that do not code for proteins. Initially considered a genomic mystery, an increasing number of lncRNAs have been shown to have vital roles in physiological and pathological conditions by regulating gene expression through diverse mechanisms depending on their subcellular localization. Dysregulated angiogenesis is responsible for various vascular oculopathies, including diabetic retinopathy, retinopathy of prematurity, age-related macular degeneration, and corneal neovascularization. While anti-VEGF treatment is available, it is not curative, and long-term outcomes are suboptimal, and some patients are unresponsive.

Results and summary
To better understand these diseases, researchers have investigated the role of lncRNAs in regulating angiogenesis and models of vascular oculopathies. This review summarizes recent research on lncRNAs in ocular angiogenesis, including the pro-angiogenic lncRNAs ANRIL, HOTAIR, HOTTIP, H19, IPW, MALAT1, MIAT, NEAT1, and TUG1, the anti-angiogenic lncRNAs MEG3 and PKNY, and the human/primate specific lncRNAs lncEGFL7OS, discussing their functions and mechanisms of action in vascular oculopathies.
Mechanisms behind gender transformative approaches targeting adolescent pregnancy in low- and middle-income countries: a realist synthesis protocol
Authors: Shukla Shruti , Abejirinde Ibukun-Oluwa Omolade , Meyer Sarah R. , Shenderovich Yulia , Steinert Janina Isabel 
Published: March 2024

Abstract
Introduction
Adolescent pregnancy is defined as pregnancy at the age of 19 or below. Pregnancy and childbirth complications are the most significant cause of death among 15–19-year-old girls. Several studies have indicated that inequitable gender norms can increase the vulnerability of adolescent girls, including violence exposure, early marriage, and adolescent pregnancy. To address these disparities, gender transformative approaches aim to challenge and transform restrictive gender norms, roles, and relations through targeted interventions, promoting progressive changes. This realist review aims to synthesise existing evidence from a broad range of data sources to understand how, why, for whom, and in what contexts gender transformative approaches succeed in reducing adolescent pregnancy in low- and middle-income countries.

Method and analysis
We employ a five-step realist synthesis approach: (1) clarify the scope of review and assessment of published literature, (2) development of initial programme theories, (3) systematic search for evidence, (4) development of refined programme theories, and (5) expert feedback and dissemination of results. This protocol presents the results of the first three steps and provides details of the next steps.
We extracted data from 18 studies and outlined eight initial programme theories on how gender transformative approaches targeting adolescent pregnancy work in the first three steps. These steps were guided by experts in the field of sexual and reproductive health, implementation science, and realist methodology. As a next step, we will systematically search evidence from electronic databases and grey literature to identify additional studies eligible to refine the initial programme theories. Finally, we will propose refined programme theories that explain how gender transformative approaches work, why, for whom, and under which circumstances.

Ethics and dissemination
Ethics approval is not required because the included studies are published articles and other policy and intervention reports. Key results will be shared with the broader audience via academic papers in open-access journals, conferences, and policy recommendations. The protocol for this realist review is registered in PROSPERO (CRD42023398293).
Clinicopathological and molecular genetic alterations in monomorphic–epitheliotropic intestinal T-cell lymphoma of the small intestine
Authors: Zhou Bing , Guo Min , Li Xiaohua , Duan Ting , Peng Lizi , Hao Hua 
Published: March 2024

Abstract
Background
Small intestinal monomorphic–epitheliotropic intestinal T-cell lymphoma (MEITL) is a rare aggressive T-cell lymphoma originating in the gastrointestinal tract. This study aimed to investigate the clinicopathological features, immunophenotypes, and molecular genetic changes of MEITL.

Methods
The clinicopathological data for three patients with surgically resected MEITL of the small intestine were collected. Next, immunohistochemical labeling, Epstein–Barr virus (EBV) in situ hybridization, assessment of clonal rearrangement of T-cell receptor (TCR) genes, and next-generation sequencing (NGS) were performed.

Results
Of the three patients, two were male and one was female, with ages of 61, 67, and 73 years, respectively. Clinical manifestations were predominantly abdominal pain and distension. Histopathology revealed infiltrative growth of small-to-medium-sized lymphocytes with a consistent morphology between the intestinal walls, accompanied by an obvious pro-epithelial phenomenon. The expression of CD3, CD8, CD43, CD56, TIA-1, CD103, H3K36me3, and Bcl-2 was detected, and the Ki-67 proliferation index ranged from 50% to 80%. All three patients tested negative for EBER. However, monoclonal rearrangement of the TCR gene was detected in them. NGS testing showed a JAK3 mutation in all three cases. Further, STAT5B, SETD2, and TP53 mutations were each observed in two cases, and a BCOR mutation was found in one case. All patients were treated with chemotherapy after surgery. Two patients died 7 and 15 month post-operation, and one patient survived for 5 months of follow-up.

Conclusions
Our findings demonstrate that mutations in JAK3 and STAT5B of the JAK/STAT pathway and inactivation of the oncogene SETD2 markedly contribute to the lymphomagenesis of MEITL.
Genomic, functional, and metabolic enhancements in multidrug-resistant Enterobacter bugandensis facilitating its persistence and succession in the International Space Station
Authors: Sengupta Pratyay , Muthamilselvi Sivabalan Shobhan Karthick , Singh Nitin Kumar , Raman Karthik , Venkateswaran Kasthuri 
Published: March 2024

Abstract
Background
The International Space Station (ISS) stands as a testament to human achievement in space exploration. Despite its highly controlled environment, characterised by microgravity, increased CO$$_{2}$$

2

levels, and elevated solar radiation, microorganisms occupy a unique niche. These microbial inhabitants play a significant role in influencing the health and well-being of astronauts on board. One microorganism of particular interest in our study is Enterobacter bugandensis, primarily found in clinical specimens including the human gastrointestinal tract, and also reported to possess pathogenic traits, leading to a plethora of infections.

Results
Distinct from their Earth counterparts, ISS E. bugandensis strains have exhibited resistance mechanisms that categorise them within the ESKAPE pathogen group, a collection of pathogens recognised for their formidable resistance to antimicrobial treatments. During the 2-year Microbial Tracking 1 mission, 13 strains of multidrug-resistant E. bugandensis were isolated from various locations within the ISS. We have carried out a comprehensive study to understand the genomic intricacies of ISS-derived E. bugandensis in comparison to terrestrial strains, with a keen focus on those associated with clinical infections. We unravel the evolutionary trajectories of pivotal genes, especially those contributing to functional adaptations and potential antimicrobial resistance. A hypothesis central to our study was that the singular nature of the stresses of the space environment, distinct from any on Earth, could be driving these genomic adaptations. Extending our investigation, we meticulously mapped the prevalence and distribution of E. bugandensis across the ISS over time. This temporal analysis provided insights into the persistence, succession, and potential patterns of colonisation of E. bugandensis in space. Furthermore, by leveraging advanced analytical techniques, including metabolic modelling, we delved into the coexisting microbial communities alongside E. bugandensis in the ISS across multiple missions and spatial locations. This exploration revealed intricate microbial interactions, offering a window into the microbial ecosystem dynamics within the ISS.

Conclusions
Our comprehensive analysis illuminated not only the ways these interactions sculpt microbial diversity but also the factors that might contribute to the potential dominance and succession of E. bugandensis within the ISS environment. The implications of these findings are twofold. Firstly, they shed light on microbial behaviour, adaptation, and evolution in extreme, isolated environments. Secondly, they underscore the need for robust preventive measures, ensuring the health and safety of astronauts by mitigating risks associated with potential pathogenic threats.
MicroRNA-148b secreted by bovine oviductal extracellular vesicles enhance embryo quality through BPM/TGF-beta pathway
Authors: Cañón-Beltrán Karina , Cajas Yulia N , Almpanis Vasileios , Egido Sandra Guisado , Gutierrez-Adan Alfonso , González Encina M , Rizos Dimitrios 
Published: March 2024

Abstract
Background
Extracellular vesicles (EVs) and their cargoes, including MicroRNAs (miRNAs) play a crucial role in cell-to-cell communication. We previously demonstrated the upregulation of bta-mir-148b in EVs from oviductal fluid of cyclic cows. This miRNA is linked to the TGF-β pathway in the cell proliferation. Our aim was to verify whether miR-148b is taken up by embryos through gymnosis, validate its target genes, and investigate the effect of miR-148b supplementation on early embryo development and quality.

Methods
Zygotes were cultured in SOF + 0.3% BSA (Control) or supplemented with: 1 µM miR-148b mimics during: D1-D7 (miR148b) or D1-D4 (miR148b-OV: representing miRNA effect in the oviduct) or D4-D7 (miR148b-UT: representing miRNA effect in the uterus) or 1 µM control mimics was used during: D1-D7 (CMimic). Embryos at ≥ 16-cells and D7 blastocysts (BD7) were collected to examine the mRNA abundance of transcripts linked to the TGF-β pathway (TGFBR2, SMAD1, SMAD2, SMAD3, SMAD5, BMPR2, RPS6KB1, POU5F1, NANOG), total cell number (TC), trophectoderm (TE), and inner cell mass (ICM) were also evaluated. One-way ANOVA was used for all analyses.

Results
We demonstrated that miR-148b can be taken up in both 16-cell embryos and BD7 by gymnosis, and we observed a decrease in SMAD5 mRNA, suggesting it’s a potential target of miR-148b. Cleavage and blastocysts rates were not affected in any groups; however, supplementation of miR-148b mimics had a positive effect on TC, TE and ICM, with values of 136.4 ± 1.6, 92.5 ± 0.9, 43.9 ± 1.3 for miR148b and 135.3 ± 1.5, 92.6 ± 1.2, 42.7 ± 0.8, for miR148b-OV group. Furthermore, mRNA transcripts of SMAD1 and SMAD5 were decreased (P ≤ 0.001) in 16-cell embryos and BD7 from miR148b and miR148b-OV groups, while POU5F1 and NANOG were upregulated (P ≤ 0.001) in BD7 and TGFBR2 was only downregulated in 16-cell embryos. pSMAD1/5 levels were higher in the miR148b and miR148b-OV groups.

Conclusions
Our findings suggest that supplementation of bta-miR-148b mimics during the entire culture period (D1 - D7) or from D1 - D4 improves embryo quality and influences the TGF-β signaling pathway by altering the transcription of genes associated with cellular differentiation and proliferation. This highlights the importance of miR-148b on embryo quality and development.
Conventional and molecular cytogenetic characterization of a Moroccan patient with WAGR syndrome
Authors: Chbel Faiza , Hamdaoui Hasna , Mossafa Houssein , Ouldim Karim , Benrahma Houda 
Published: March 2024

Abstract
Background
WAGR syndrome is a rare genetic disorder characterized by a de novo deletion of 11p13 and is usually clinically associated with Wilms’ tumor, aniridia, genitourinary anomalies, and mental retardation (W-A-G-R). Although the genotypic defects in WAGR syndrome have been well established. The congenital aniridia is caused, in nearly 90% of cases by mutations in the gene PAX6. In the face of congenital aniridia, it is imperative to specify whether it falls within the scope of a WAGR syndrome or if it is an isolated congenital aniridia or inherited by performing karyotype, FISH (Fluorescence In Situ Hybridization) or a CGH array for genetic counseling.

Case presentation
We report here a case of genetic testing for newborn with aniridia, to detect 11p13 rearrangements, using karyotyping and CGH array to complete picture of the chromosomal deletions and breakpoints in aniridia. Results show either a loss of 3811.196 kb on chromosome 11 delimited by the bands p14.1 and p13 with formula or a loss of a 1867.287 kb on chromosome 18 fragment delimited by q21.33 and q22.1 bands, that has not been detected by karyotype analysis.

Conclusions
Cytogenetics screening is a good strategy for the genetic diagnosis of aniridia and associated syndromes, allowing for a better identification of breakpoints. Our results underline the clinical importance of performing exhaustive and accurate analysis of chromosomal rearrangements for patients with aniridia, especially newborns to improve survival and quality of life for affected individuals.
Von Duden bis Deepl: zur Verwendung lexikografischer Ressourcen im Südtiroler Sprachunterricht (L1, L2, L3) im Spannungs-feld normativer Vorgaben und schulischer Praxis
Authors: Abel Andrea 
Published: March 2024

The paper deals with the role of lexicographic resources in the South Tyrolean (i. e. the Autonomous Province of Bolzano/Bozen, Italy) educational context against the backdrop of legal provisions (Das neue Autonomiestatut 2019/1972) and the relevance of language education on the part of educational institutions (Rahmenrichtlinien DE, Rahmenrichtlinien IT), taking into account both normative requirements and their application in practice. The focus is on two questions that have been little researched so far, not only in the specific context but also internationally (cf. Abel 2022; Nied Curcio 2022): To what extent are lexicographic resources represented in the school framework guidelines? How are they actually used in schools? For the case study presented here, the South Tyrolean framework guidelines provided by the German and the Italian school boards at all levels of education for German and Italian as first (L1) and second (L2) languages, as well as for English as a foreign language (L3) were examined by means of a document analysis. In a second step, a questionnaire survey with language teachers at all school levels (German and Italian as L1/L2, English as L3; number of survey respondents: 644) determined the actual use of lexicographic resources.
In search of a prerequisite for infant participation in pregnancy: a depth-hermeneutical interpretation of conversations between coming mothers and midwives
Authors: Bakkenget Brynulf , Finholt-Pedersen Sissel Merete , Håkansson Ulrika Christina , Våpenstad Eystein Victor 
Published: March 2024

Based on the fact that the United Nations Convention on the Rights of the Child (UNCRC) gives the right to participate and be heard in situations that affect their lives to all children, even pre-verbal infants, we have looked for the infant voice in parental narratives about their child. Conversations between 16 mothers and a professional at two stages were videotaped and transcribed. The first conversation between mother and midwife took place in pregnancy and, the second, between mother and health nurse, was completed when the child was about six months old. We wanted to invent a method that could find the voice of pre-verbal children, even before birth, a method capable of registering the child’s impact on us and decoding this influence into common language and practical action. Based on infant research on intersubjectivity and qualitative methodology from psychosocial research, we developed a procedure of depth-hermeneutical interpretation of the parental narratives. In this article we describe the results from the interpretation of the narratives made in pregnancy. Through the procedure of Scenic-Narrative Microanalysis, a very suitable method of depth-hermeneutic group interpretation, we identified three different areas of conflict or tension in the data material: container versus oneness; openness versus narrowness; and control versus curiosity. A description of the epistemological foundations and the research procedures from data collection to interpretation will be given.
The results from the second round of interpretation will be analysed and compared with the results from the pregnancy narratives, and published in a future article.
Information System Development for Reading and Writing Qur'an at Tarbiyah and Teacher Training Faculty of UIN Sunan Kalijaga
Authors: Nur Hidayat  , Kasyful Albab Al Musthofa  , Adhi Setiyawan  
Published: March 2024

Some Postgraduate and Doctoral Alumni of UIN Sunan Kalijaga, Faculty of Tarbiyah Sciences do not yet have Quranic literacy skills, so the Faculty of Tarbiyah and Teacher Training held standardization for students who will graduate by adding conditions to be able to take part in the munaqasah session by passing the Quran Literacy Exam. This research uses the plomp method and the assure method because it can simplify the stages systematically. The results of this quranic literacy examination research graduates from postgraduate or doctoral from the faculty of tarbiyah science and teacher training can read and write the Quran all and make student output better than the previous year’.
Abstrak
Beberapa Alumni Pascasarjana dan Doktoral UIN Sunan Kalijaga Fakultas Ilmu Tarbiyah belum memiliki kemampuan baca tulis Alquran, sehingga Fakultas Ilmu Tarbiyah dan Keguruan mengadakan standarisasi bagi mahasiswa yang akan diwisuda dengan menambahkan syarat untuk dapat mengikuti sidang munaqasah yaitu lulus Ujian Baca Tulis Alquran. Penelitian ini menggunakan metode plomp dan metode assure karena dapat menyederhanakan tahapan-tahapan secara sistematis. Hasil dari penelitian ujian baca tulis alquran ini lulusan dari pascasarjana atau doktoral dari fakultas ilmu tarbiyah dan keguruan dapat membaca dan menulis alquran semua dan menjadikan output mahasiswa lebih baik dari tahun sebelumnya
Anti-parasitic activity and computational studies on a novel labdane diterpene from the roots of Vachellia nilotica
Authors: Al-Tannak Naser F. , Anyam John V. , Santali Eman Y. , Gray Alexander I. , Ibeji Collins U. , Igoli John O. 
Published: March 2024

Abstract
A new labdane diterpene characterized as 18α-O-trans-p-feruloyl-15-methyl-8(17)-labdanoate has been isolated from the roots of Vachellia nilotica. Also isolated were p-coumaric acid, ferulic acid, stearic acid, lupeol, and a mixture of β-sitosterol and stigmasterol. The compounds were obtained after a series of column chromatography on silica gel, and their structures were elucidated using NMR and LC-MS analyses. The new diterpene showed good anti-parasitic activity with an IC50 of 0.0177 µM against Trypanosoma brucei and 0.0154 µM against Leishmania major using an Alamar Blue assay. The compound also displayed very good inhibitory activity against Leishmania major compared to Trypanosoma brucei rhodesiense with a binding energy of −10.5 and −7.8 kcal/mol, respectively. Density functional theory analysis showed that the studied compound has low LUMO–HOMO energy, signifying a high chemical reactivity with the ability to donate electrons to electron-accepting species.
Density functional theory to study stopping power of proton in water, lung, bladder, and intestine
Authors: Jasim Wejdan A. , Kadhim Rashid O. 
Published: March 2024

Abstract
Stopping power, range, and time of proton in water, lung, bladder, and intestinal human tissues are calculated using density functional theory and Beth’s relativistic equation in range of proton energy (0.01–1,000 MeV). The experimental data extracted from SRIM-2013 program were used to proton to the same human tissues applied in the MATLAB-2021 program, and the mean ionization potential of water and the studied tissues is calculated using Gaussian 09W program. A good agreement has been found between our calculations for stopping power, range, and time of protons in the studied human body tissues and SRIM-2013 program calculations.
Recording, Sharing and Linking Micromorphological Data: A Two-Pillar Database System
Authors: Russo Sarah Lo , Brönnimann David , Pümpin Christine , Ismail-Meyer Kristin , Rentzel Philippe , Gautschy Rita , Wimmer Johannes , Devos Yannick , Nys Karin 
Published: March 2024

Abstract
In archaeological soil and sediment micromorphology, research is grounded in observations made with petrographic microscopes. These observations are recorded using standardised terms and microphotographs. The two-pillar database system allows a user-friendly recording of these observations with I-GEOARCHrec and the possibility to link these data to field pictures and microphotographs publicly available in I-GEOARCHive.