bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic distance analysis of Lingnan, Arab, and Kedu chicken as parental lines based on mitochondrial DNA
Authors: Pambuko Galih , Hendi Nur Pratama Muhammad , Kusumaningrum Rahayu , Widyas Nuzul , Sumarno Lanjar , Prastowo Sigit
Published: June 2024

Lingnan, Arab, and Kedu chickens are the main breeds used as parental lines to develop Maron chickens. The genetic distance between Maron chicken parental lines is critical to achieving heterosis. D-Loop Mitochondria’s Hypervariable 1 (HV1) region is a genetic distance marker. This study aims to determine the genetic distance between the Maron chicken parental lines using the mitochondria HV1 marker. A total of 73 blood samples were collected from Lingnan, Arab, and Kedu chicken. In this study, Polymerase Chain Reaction was employed to amplify D-loop HV1 region in mitochondria, followed by DNA sequencing. A maximum likelihood (ML) analysis then used to generate phylogenetic reconstruction. As a result, eight haplotypes were identified, 21 being the highest, and 1 belonging to the lowest. All pairwise comparisons reveal significant population differences (Fst = 0.67 - 0.962). PCA analysis revealed that Lingnan, Arab, and Kedu populations are different from one to another. Then it is concluded that Lingnan, Arab, and Kedu chickens have a significant genetic distance, which can be used to guide the breeding process of Maron chicken.
The role of women in agrotourism development: gender analysis (case study of Ngargoyoso District)
Authors: Setyowati R , Lestari E , Rusdiyana E , Sugihardjo  , Widiyanto  , Maharani R F
Published: June 2024

Agrotourism development in Ngargoyoso District requires the optimization of women’s role in its operation. Women’s participation in tourism can reduce gender inequality in development, especially in 3 villages: Berjo, Kemuning, and Jatirejo. Therefore, researchers want to study in more depth women’s role and participation in agrotourism development in Ngargoyoso District. The research method used was a case study with a qualitative approach. Focus Group Discussion, interviews, documentation, and field observation were the data collection techniques used in this research. The results showed the active role played by women in Ngargoyoso sub-district, especially in Berjo, Jatirejo, and Kemuning villages, in developing agrotourism through their participation in MSMEs management, photography, Women’s Farmer Groups, agrotourism managers, tourism promotion, maintaining ticket counters, and joining ojek and jeep communities. Women in Ngargoyoso sub-district, especially in the 3 villages, participate in agrotourism management for economic reasons and want to be independent without depending on others. However, the village government has not supported them yet. Further assistance is expected to be given to women in the attempt of developing tourist villages in Ngargoyoso District.
Sustainable tourism for rural livelihood sustainability (A case study of agrotourism in Karanganyar Regency, Central Java)
Authors: Widiyanto  , Setyowati R , Lestari E , Rusdiyana E , Sugihardjo  , Arwindianti M L
Published: June 2024

Sustainable tourism development is a concept appearing to overcome the negative impacts of tourism development. This study aims to analyze sustainable tourism development to achieve economic, socio-cultural, and environmental sustainability goals in Ngargoyoso District. The research method used in this study was a descriptive qualitative method with FGD, direct interviews, documentation, and field observation being the techniques of collecting data. Tourist villages in Ngargoyoso District, especially in Jatirejo, Kemuning, and Berjo are supported by stakeholders, namely the government, private parties, and the community who synergize with each other to achieve community welfare. Considering the findings of study, it can be seen that the positive impacts of the existence of tourist villages include increased economic level, increased fame in the public, and reduced unemployment rate, while the negative impacts occurring include increasingly accumulated garbage, infrastructural damage, and traffic jam.
Nutrient content, phytochemical profile and anti-methanogen potential of Chaya (Cnidoscolus aconitifolius) leaf extracts
Authors: Setiasih S , Anggraeny Y N , Latifah E , Baswarsiati  , Antonius  , Puspito S , Istiqomah N , Bakrie B , Hidayah N , Indriatie R , Ramsiati DT. , Wardi  , Rachmawati D
Published: June 2024

Chaya leaves (Cnidoscolus aconitifolius) contain many nutrients and phytochemicals expected to reduce ruminants’ methane emissions. This study aims to determine the nutritional quality, phytochemical content and potential inhibitory power of Chaya leaf extract against the growth of rumen fluid methanogen bacteria. The methods used to determine nutrient content were proximate and fibre analysis. The phytochemical content tested were total phenols, tannins and flavonoids. Anti-methanogen test through inhibitory power using liquid culture selective media for methanogens. The results showed that Chaya leaves are a source of fibre feed, which also contains high crude protein (23 - 29%). The highest total phenol and tannin content in ethanol extract of Chaya leaves is 8.62 mg/g and 31.34 ppm, respectively. In contrast, ethyl acetate extract’s highest total flavonoid content is 13.96 mg/g. The highest potential inhibitory power against methanogen bacteria was shown by ethanol extract (50 mg/mL), causing inhibition of 44.56%. This study concludes that Chaya leaves have the potential to be used as ruminant animal feed and as a suppressor of methanogen bacteria, and further tests are recommended for methane gas production in vitro.
Changes of physiological traits on red chili pepper (Capsicum annum L.) exposed by short-term waterlogging
Authors: Siaga E , Rini D S , Sakagami J I , Yabuta S , Meihana M , Lumbantoruan S M
Published: June 2024

Tropical riparian wetland known as non-tidal lowland is potential land for agriculture, especially for vegetable cultivation such as red chili pepper (Capsicum annum L.). Transitional period (dry to rainy season) has a chance for red chili pepper cultivation in the field (at low tide conditions), but has risk of experiencing dynamic water table to waterlogging in early rainy season. The aim of this research was to determine the effects of physiological traits of red chili pepper exposure on short-term (4 days) waterlogging. This study was done at the Tropical Crop Science Laboratory, Kagoshima University, Japan. The experiment was designed as a completely randomized factorial design. The first factor was control/field capacity and waterlogging (entire growing media was submerged). The second factor was chili variety, consisting of Laris and Romario. Treatments began 14 days after transplanting, lasted four days, then followed by seven days of recovery. The results of this study showed that there were changes in photosynthetic characters between before waterlogging, after waterlogging and after recovery time, between control and waterlogging, and also between Laris and Romario. Photosynthetic and transpiration rates decreased sharply under waterlogging in after waterlogging, but increased in after recovery period on Laris, opposite on Romario. Changes occur were associated with the decline in stomatal conductance and chlorophyll fluorescence as a response to waterlogging stress. Laris as a resistant variety has the ability to recover under short-term stress conditions, so it needs to be further developed for cultivation in tropical riparian wetlands.
Business Analysis of Black Ear Mushroom (Auricularia polytrhica (Mont.) Sacc.) in Berjo Village, Ngargoyoso District, Karanganyar Regency
Authors: Hafizh G Z T , Agustina A , Pertiwi Y A B , Supriyadi  , Syahputra A W , Jannah A F , Noviyanti D , Tamami I , Jaatsiyah I , Wicaksono R H , Marom S
Published: June 2024

Black ear mushroom (Auricularia polytricha (Mont.) Sacc.) are edible mushroom that has been widely processed into food and medicine. Thus, due to its high demand, the black ear mushroom has been widely cultivated. The aim of the present study was to determine the feasibility of mushroom cultivation businesses in Berjo Village, Ngargoyoso District, Karanganyar Regency, Central Java. An interview was conducted to three black ear mushroom cultivation business owners. Business performance analysis was carried out. Furthermore, revenue analysis, business efficiency, benefit-cost (B/C) ratio, break-even point (BEP), payback period, and depreciation cost were determined. The average area of mushroom house was 776 m2 with capacity of 18,000 baglogs. Business owners managed their business in the traditional way. For example, watering and pest control was conducted manually. The average revenue of black ear mushroom cultivation was Rp49,555,667/period. In addition, the business efficiency, B/C ratio, BEP unit and price were 1.93, 0.93, 4644 kg, and Rp5,924/kg, respectively. Meanwhile, the payback period and depreciation costs were 0.69 years and Rp6,357,000. Therefore, based on the results obtained in the present study, black ear mushrooms were feasible to be developed into a business.
Intestinal bacterial composition in laying pullet reared in tropical climate received betaine supplementation
Authors: Al Wahid Z , Pradista L A , Prastowo S , Ratriyanto A
Published: June 2024

Intestinal bacterial composition is one of the markers that can be observed in poultry under heat-stress conditions. This study evaluated the effects of dietary betaine on the intestinal bacterial composition of growing pullets reared in a tropical climate. The ninety-six Lohmann laying hens aged three weeks old were distributed into two dietary groups, each comprising six replicates of eight birds. This experiment used PAR-DOC (Japfa Comfeed ©) as basal diet (T0) and basal diet with 1.2g/kg betaine supplementation (T1). The next-generation sequencing method of the 16S rRNA gene region V3–V4 was applied to explore the taxonomy profile. Bacteria from the genus Faecalibacterium, Akkermansia, Desulfovibrio, and Lachnospiraceae UCG-002 were reported as markers in the heat stress condition. A t-test was applied using R software to evaluate the effect of each treatment. The relative abundance from the genus Akkermansia as a marker heat stress response in T1 treatment showed significantly lower than T0 (p<0.05). Based on this result, we concluded that the lower population of the genus Akkermansia indicated that betaine supplementation could alleviate heat stress conditions in growing pullets.
Effect of BAP concentration on the growth of several types of rambutan plants (Nephelium lappaceum L.) in vitro
Authors: Yuniastuti E , Nugroho F S A , Sukaya  , Nandariyah
Published: June 2024

In vitro seed propagation is needed as an alternative to providing superior rambutan planting material. This research aimed to examine the effect of BAP on the growth of several varieties of rambutan in vitro. The method used was a completely randomized design with 2 factors, the first factor was rambutan varieties (binjai, rapiah, and ace), and the second factor was BAP concentrations (0, 2, 4, and 6 ppm). There were 12 treatment combinations and 3 times replications. Variables observed was analyzed using analysis of variance followed by 5% Duncan’s Multiple Range Test and other data (leaf emergence time, number of leaves, root emergence time, number of roots, and root length) were analyzed descriptively. The results showed that the combination of 0 ppm BAP and binjai variety gave the best results on the shoot length, number of leaves, and number of roots. The 0 ppm BAP treatment gave the best results on the number of shoots, shoot length, number of leaves, number of roots, and root length. Binjai variety treatment gave the best results on the time of shoot emergence, shoot length, time of leaf appearance, number of leaves, time of root appearance, and number of roots.
Information Exposure to National Strategic Projects of Toll Road in Central Java
Authors: Utami B W , Hariadi S S , Raya A B
Published: June 2024

This paper takes part in the research on the response of affected farmers to National Strategic Projects. This article reviews the information exposure. The present study aims to examine how farmers assess the frequency of exposure, the credibility of information sources, and the strength of reference groups in constructing the Solo-Yogyakarta toll road in Klaten Regency. The results showed the frequency of information from the government and the largest share of farmers rated as “sometimes”. Meanwhile, the frequency of information from offline (neighbors) and online (media) sources were both considered “never”. Meanwhile, in terms of the credibility (trust and expertise) of information sources, the majority of affected farmers admitted their trust in the government. In terms of the trustworthiness of offline and online reference groups, most farmers doubted the information provided by the offline reference groups and did not trust the information from the online reference groups. Smallholder farmers considered the frequency of information exposure on the land use conversion policy for toll road construction from the government required improvement. However, when compared to the information from neighbors and media, the affected farmers admitted their trust in the official information from the government.
Disease Incidence of Bacterial Pustules (Xanthomonas axonopodis pv. glycines) on Some Soybean Varieties Planted in Mahogany Agroforestry System in Alas Bromo Forestry
Authors: Hadiwiyono  , Firda A L Y
Published: June 2024

Soybean production in Indonesia needs to supply for domestic needs sufficiently. One of the things that influence is the reduction of soybean harvest areas in Indonesia. One of the solutions to the problem is through extensification by utilizing land under shade, which is called an agroforestry system. Agroforestry systems will change intercrop environmental conditions such as reducing light intensity, temperature and increasing humidity. The condition will affect disease development in soybean plants, especially bacterial pustule disease caused byXanthomonas axonopodispv. Glycines.X. axonopodisbacteria can reduce soybean productivity by up to 57.61% in susceptible hosts and favorable environmental conditions. In this research, observations were made regarding the symptoms and incidence of bacterial pustules infection on seven varieties under the shade of mahogany. The varieties used were Anjasmoro, Argomulyo, Dena-1, Dena-2, Denasa-1, Denasa-2, and Devon-1. The research was conducted for three months at KHDTK (Kawasan Hutan dengan Tujuan Khusus) Alas Bromo, Karanganyar, Central Java, Indonesia. The research showed that the lowest incidence of bacterial pustule occurred in the Anjasmoro varieties, with an incidence value of 0%. In comparison, the highest incidence of attacks occurred on the Denasa-1 variety, up to 23.3%.
dCCA: detecting differential covariation patterns between two types of high-throughput omics data
Authors: Lee Hwiyoung , Ma Tianzhou , Ke Hongjie , Ye Zhenyao , Chen Shuo
Published: June 2024

Motivation

The advent of multimodal omics data has provided an unprecedented opportunity to systematically investigate underlying biological mechanisms from distinct yet complementary angles. However, the joint analysis of multi-omics data remains challenging because it requires modeling interactions between multiple sets of high-throughput variables. Furthermore, these interaction patterns may vary across different clinical groups, reflecting disease-related biological processes.

Results

We propose a novel approach called Differential Canonical Correlation Analysis (dCCA) to capture differential covariation patterns between two multivariate vectors across clinical groups. Unlike classical Canonical Correlation Analysis, which maximizes the correlation between two multivariate vectors, dCCA aims to maximally recover differentially expressed multivariate-to-multivariate covariation patterns between groups. We have developed computational algorithms and a toolkit to sparsely select paired subsets of variables from two sets of multivariate variables while maximizing the differential covariation. Extensive simulation analyses demonstrate the superior performance of dCCA in selecting variables of interest and recovering differential correlations. We applied dCCA to the Pan-Kidney cohort from the Cancer Genome Atlas Program database and identified differentially expressed covariations between noncoding RNAs and gene expressions.

Availability and Implementation

The R package that implements dCCA is available at https://github.com/hwiyoungstat/dCCA.
Evergene: an interactive webtool for large-scale gene-centric analysis of primary tumours
Authors: Kennedy Anna , Richardson Ella , Higham Jonathan , Kotsantis Panagiotis , Mort Richard , Shih Barbara Bo-Ju
Published: June 2024

Motivation

The data sharing of large comprehensive cancer research projects, such as The Cancer Genome Atlas (TCGA), has improved the availability of high-quality data to research labs around the world. However, due to the volume and inherent complexity of high-throughput omics data, analysis of this is limited by the capacity for performing data processing through programming languages such as R or Python. Existing webtools lack functionality that supports large-scale analysis; typically, users can only input one gene, or a gene list condensed into a gene set, instead of individual gene-level analysis. Furthermore, analysis results are usually displayed without other sample-level molecular or clinical annotations. To address these gaps in the existing webtools, we have developed Evergene using R and Shiny.

Results

Evergene is a user-friendly webtool that utilizes RNA-sequencing data, alongside other sample and clinical annotation, for large-scale gene-centric analysis, including principal component analysis (PCA), survival analysis (SA), and correlation analysis (CA). Moreover, Evergene achieves in-depth analysis of cancer transcriptomic data which can be explored through dimensional reduction methods, relating gene expression with clinical events or other sample information, such as ethnicity, histological classification, and molecular indices. Lastly, users can upload custom data to Evergene for analysis.

Availability and implementation

Evergene webtool is available at https://bshihlab.shinyapps.io/evergene/. The source code and example user input dataset are available at https://github.com/bshihlab/evergene.
RNA m6A detection using raw current signals and basecalling errors from Nanopore direct RNA sequencing reads
Authors: Ni Peng , Xu Jinrui , Zhong Zeyu , Luo Feng , Wang Jianxin
Published: June 2024

Motivation

Nanopore direct RNA sequencing (DRS) enables the detection of RNA N6-methyladenosine (m6A) without extra laboratory techniques. A number of supervised or comparative approaches have been developed to identify m6A from Nanopore DRS reads. However, existing methods typically utilize either statistical features of the current signals or basecalling-error features, ignoring the richer information of the raw signals of DRS reads.

Results

Here, we propose RedNano, a deep-learning method designed to detect m6A from Nanopore DRS reads by utilizing both raw signals and basecalling errors. RedNano processes the raw-signal feature and basecalling-error feature through residual networks. We validated the effectiveness of RedNano using synthesized, Arabidopsis, and human DRS data. The results demonstrate that RedNano surpasses existing methods by achieving higher area under the ROC curve (AUC) and area under the precision-recall curve (AUPRs) in all three datasets. Furthermore, RedNano performs better in cross-species validation, demonstrating its robustness. Additionally, when detecting m6A from an independent dataset of Populus trichocarpa, RedNano achieves the highest AUC and AUPR, which are 3.8%–9.9% and 5.5%–13.8% higher than other methods, respectively.

Availability and implementation

The source code of RedNano is freely available at https://github.com/Derryxu/RedNano.
A protocol to isolate, identify, and verify glucose- or carbohydrate-binding receptors
Authors: Rashid Nadia , Chhabra Kavaljit H
Published: June 2024

Sensing, transport, and utilization of glucose is pivotal to the maintenance of energy homeostasis in animals. Although transporters involved in mobilizing glucose across different cellular compartments are fairly well known, the receptors that bind glucose to mediate its effects independently of glucose metabolism remain largely unrecognized. Establishing precise and reproducible methods to identify glucose receptors in the brain or other peripheral organs will pave the way for comprehending the role of glucose signaling pathways in maintaining, regulating, and reprogramming cellular metabolic needs. Identification of such potential glucose receptors will also likely lead to development of effective therapeutics for treatment of diabetes and related metabolic disorders. Commercially available biotin or radiolabeled glucose conjugates have low molecular weight; therefore, they do not provide enough sensitivity and density to isolate glucose receptors. Here, we describe a protocol to isolate, identify, and verify glucose-binding receptor/s using high molecular weight glucose (or other carbohydrate) conjugates. We have produced 30 kDa glucose– (or other carbohydrate–) biotin–polyacrylamide (PAA) conjugates with mole fractions of 80:5:15% respectively. These conjugates are used with biotin-streptavidin biochemistry, In-cell ELISA, and surface plasmon resonance (SPR) methods to isolate, identify, and verify glucose- or carbohydrate-binding receptors. We first demonstrate how streptavidin-coated magnetic beads are employed to immobilize glucose–biotin–PAA conjugates. Then, these beads are used to enrich and isolate glucose-binding proteins from tissue homogenates or from single-cell suspensions. The enriched or isolated proteins are subjected to mass spectrometry/proteomics to reveal the identity of top candidate proteins as potential glucose receptors. We then describe how the In-cell ELISA method is used to verify the interaction of glucose with its potential receptor through stable expression of the receptor in-vitro. We further demonstrate how a highly sensitive SPR method can be used to measure the binding kinetics of glucose with its receptor. In summary, we describe a protocol to isolate, identify, and verify glucose- or carbohydrate-binding receptors using magnetic beads, In-cell ELISA, and SPR. This protocol will form the future basis of studying glucose or carbohydrate receptor signaling pathways in health and in disease.
The early after discharge cardiac CT for low-risk chest pain study: the ED-CT study
Authors: Cronin Michael , Gill Aisling , Blake Eve , Dunne Niamh , Sheehy Niall , McMahon Geraldine , Murphy Ross , Daly Caroline
Published: June 2024

Objectives

An accelerated diagnostic pathway is created to aid the management of low-risk patients presenting to the emergency room with chest pain. Records are taken of patient outcomes and factors influencing physician decision-making between inpatient invasive angiography versus early outpatient cardiac CT angiography.

Methods

A cohort study at 30 days post discharge is undertaken over 1 year. Differences are observed between a population of patients who underwent early outpatient CT and a population of ambulatory haemodynamically stable patients who underwent inpatient fluoroscopic angiography.

Results

Totally, 369 patients underwent CT (F = 46%) and 37 underwent angiography (F = 30%). Median outpatient CT was at 14 days. At 30 days, 0 patients suffered mortality or myocardial infarction. Eleven percent were recommended for invasive angiography. Two percent of CT patients underwent coronary revascularization. Median calcium score was 0. Twenty percent of the CT population were commenced on high-potency statin or had their pre-existing statin dose intensified. Calcium score affected a composition of statin commencement, angiography, and revascularization (OR 59, P < .001). Age, troponin, vascular disease, and previous coronary revascularization appeared to influence choice between coronary computed tomography angiography (CCTA) and invasive angiography.

Conclusion

An accelerated diagnostic pathway for outpatient cardiac CT for chest pain resulted in no mortality or myocardial infarction, with a low level of downstream testing and coronary revascularization.

Advances in knowledge

At a median time to CCTA of 14 days post discharge from the emergency department, there is no effect on patient major adverse cardiac events.
Four dimensions of naturalistic language production in aphasia after stroke
Authors: Casilio Marianne , Kasdan Anna V , Bryan Katherine , Shibata Kiiya , Schneck Sarah M , Levy Deborah F , Entrup Jillian L , Onuscheck Caitlin , de Riesthal Michael , Wilson Stephen M
Published: June 2024

There is a rich tradition of research on the neuroanatomical correlates of spoken language production in aphasia using constrained tasks (e.g. picture naming), which offer controlled insights into the distinct processes that govern speech and language (i.e. lexical-semantic access, morphosyntactic construction, phonological encoding, speech motor programming/execution). Yet these tasks do not necessarily reflect everyday language use. In contrast, naturalistic language production (also referred to as ‘connected speech’ or ‘discourse’) more closely approximates typical processing demands, requiring the dynamic integration of all aspects of speech and language. The brain bases of naturalistic language production remain relatively unknown, however, in part because of the difficulty in deriving features that are salient, quantifiable and interpretable relative to both speech-language processes and the extant literature. The present cross-sectional observational study seeks to address these challenges by leveraging a validated and comprehensive auditory-perceptual measurement system that yields four explanatory dimensions of performance—Paraphasia (misselection of words and sounds), Logopenia (paucity of words), Agrammatism (grammatical omissions) and Motor speech (impaired speech motor programming/execution).

We used this system to characterize naturalistic language production in a large and representative sample of individuals with acute post-stroke aphasia (n = 118). Scores on each of the four dimensions were correlated with lesion metrics, and multivariate associations among the dimensions and brain regions were then explored.

Our findings revealed distinct yet overlapping neuroanatomical correlates throughout the left-hemisphere language network. Paraphasia and logopenia were associated primarily with posterior regions, spanning both dorsal and ventral streams, which are critical for lexical-semantic access and phonological encoding. In contrast, agrammatism and motor speech were associated primarily with anterior regions of the dorsal stream that are involved in morphosyntactic construction and speech motor planning/execution, respectively.

Collectively, we view these results as constituting a brain–behaviour model of naturalistic language production in aphasia, aligning with both historical and contemporary accounts of the neurobiology of spoken language production.
Risk-stratified analysis of long-term clinical outcomes and cumulative costs in Finnish patients with recent acute coronary syndrome or coronary revascularization: a 5-year real-world study using electronic health records
Authors: Oksanen Minna , Parviainen Jenna , Asseburg Christian , Hageman Steven , Rissanen Tuomas T , Kivelä Annukka , Taipale Kristian , Visseren Frank , Martikainen Janne
Published: June 2024

Aims

Risk assessment is essential in the prevention of cardiovascular disease. In patients with recent acute coronary syndrome (ACS) or coronary revascularization, risk prediction tools, like the European Society of Cardiology guideline recommended SMART-REACH risk score, are increasingly used to predict the risk of recurrent cardiovascular events enabling risk-based personalized prevention. However, little is known about the association between risk stratification and the social and healthcare costs at a population level. This study evaluated the associations between baseline SMART-REACH risk scores, long-term recurrent clinical events, cumulative costs, and post-index event LDL-C goal attainment in patients with recent ACS and/or revascularization.

Methods and results

This retrospective study used electronic health records and was conducted in the North Karelia region of Finland. The study cohort included all patients aged 45–85 admitted to a hospital for ACS or who underwent percutaneous coronary intervention or coronary artery bypass surgery between 1 January 2017 and 31 December 2021. Patients were divided into quintiles based on their baseline SMART-REACH risk scores to examine the associations between predicted 5-year scores and selected clinical and economic outcomes. In addition, simple age-based stratification was conducted as a sensitivity analysis. The observed 5-year cumulative incidence of recurrent events ranged from 20% in the lowest to 41% in the highest risk quintile, whereas the corresponding predicted risks ranged from 13% to 51%, and cumulative 5-year mean total costs per patient ranged from 15 827 to 46 182€, respectively. Both monitoring and attainment of low LDL-C values were suboptimal.

Conclusion

The use of the SMART-REACH quintiles as a population-level risk stratification tool successfully stratified patients into subgroups with different cumulative numbers of recurrent events and cumulative total costs. However, more research is needed to define clinically and economically optimal threshold values for a population-level stratification.
Remembering Episcopalian Conformity in Restoration England
Authors: White William
Published: June 2024

This article examines how the phenomenon of episcopalian conformity in the late 1640s and 1650s was remembered, debated and explained after the Restoration. Drawing on petitions, pamphlets, funeral sermons and clerical biographies, it shows that both personal ambition and polemical advantage encouraged episcopalians to suppress evidence of Interregnum conformity from the moment the king returned in May 1660. Crucially, however, this kind of whitewashing was by no means the only—or even the principal—way in which episcopalian conformists retrospectively presented their own careers. Many clergymen after 1660 were eager to defend their decision to continue ministering publicly under the English Republic, claiming that their proselytising activities in these years had ultimately helped to advance the interests of Church and king. It is argued that these contrasting approaches to remembering conformity reflect the unstable, contested meaning of loyalty, especially after 1649. As well as adding a new dimension to recent literature on the significance of memories of the English Revolution in the late seventeenth century, the article therefore enhances our understanding of episcopalian identities during the 1640s and 1650s, helping to explain why clergymen who considered themselves loyal to the pre-war order could embark on such divergent trajectories when confronted with defeat, disestablishment and regicide.
Regulation of memory CD4+ T-cell generation by intrinsic and extrinsic IL-27 signaling during malaria infection
Authors: Tsogtsaikhan Sanjaadorj , Inoue Shin-Ichi , Bayarsaikhan Ganchimeg , Macalinao Maria Lourdes , Kimura Daisuke , Miyakoda Mana , Yamamoto Masahiro , Hara Hiromitsu , Yoshida Hiroki , Yui Katsuyuki
Published: June 2024

The generation and maintenance of memory T cells are regulated by various factors, including cytokines. Previous studies have shown that IL-27 is produced during the early acute phase of Plasmodium chabaudi chabaudi AS (Pcc) infection and inhibits the development of Th1-type memory CD4+ T cells. However, whether IL-27 acts directly on its receptor on Plasmodium-specific CD4+ T cells or indirectly via its receptor on other immune cells remains unclear. We aimed to determine the role of IL-27 receptor signaling in different immune cell types in regulating the generation and phenotype of memory CD4+ T cells during Plasmodium infection. We utilized Plasmodium-specific T-cell antigen receptor (TCR) transgenic mice, PbT-II, and Il27rα−/− mice to assess the direct and indirect effects of IL-27 signaling on memory CD4+ T-cell generation. Mice were transferred with PbT-II or Il27rα−/− PbT-II cells and infected with Pcc. Conditional knockout mice lacking the IL-27 receptor in T cells or dendritic cells were employed to discern the specific immune cell types involved in IL-27 receptor signaling. High levels of memory in PbT-II cells with Th1-shift occurred only when both PbT-II and host cells lacked the IL-27 receptor, suggesting the predominant inhibitory role of IL-27 signaling in both cell types. Furthermore, IL-27 receptor signaling in T cells limited the number of memory CD4+ T cells, while signaling in both T and dendritic cells contributed to the Th1 dominance of memory CD4+ T cells. These findings underscore the complex cytokine signaling network regulating memory CD4+ T cells during Plasmodium infection.
SeqCode in the golden age of prokaryotic systematics
Authors: Jiménez Diego Javier , Rosado Alexandre Soares
Published: June 2024

The SeqCode is a new code of prokaryotic nomenclature that was developed to validate taxon names using genome sequences as the type material. The present article provides an independent view about the SeqCode, highlighting its history, current status, basic features, pros and cons, and use to date. We also discuss important topics to consider for validation of novel prokaryotic taxon names using genomes as the type material. Owing to significant advances in metagenomics and cultivation methods, hundreds of novel prokaryotic species are expected to be discovered in the coming years. This manuscript aims to stimulate and enrich the debate around the use of the SeqCode in the upcoming golden age of prokaryotic taxon discovery and systematics.
Treatment of persistent focalized Q fever: time has come for an international randomized controlled trial
Authors: Delahaye Audrey , Eldin Carole , Bleibtreu Alexandre , Djossou Félix , Marrie Thomas J , Ghanem-Zoubi Nesrin , Roeden Sonja , Epelboin Loïc
Published: June 2024

Q fever is a worldwide zoonosis due to Coxiella burnetii, responsible for endocarditis and endovascular infections. Since the 1990s, the combination hydroxychloroquine + doxycycline has constituted the curative and prophylactic treatment in persistent focalized Q fever. This combination appears to have significantly reduced the treatment’s duration (from 60 to 26 months), yet substantial evidence of effectiveness remains lacking. Data are mostly based on in vitro and observational studies. We conducted a literature review to assess the effectiveness of this therapy, along with potential alternatives. The proposed in vitro mechanism of action describes the inhibition of Coxiella replication by doxycycline through the restoration of its bactericidal activity (inhibited in acidic environment) by alkalinization of phagolysosome-like vacuoles with hydroxychloroquine. So far, the rarity and heterogeneous presentation of cases have made it challenging to design prospective studies with statistical power. The main studies supporting this treatment are retrospective cohorts, dating back to the 1990s–2000s. Retrospective studies from the large Dutch outbreak of Q fever (>4000 cases between 2007 and 2010) did not corroborate a clear benefit of this combination, notably in comparison with other regimens. Thus, there is still no consensus among the medical community on this issue. However insufficient the evidence, today the doxycycline + hydroxychloroquine combination remains the regimen with the largest clinical experience in the treatment of ‘chronic’ Q fever. Reinforcing the guidelines’ level of evidence is critical. We herein propose the creation of an extensive international registry, followed by a prospective cohort or ideally a randomized controlled trial.
Genetic profile and characterization of antimicrobial resistance in Acinetobacter baumannii post-COVID-19 pandemic: a study in a tertiary hospital in Recife, Brazil
Authors: Rocha Igor Vasconcelos , Martins Lamartine Rodrigues , Pimentel Maria Izabely Silva , Mendes Renata Pessôa Germano , Lopes Ana Catarina de Souza
Published: June 2024

Aims

To investigate the genetic profile and characterize antimicrobial resistance, including the main β-lactam antibiotic resistance genes, in Acinetobacterbaumannii isolates from a tertiary hospital in Recife-PE, Brazil, in the post-COVID-19 pandemic period.

Methods and Results

Acinetobacter baumannii isolates were collected between 2023 and 2024 from diverse clinical samples. Antimicrobial resistance testing followed standardized protocols, with β-lactamase-encoding genes detected via PCR and sequencing. Investigation into ISAba1 upstream of blaOXA-carbapenemase and blaADC genes was also conducted. Genetic diversity was assessed through ERIC-PCR. Among the 78 A. baumannii, widespread resistance to multiple antimicrobials was evident. Various acquired β-lactamase-encoding genes (blaOXA-23,-24,-58,-143, blaVIM, and blaNDM) were detected. Furthermore, this is the first report of blaVIM-2 in A. baumannii isolates harboring either the blaOXA-23-like or the blaOXA-143 gene in Brazil. Molecular typing revealed a high genetic heterogeneity among the isolates, and multi-clonal dissemination.

Conclusion

The accumulation of genetic resistance determinants underscores the necessity for stringent infection control measures and robust antimicrobial stewardship programs to curb multidrug-resistant strains.
Clinical trial recruitment of people who speak languages other than English: a Children’s Oncology Group report
Authors: Beauchemin Melissa P , Ortega Maria , Santacroce Sheila J , Robles Joanna M , Ruiz Jenny , Hall Anurekha G , Kahn Justine M , Fu Cecilia , Orjuela-Grimm Manuela , Hillyer Grace C , Solomon Samrawit , Pelletier Wendy , Montiel-Esparza Raul , Blazin Lindsay J , Kline Cassie , Seif Alix E , Aristizabal Paula , Winestone Lena E , Velez Maria C
Published: June 2024

Background

Persons who speak languages other than English are underrepresented in clinical trials, likely in part because of inadequate multilevel resources. We conducted a survey of institutions affiliated with the Children’s Oncology Group (COG) to characterize current research recruitment practices and resources regarding translation and interpretation services.

Methods

In October 2022, a 20-item survey was distributed electronically to institutions affiliated with COG to assess consent practices and resources for recruiting participants who speak languages other than English to COG trials. Descriptive statistics were used to summarize responses; responses were compared by institution size and type as well as respondent role.

Results

The survey was sent to 230 institutions, and the response rate was 60% (n = 139). In total, 60% (n = 83) of those respondents had access to short-form consent forms. Full consent form translation was required at 50% of institutions, and 12% of institutional review boards restricted use of centrally translated consent forms. Forty-six percent (n = 64) of institutions reported insufficient funding to support translation costs; 19% (n = 26) had access to no-cost translation services. Forty-four percent (n = 61) were required to use in-person interpreters for consent discussions; the most frequently cited barrier (56%) to obtaining consent was lack of available in-person interpreters. Forty-seven percent (n = 65) reported that recruiting persons who speak languages other than English to clinical trials was somewhat or very difficult.

Conclusions

Institutions affiliated with COG face resource-specific challenges that impede recruitment of participants who speak languages other than English for clinical trials. These findings indicate an urgent need to identify strategies aimed at reducing recruitment barriers to ensure equitable access to clinical trials.
(035) WOMEN IN PROSTHETIC UROLOGY: MENTORSHIP, SPONSORSHIP, AND CAREER ADVANCEMENT
Authors: Paulsen O , Orozco Rendon D , King S , Hehemann M , Ramasamy R , L  Bernie H
Published: June 2024

Introduction

Mentorship is a dynamic, reciprocal personal relationship in which a more experienced member of the organization (mentor), acts as a guide, role model, teacher, and sponsor of a less experienced person (mentee). Sponsorship involves the mentor making a personal investment in the advancement of the mentee. Women currently in and looking to enter prosthetic urology are not afforded the same quality or quantity of these dynamic relationships compared to men.

Objective

The goals of this manuscript are to discuss obstacles and barriers faced by women in prosthetic urology, highlight the benefits of mentorship and sponsorship in advancing the careers of women in this field, and provide recommendations for creating a more inclusive and supportive environment for women to excel in prosthetic urology.

Methods

Six authors carefully reviewed full-text, published articles related to the climate of [women in urology], [prosthetic urology], and available [mentorship], [sponsorship], and [leadership], and data from the 2022 American Urologic Association (AUA) census. Thirty-two sources were included.

Results

Urology and specifically, prosthetic urology, has a long history of being male-prominent. Several factors play into this truth, including gender roles, societal influences, implicit biases, medical history, and a lack of early exposure, mentorship, and sponsorship. Despite strides made in gender equity in medicine, women remain underrepresented in urology making up only 11.6% of practicing urologists in the United States. In subspecialties such as prosthetic urology, women make up even less of the pool. These factors also contribute to the lack of women in leadership positions. As of 2023, women occupy just 3 of the 13 board member positions and 7 of the 29 committee chair positions in the SMSNA.

Conclusions

Implementing successful mentorship involves recognizing the gender disparities that exist in prosthetic urology, having male mentors and sponsors, and breaking the traditional mentor-mentee hierarchies. Additionally, mentees can foster effective mentorship by establishing SMART goals and getting involved in women affinity groups. By creating an inclusive, diverse environment that not only welcomes, but mentors, and sponsors women, prosthetic urology can harness its full potential.

Disclosure

No.
(036) BASELINE CHARACTERISTICS OF PATIENTS UNDERGOING GENDER AFFIRMING HYSTERECTOMIES
Authors: De Moya A , Watson K , Rowen T
Published: June 2024

Introduction

Gender affirming hysterectomies (GAH) are one of the many interventions offered to people with uteruses who are seeking gender affirming care. Gender affirming care, especially hormones, has been shown to improve sexual satisfaction outcomes, but no research currently exists on sexual function or orgasm experience after gender affirming hysterectomy in particular. Post-hysterectomy sexual function has only been examined in cisgender populations, and has found mixed results on sexual health, wellness, and function. Research on sexual function and orgasm experience after GAH is needed to inform evidence-based recommendations and advance our understanding of sexual pleasure in a population that has historically been under-researched.

Objective

To achieve a better understanding of how gender affirming hysterectomies impact the experience of sex through a standardized analysis of orgasms and sexual function.

Methods

This project is a prospective study of patients receiving gender affirming hysterectomies at a single tertiary care center (November 2023-ongoing). Baseline characteristics (pre-hysterectomy) have been collected and analyzed via surveys asking about demographics, sexual practices, medical history, orgasm satisfaction (Orgasm Rating Scale) and sexual function (Transmasculine Sexual Functioning Index).

Results

We currently have 5 patients enrolled and anticipate a sample size of 30 participants by mid-February 2024. We plan to present pre-hysterectomy data describing participants’ overall sexual function and satisfaction. We anticipate a diversity of sexual practices and wellbeing.

Conclusions

There is a dearth in the current literature describing sexual function of individuals pursuing GAH. Further characterizing this population's pre-operative sexual practices and satisfaction will improve our ability to counsel patients considering GAH. Comparing this baseline data to sexual function post-GAH will provide insight into how GAH impacts ability to perform sexually and its influence on overall sexual satisfaction. This data will allow us to provide evidence-based recommendations regarding the impact of hysterectomy on orgasm and sexual function in patients seeking GAH.

Disclosure

No.
(062) IMPLEMENTING A VALIDATED SEXUAL DYSFUNCTION SCREENING TOOL AT AN INNER-CITY WOMEN’S HEALTH CLINIC
Authors: Zandvliet R , Wortel S , Hartnett J , Lindsay S
Published: June 2024

Introduction

The American College of Obstetricians and Gynecologists (ACOG) reports 43% of American women experience sexual health problems, including Female Sexual Interest and Arousal Disorder, Female Orgasmic Disorder, Genito–Pelvic Pain and Penetration Disorder, and Substance or Medication-Induced Sexual Dysfunction.

Objective

At Women’s Ambulatory Health Services (WAHS), an inner-city clinic associated with Hartford HealthCare, at which UConn Health ObGyn residents work, there is no routine screening in place for sexual dysfunction. This project aimed to implement the Female Sexual Function Index (FSFI) for screening for sexual dysfunction at this clinic to identify patients who may benefit from treatment.

Methods

We implemented the FSFI-short version, a six-question screening tool for sexual dysfunction that has been validated in English and Spanish and utilized in many countries on July 1st, 2022. Patients presenting for a new gynecologic visit or an annual gynecologic exam were asked to complete the screening tool. Patients who scored equal to or less than 18 on the FSFI-short version were identified as at risk for female sexual dysfunction and were offered referral to a health psychologist specializing in sexual dysfunction. We utilized the RE-AIM framework for implementation science to guide the implementation evaluation. We collected data on patients from July 1 through December 1, 2022. We collected patient demographics and implementation outcomes, including rate of survey completion, candidacy for referral and referral completion.

Results

196 surveys were reviewed between July 1st and December 1st of 2022. 44 surveys were excluded for various reasons, including not meeting study inclusion criteria or invalid responses. 152 screening forms were included and 45 patients screened positive. Subjective patient barriers were gathered from comments written directly onto the paper survey as well as quotes documented by their providers in the visit note. These subjective barriers included hesitancy to discuss sexual health and lacking knowledge that the gynecologist provider offers assessment and management for these disorders.

Conclusions

The introduction of the FSFI-sv at WAHS has both expanded the resources offered to patients, enhanced the environment surrounding topics of women’s health both between staff members as well as within the patient-provider relationship, and has unearthed multiple opportunities for improving the screening process, referral selection and work flow for sexual dysfunction amongst the patient population.

Disclosure

No.