bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combined surgical and chemotherapy treatment for invasive primary urethral cancer: a case presentation
Authors: Simsek Alper , Butun Salih , Duran Mesut Berkan , Kucuker Kursat , Celen Sinan , Ozlulerden Yusuf , Tuncay Omer Levent 
Published: February 2024

Abstract
Background
The European Association of Urology (EAU) defines primary urethral carcinoma (PUC) as a carcinoma that arises in the urethra without a previous diagnosis of carcinoma elsewhere in the urinary system. It is considered as a rare cancer, accounting for less than 1% of all malignant tumors and 5% of malignant tumors of the urinary system. The difficulty in diagnosis and its rarity can lead to delayed diagnosis and decreased survival. We think that a case report to be made in the literature for this rare disease with no consensus on treatment will contribute to disease management.

Case presentation
In this article, we describe the diagnosis and treatment process of a 75-year-old patient who was diagnosed with primary urethral cancer and had urethral discharge and difficulty in urination. The biopsy result from the suspected hyperemic area in the urethra in cystourethroscopy was primary urethral cancer. Urethrectomy followed by urethroplasty was performed on the patient's 2-cm primary urethral cancerous tissue. In the postoperative first month, an F-18 FDG whole-body PET scan for oncological evaluation showed increased pathological F-18 FDG uptake in the periphery of the mass in the penile urethra and indistinguishable boundaries from the prostatic urethra. After this, adjuvant gemcitabine and carboplatin therapy was planned by the oncology team.

Conclusions
Based on our outcome in this case, we believe that chemotherapy combined with surgery increases the chance of successful treatment in locally advanced urethral cancer.
Protein embedding based alignment
Authors: Iovino Benjamin Giovanni , Ye Yuzhen 
Published: February 2024

Abstract
Purpose
Despite the many progresses with alignment algorithms, aligning divergent protein sequences with less than 20–35% pairwise identity (so called "twilight zone") remains a difficult problem. Many alignment algorithms have been using substitution matrices since their creation in the 1970’s to generate alignments, however, these matrices do not work well to score alignments within the twilight zone. We developed Protein Embedding based Alignments, or PEbA, to better align sequences with low pairwise identity. Similar to the traditional Smith-Waterman algorithm, PEbA uses a dynamic programming algorithm but the matching score of amino acids is based on the similarity of their embeddings from a protein language model.

Methods
We tested PEbA on over twelve thousand benchmark pairwise alignments from BAliBASE, each one extracted from one of their multiple sequence alignments. Five different BAliBASE references were used, each with different sequence identities, motifs, and lengths, allowing PEbA to showcase how well it aligns under different circumstances.

Results
PEbA greatly outperformed BLOSUM substitution matrix-based pairwise alignments, achieving different levels of improvements of the alignment quality for pairs of sequences with different levels of similarity (over four times as well for pairs of sequences with <10% identity). We also compared PEbA with embeddings generated by different protein language models (ProtT5 and ESM-2) and found that ProtT5-XL-U50 produced the most useful embeddings for aligning protein sequences. PEbA also outperformed DEDAL and vcMSA, two recently developed protein language model embedding-based alignment methods.

Conclusion
Our results suggested that general purpose protein language models provide useful contextual information for generating more accurate protein alignments than typically used methods.
Differential regulation of miRNAs involved in the susceptible and resistance responses of wheat cultivars to wheat streak mosaic virus and Triticum mosaic virus
Authors: Soylu Inanc , Lakshman Dilip K. , Tatineni Satyanarayana , Galvez Leny C. , Mitra Amitava 
Published: February 2024

Abstract
Background
Wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV) are components of the wheat streak mosaic virus disease complex in the Great Plains region of the U.S.A. and elsewhere. Co-infection of wheat with WSMV and TriMV causes synergistic interaction with more severe disease symptoms compared to single infections. Plants are equipped with multiple antiviral mechanisms, of which regulation of microRNAs (miRNAs) is a potentially effective constituent. In this investigation, we have analyzed the total and relative expression of miRNA transcriptome in two wheat cultivars, Arapahoe (susceptible) and Mace (temperature-sensitive-resistant), that were mock-inoculated or inoculated with WSMV, TriMV, or both at 18 °C and 27 °C.

Results
Our results showed that the most abundant miRNA family among all the treatments was miRNA166, followed by 159a and 168a, although the order of the latter two changed depending on the infections. When comparing infected and control groups, twenty miRNAs showed significant upregulation, while eight miRNAs were significantly downregulated. Among them, miRNAs 9670-3p, 397-5p, and 5384-3p exhibited the most significant upregulation, whereas miRNAs 319, 9773, and 9774 were the most downregulated. The comparison of infection versus the control group for the cultivar Mace showed temperature-dependent regulation of these miRNAs. The principal component analysis confirmed that less abundant miRNAs among differentially expressed miRNAs were strongly correlated with the inoculated symptomatic wheat cultivars. Notably, miRNAs 397-5p, 398, and 9670-3p were upregulated in response to WSMV and TriMV infections, an observation not yet reported in this context. The significant upregulation of these three miRNAs was further confirmed with RT-qPCR analysis; in general, the RT-qPCR results were in agreement with our computational analysis. Target prediction analysis showed that the miRNAs standing out in our analysis targeted genes involved in defense response and regulation of transcription.

Conclusion
Investigation into the roles of these miRNAs and their corresponding targets holds promise for advancing our understanding of the mechanisms of virus infection and possible manipulation of these factors for developing durable virus resistance in crop plants.
Biology of Nicotiana glutinosa L., a newly recorded species from an archaeological excavation site in Egypt
Authors: Heneidy Selim Z. , Al-Sodany Yassin M. , Fakhry Amal M. , Kamal Sania A. , Halmy Marwa Waseem A. , Bidak Laila M. , kenany Eman T. El , Toto Soliman M. 
Published: February 2024

Abstract
Background
During a field survey of urban flora in Alexandria city in 2019–2022, an interesting species belonging to the Solanaceae was collected from a newly archaeological excavation site and identified as Nicotiana glutinosa L. Many visits were made to the herbaria of Egypt to confirm the species records, but no single record was found. Reviewing the available literature revealed that this tropical American taxon was never recorded in the flora of Egypt.

Aims
The present study was focused on N. glutinosa growth structure and plant macro- and micromorphology.

Methods
Ten sampling sites were covered for N. glutinosa size structure. Plant samples were examined for stem anatomy, leaf, seed, and pollen morphology.

Results
The species size structure reveals that the individual size index ranges from 1.33 to 150 cm, while its density ranges from 4 to 273 individuals /100 m−2.
N. glutinosa has successfully established itself in one of the archaeological sites in Egypt, showing a “healthy” population with a high degree of size inequality, characterized by a relative majority of the juvenile individuals. Voucher specimens were deposited in the Herbarium of Alexandria University (ALEX) Faculty of Science, another specimen is processed to make herbarium specimens at the Herbarium of the Botanic Garden (Heneidy et al. collection, deposition number. 5502).

Conclusions
From our observations, N. glutinosa seems to have invasive potential, as it shows characteristics shared by most invasive species that are thought to help in their successful establishment in new habitats. This article emphasizes the importance of monitoring and regularly reporting the threats of alien invasive species to avoid any possible negative impacts on indigenous biodiversity in the future.
Transcriptomic analysis identifies candidate genes for Aphanomyces root rot disease resistance in pea
Authors: Kälin Carol , Piombo Edoardo , Bourras Salim , Brantestam Agnese Kolodinska , Dubey Mukesh , Elfstrand Malin , Karlsson Magnus 
Published: February 2024

Abstract
Background
Aphanomyces euteiches is a soil-borne oomycete that causes root rot in pea and other legume species. Symptoms of Aphanomyces root rot (ARR) include root discoloration and wilting, leading to significant yield losses in pea production. Resistance to ARR is known to be polygenic but the roles of single genes in the pea immune response are still poorly understood. This study uses transcriptomics to elucidate the immune response of two pea genotypes varying in their levels of resistance to A. euteiches.

Results
In this study, we inoculated roots of the pea (P. sativum L.) genotypes ‘Linnea’ (susceptible) and ‘PI180693’ (resistant) with two different A. euteiches strains varying in levels of virulence. The roots were harvested at 6 h post-inoculation (hpi), 20 hpi and 48 hpi, followed by differential gene expression analysis. Our results showed a time- and genotype-dependent immune response towards A. euteiches infection, involving several WRKY and MYB-like transcription factors, along with genes associated with jasmonic acid (JA) and abscisic acid (ABA) signaling. By cross-referencing with genes segregating with partial resistance to ARR, we identified 39 candidate disease resistance genes at the later stage of infection. Among the genes solely upregulated in the resistant genotype ‘PI180693’, Psat7g091800.1 was polymorphic between the pea genotypes and encoded a Leucine-rich repeat receptor-like kinase reminiscent of the Arabidopsis thaliana FLAGELLIN-SENSITIVE 2 receptor.

Conclusions
This study provides new insights into the gene expression dynamics controlling the immune response of resistant and susceptible pea genotypes to A. euteiches infection. We present a set of 39 candidate disease resistance genes for ARR in pea, including the putative immune receptor Psat7g091800.1, for future functional validation.
Alleviating the drought stress and improving the plant resistance properties of Triticum aestivum via biopriming with aspergillus fumigatus
Authors: George Nelly Michel , Hany-Ali Gehad , Abdelhaliem Ekram , Abdel-Haleem Mohamed 
Published: February 2024

Abstract
Background
Wheat (Triticum aestivum L.) is one of the most widely grown and vital cereal crops, containing a high percentage of basic nutrients such as carbohydrates and proteins. Drought stress is one of the most significant limitations on wheat productivity. Due to climate change influences plant development and growth, physiological processes, grain quality, and yield. Drought stress has elicited a wide range of plant responses, namely physiological and molecular adaptations. Biopriming is one of the recent attempts to combat drought stress. Mitigating the harmful impact of abiotic stresses on crops by deploying extreme-habitat-adapted symbiotic microbes. The purpose of this study was to see how biopriming Triticum aestivum grains affected the effects of inoculating endophytic fungi Aspergillus fumigatus ON307213 isolated from stressed wheat plants in four model agricultural plants (Gemmiza-7, Sids-1, Sakha8, and Giza 168). And its viability in reducing drought stress through the use of phenotypic parameters such as root and shoot fresh and dry weight, shoot and root length, and so on. On a biochemical and physiological level, enzymatic parameters such as catalase and superoxidase dismutase are used. Total phenolics, flavonoids, and photosynthetic pigments are non-enzymatic parameters. Making use of molecular techniques such as reverse transcriptase polymerase chain reaction (RT-PCR).

Results
It has been found that using Aspergillus fumigatus as a biological biopriming tool can positively impact wheat plants experiencing drought stress. The total biomass of stressed wheat plants that had been bio-primed rose by more than 40% as compared to wheat plants that had not been bio-primed. A. fumigatus biopriming either increased or decreased the amount of enzymatic and non-enzymatic substances on biochemical scales, aside from the noticeable increase in photosynthetic pigment that occurs in plants that have been bio-primed and stressed. Drought-resistant genes show a biopriming influence in gene expression.

Conclusions
This is the first paper to describe the practicality of a. fumigatus biopriming and its effect on minimizing the degrading effects of drought through water limitation. It suggests the potential applications of arid habitat-adapted endophytes in agricultural systems.
Scoping review of values elicitation tools for treatment decisions in hepatocellular carcinoma
Authors: Ritaccio Gabrielle , Barritt IV A. Sidney , Conklin Jamie L. , Richardson Daniel R. , Evon Donna M. , Sanoff Hanna K. , Basch Ethan , Wheeler Stephanie B. , Moon Andrew M. 
Published: February 2024

Abstract
Background
Treatment choices in hepatocellular carcinoma (HCC) involve consideration of tradeoffs between the benefits, toxicities, inconvenience, and costs. Stated preference elicitation methods have been used in the medical field to help evaluate complex treatment decision-making. The aim of this study was to conduct a scoping review to assess the evidence base for the use of preference elicitation tools or willingness to pay/willingness to accept methods for HCC treatment decision-making from both the patient and provider perspective.

Methods
We performed a scoping review to identify abstracts or manuscripts focused on the role preference elicitation tools or willingness to pay/willingness to accept methods for HCC treatment options among patients, caregivers, and/or providers. Two researchers independently screened full-text references and resolved conflicts through discussion. We summarized key findings, including the type and setting of preference-elicitation tools used for HCC treatment decisions.

Results
Ten published abstracts or manuscripts evaluated the role of preference elicitation tools for HCC treatments. The studies revealed several attributes that are considered by patients and providers making HCC treatment decisions. Many of the studies reviewed suggested that while patients place the most value on extending their overall survival, they are willing to forgo overall survival to avoid risks of treatments and maintain quality of life. Studies of physicians and surgeons found that provider preferences are dependent on patient characteristics, provider specialty, and surgeon or hospital-related factors.

Conclusion
This scoping review explored both patient and physician preferences towards treatment modalities in all stages of HCC. The studies revealed a large scope of potential attributes that may be important to patients and that many patients are willing to forgo survival to maintain quality of life. Further research should explore both preference elicitation of currently available and emerging therapies for HCC as well as the use of this data to develop patient-facing tools to assist in navigating treatment options.
Risk factors for falls in older adults with diabetes mellitus: systematic review and meta-analysis
Authors: Freire Larissa Barros , Brasil-Neto Joaquim Pereira , da Silva Marianne Lucena , Miranda Milena Gonçalves Cruz , de Mattos Cruz Lorrane , Martins Wagner Rodrigues , da Silva Paz Leonardo Petrus 
Published: February 2024

Abstract
Aim
To identify risk factors for falls in older adults with Type 2 Diabetes Mellitus (T2DM).

Methods
The eligible studies identified factors associated with the risk of falls in older adults with T2DM. We searched PubMed, Cinahl, Web of Science, Scopus, and the Cochrane Library databases. The review has been updated and the last review date was November 30, 2023 (CRD42020193461).

Results
Twelve studies met the inclusion criteria, and eight studies were included in the meta-analysis. These studies included a total of 40,778 older adults with T2DM, aged 60 to 101 years. The risk of developing the outcome falls in older adults with T2DM is 63% higher compared to the risk in older adults without T2DM (HR 1.63; 95% CI [1.30 - 2.05]). The overall chance of falling in older adults with T2DM is 59% higher than that of non-diabetic older adults (OR 1.59; 95% CI [1.36 -1.87]), and in older adults with T2DM who take insulin the chance of falling is 162% higher (OR 2.62; 95% CI [1.87 - 3.65]). No results on diabetic polyneuropathy were found in the studies.

Conclusion
Older adults with T2DM present a higher risk of falls compared to non-diabetics. Among the included older adults with T2DM, the most important factor associated with a higher risk of falls was insulin use.

Trial registration
Registered in the International Prospective Register of Systematic Reviews (CRD42020193461).
Cross-country analysis of contextual factors and implementation strategies in under-5 mortality reduction in six low- and middle-income countries 2000–2015
Authors: Binagwaho Agnes , VanderZanden Amelia , Garcia Patricia J. , Huda Fauzia Akhter , Maskey Mahesh , Sall Mohamadou , Sayinzoga Felix , Subedi Raj Kumar , Teklu Alula M. , Donahoe Kateri , Frisch Miriam , Ntawukuriryayo Jovial Thomas , Udoh Kelechi , Hirschhorn Lisa R. 
Published: February 2024

Abstract
Background
The Exemplars in Under-5 Mortality (U5M) was a multiple cases study of how six low- and middle-income countries (LMICs), Bangladesh, Ethiopia, Nepal, Peru, Rwanda, and Senegal, implemented health system-delivered evidence-based interventions (EBIs) to reduce U5M between 2000 and 2015 more effectively than others in their regions or with similar economic growth. Using implementation research, we conducted a cross-country analysis to compare decision-making pathways for how these countries chose, implemented, and adapted strategies for health system-delivered EBIs that mitigated or leveraged contextual factors to improve implementation outcomes in reducing amenable U5M.

Methods
The cross-country analysis was based on the hybrid mixed methods implementation research framework used to inform the country case studies. The framework included a common pathway of Exploration, Preparation, Implementation, Adaptation, and Sustainment (EPIAS). From the existing case studies, we extracted contextual factors which were barriers, facilitators, or determinants of strategic decisions; strategies to implement EBIs; and implementation outcomes including acceptability and coverage. We identified common factors and strategies shared by countries, and individual approaches used by countries reflecting differences in contextual factors and goals.

Results
We found the six countries implemented many of the same EBIs, often using similar strategies with adaptations to local context and disease burden. Common implementation strategies included use of data by decision-makers to identify problems and prioritize EBIs, determine implementation strategies and their adaptation, and measure outcomes; leveraging existing primary healthcare systems; and community and stakeholder engagement. We also found common facilitators included culture of donor and partner coordination and culture and capacity of data use, while common barriers included geography and culture and beliefs. We found evidence for achieving implementation outcomes in many countries and EBIs including acceptability, coverage, equity, and sustainability.

Discussion
We found all six countries used a common pathway to implementation with a number of strategies common across EBIs and countries which contributed to progress, either despite contextual barriers or by leveraging facilitators. The transferable knowledge from this cross-country study can be used by other countries to more effectively implement EBIs known to reduce amenable U5M and contribute to strengthening health system delivery now and in the future.
Inequity in the face of success: understanding geographic and wealth-based equity in success of facility-based delivery for under-5 mortality reduction in six countries
Authors: Ntawukuriryayo Jovial Thomas , VanderZanden Amelia , Amberbir Alemayehu , Teklu Alula , Huda Fauzia Akhter , Maskey Mahesh , Sall Mohamadou , Garcia Patricia J. , Subedi Raj Kumar , Sayinzoga Felix , Hirschhorn Lisa R. , Binagwaho Agnes 
Published: February 2024

Abstract
Background
Between 2000–2015, many low- and middle-income countries (LMICs) implemented evidence-based interventions (EBIs) known to reduce under-5 mortality (U5M). Even among LMICs successful in reducing U5M, this drop was unequal subnationally, with varying success in EBI implementation. Building on mixed methods multi-case studies of six LMICs (Bangladesh, Ethiopia, Nepal, Peru, Rwanda, and Senegal) leading in U5M reduction, we describe geographic and wealth-based equity in facility-based delivery (FBD), a critical EBI to reduce neonatal mortality which requires a trusted and functional health system, and compare the implementation strategies and contextual factors which influenced success or challenges within and across the countries.

Methods
To obtain equity gaps in FBD coverage and changes in absolute geographic and wealth-based equity between 2000–2015, we calculated the difference between the highest and lowest FBD coverage across subnational regions and in the FBD coverage between the richest and poorest wealth quintiles. We extracted and compared contextual factors and implementation strategies associated with reduced or remaining inequities from the country case studies.

Results
The absolute geographic and wealth-based equity gaps decreased in three countries, with greatest drops in Rwanda – decreasing from 50 to 5% across subnational regions and from 43 to 13% across wealth quintiles. The largest increases were seen in Bangladesh – from 10 to 32% across geography – and in Ethiopia – from 22 to 58% across wealth quintiles. Facilitators to reducing equity gaps across the six countries included leadership commitment and culture of data use; in some countries, community or maternal and child health insurance was also an important factor (Rwanda and Peru). Barriers across all the countries included geography, while country-specific barriers included low female empowerment subnationally (Bangladesh) and cultural beliefs (Ethiopia). Successful strategies included building on community health worker (CHW) programs, with country-specific adaptation of pre-existing CHW programs (Rwanda, Ethiopia, and Senegal) and cultural adaptation of delivery protocols (Peru). Reducing delivery costs was successful in Senegal, and partially successful in Nepal and Ethiopia.

Conclusion
Variable success in reducing inequity in FBD coverage among countries successful in reducing U5M underscores the importance of measuring not just coverage but also equity. Learning from FBD interventions shows the need to prioritize equity in access and uptake of EBIs for the poor and in remote areas by adapting the strategies to local context.