bluuebunny/crossref_metadata_2025_split huggingface dataset:
ПРАКТИЧЕСКИЙ ОПЫТ СЕКВЕНИРОВАНИЯ ХЛОРОПЛАСТНЫХ ГЕНОМОВ КОРОТКИМИ РИДАМИ
Authors: Шевцов А.Б. , Ержанова Н.С. , Амиргазин А.О. , Тұрсұнбай Н.Е. 
Published: September 2024

Хлоропласты (пластиды) представляют собой растительные органеллы с автономной кольцевой молекулой ДНК размером от 72 до 217 тысяч пар нуклеотидов, кодирующей около 130 генов вовлеченных в фотосинтез. Хотя геномы хлоропластов содержат высококонсервативные гены, необходимые для роста и развития растений, они также содержат вариабельные области, т.е. межгенные области и структурные вариации внутри генов, что отражает важную эволюционную информацию растений. Полные последовательности генома хлоропластов могут быть использованы для эволюционных исследований внутри и между различными группами растений.
Для полногеномного секвенирования хлоропластных геномов (хпДНК) применяется две стратегии: амплификация всего генома хлоропластов из тотальной ДНК с использованием длинной полимеразной цепной реакции (ПЦР) и прямое выделение хпДНК из свежего растительного материала с последующим секвенированием с использованием высокопропускных секвенаторов. В последнем случае качество и чистота выделенной хлоропластной ДНК напрямую влияет на полученный результат. Предложен ряд методов для отделения хлоропластов и выделения ДНК. Некоторые методы, такие как центрифугирование хлоропластов в градиенте с сахарозой требуют наличия дорогостоящего оборудования, а методы основанные на применение ДНКаз не всегда эффективны. На наш взгляд, осаждение хлоропластов в растворах с повышенной ионной силой позволяет получить достаточно очищенные препараты хлоропластной ДНК пригодные для секвенирвоания на NGS платформах. Детальный протокол описан в работе Shi C. с соавторами (2012).
За период 2023 года сотрудниками Национального центра биотехнологии было проведено выделение хпДНК из листьев 71 одного вида растений. Концентрация ДНК в 1 мкл раствора варьировала от 2,4 до 32,1 нг, что достаточно для секвенирвоания на MiSeq (Illumina).
Секвенирование 14 образцов позволило получить от 1,2 до 2 млн. ридов на образец. Картирование ридов на собранный хлоропластный геном показывает целевое секвенирвоание на уровне 50-86%.
Применяемая технология может быть использована для изучения и подтверждения таксономического статуса высших сосудистых растений Казахстана.
Increased intracellular H
2
S levels enhance iron uptake in
Escherichia coli
Authors: Nonoyama Shouta , Maeno Shintaro , Gotoh Yasuhiro , Sugimoto Ryota , Tanaka Kan , Hayashi Tetsuya , Masuda Shinji 
Published: September 2024

ABSTRACT

We investigated the impact of intracellular hydrogen sulfide (H
2
S) hyperaccumulation on the transcriptome of
Escherichia coli
. The wild-type (WT) strain overexpressing
mstA
, encoding 3-mercaptopyruvate sulfur transferase, produced significantly higher H
2
S levels than the control WT strain. The
mstA
-overexpressing strain exhibited increased resistance to antibiotics, supporting the prior hypothesis that intracellular H
2
S contributes to oxidative stress responses and antibiotic resistance. RNA-seq analysis revealed that over 1,000 genes were significantly upregulated or downregulated upon
mstA
overexpression. The upregulated genes encompassed those associated with iron uptake, including siderophore synthesis and iron import transporters. The
mstA
-overexpressing strain showed increased levels of intracellular iron content, indicating that H
2
S hyperaccumulation affects iron availability within cells. We found that the H
2
S-/supersulfide-responsive transcription factor YgaV is required for the upregulated expression of iron uptake genes in the
mstA
-overexpression conditions. These findings indicate that the expression of iron uptake genes is regulated by intracellular H
2
S, which is crucial for oxidative stress responses and antibiotic resistance in
E. coli
.

IMPORTANCE

H
2
S is recognized as a second messenger in bacteria, playing a vital role in diverse intracellular and extracellular activities, including oxidative stress responses and antibiotic resistance. Both H
2
S and iron serve as essential signaling molecules for gut bacteria. However, the intricate intracellular coordination between them, governing bacterial physiology, remains poorly understood. This study unveils a close relationship between intracellular H
2
S accumulation and iron uptake activity, a relationship critical for antibiotic resistance. We present additional evidence expanding the role of intracellular H
2
S synthesis in bacterial physiology.
Gill-associated ammonia oxidizers are widespread in teleost fish
Authors: Mes Wouter , Lücker Sebastian , Jetten Mike S.M. , Siepel Henk , Gorissen Marnix , van Kessel Maartje A.H.J. 
Published: September 2024

ABSTRACT

Recent advances in sequencing methods have greatly expanded the knowledge of teleost-associated microorganisms. While fish-gut microbiomes are comparatively well studied, less attention has gone toward other, external organ-microbiome associations. Gills are particularly interesting to investigate due to their functions in gas exchange, osmoregulation, and nitrogen excretion. We recently discovered a branchial symbiosis between nitrogen-cycling bacteria and teleosts (zebrafish and carp), in which ammonia-oxidizing
Nitrosomonas
and denitrifying bacteria together convert toxic ammonia excreted by the fish into harmless dinitrogen (N
2
) gas. This symbiosis can function as a “natural biofilter” in fish gills and can potentially occur in all ammonotelic fish species, but it remains unknown how widespread this symbiosis is. In this study, we analyzed all publicly available gill microbiome data sets and checked for the presence of
Nitrosomonas
. We discovered that more than half of the described fish gill microbiomes contain 16S rRNA gene sequences of ammonia-oxidizing bacteria (AOB). The presence of gill-specific AOB was shown in both wild and aquacultured fish, as well as in marine and freshwater fish species. Based on these findings, we propose that ammonia oxidizers are widespread in teleost fish gills. These gill-associated AOB can significantly affect fish nitrogen excretion, and the widespread nature of this association suggests that the gill-associated AOB can have similar impacts on more fish species. Future research should address the contribution of these microorganisms to fish nitrogen metabolism and the fundamental characteristics of this novel symbiosis.

IMPORTANCE
Recent advances in sequencing have increased our knowledge of teleost-associated microbiota, but the gill microbiome has received comparatively little attention. We recently discovered a consortium of nitrogen-cycling bacteria in the gills of common carp and zebrafish, which are able to convert (toxic) ammonia into harmless dinitrogen gas. These microorganisms thus function as a natural nitrogen biofilter. We analyzed all available gill microbiome data sets to determine how widespread gill-associated ammonia-oxidizing bacteria (AOB) are. More than half of the data sets contained AOB, representing both aquacultured and wild fish from freshwater and marine habitats. In total, 182 amplicon sequencing variants were obtained, of which 115 were found specifically in the gills and not the environmental microbiomes. As gill-associated AOB are apparently widespread in teleost fish, it is important to study their impact on host nitrogen excretion and the potential to reduce ammonia accumulation in (recirculating) aquaculture of relevant fish species.
Irreversible neurological manifestations in undiagnosed disseminated gonococcal infection
Authors: Lin Andrea , Julien Justine , Mauney Sarah , Grogan James 
Published: September 2024

Neisseria gonorrhoeae causes a common sexually transmitted infection with manifestations ranging from asymptomatic to urethritis and pelvic inflammatory disease to disseminated infections including septic arthritis. Serious complications may arise in unrecognised or inappropriately treated infections.We report a young, healthy woman who developed fever and joint pain and was diagnosed with an inflammatory arthritis. After starting immune suppressing treatments, she experienced right wrist drop and progressive muscle atrophy, joint contractures and sensory loss. Electrodiagnostic studies showed patchy, mixed neurogenic and myopathic features. Areas of muscle oedema on extremity MRI led to a right brachioradialis biopsy, which showed only nonspecific changes. Other testing, including lumbar puncture and MRI of the brain/spine was noncontributory. Additional history revealed unprotected intercourse with a new partner prior to symptom onset. Urine gonorrhoeae PCR was positive, and right shoulder arthrocentesis confirmed septic arthritis. After intravenous antibiotic treatment with ceftriaxone, she demonstrated slow, incomplete symptomatic improvement.
Familial catamenial coronary spasms
Authors: de Groot Elisabeth A A , van Heerebeek Loek , Vink Maarten A , Kuipers Remko S 
Published: September 2024

Coronary artery spasms represent important causes of myocardial ischaemia and infarction in patients with non-obstructive coronary artery disease. They are notably seen in younger people and occur almost equally in men and women. Besides traditional risk factors (ie, smoking), female hormones might also play a role.We report of two young sisters who presented with myocardial infarction caused by catamenial coronary spasms (CS), that is, during menstruation. In one of these women, this resulted in heart failure with a severely reduced ejection fraction and ultimately a heart transplant because of intractable ventricular arrhythmias.CS might result from changing hormone levels (especially oestrogen) during menstruation. Increased awareness of the occurrence of catamenial CS is essential for diagnosis and consequent treatment with coronary vasodilators and/or specific oestrogen/progesterone regimens.
Extravascular lipoma over the subclavian vein
Authors: Thariq Ajmal Imran , Thiyagarajan Amrithraj , Anand Felix , Muralidhar Venkiteswaran 
Published: September 2024

A rare instance of extravascular lipomas located over the subclavian vein in a woman in her early 60s presented unique diagnostic and therapeutic challenges due to their close proximity to critical structures. Lipomas, which are the most commonly occurring benign soft tissue tumours, are typically composed of mature adipocytes. Although lipomas can develop in any region of the body, they are most commonly found in the subcutaneous tissues of the trunk and proximal limbs. Extravascular lipomas, especially those near major blood vessels like the subclavian vein, are extremely uncommon.In this particular case, the tumour was extensively in contact with the right subclavian vein, though there was no intravascular involvement. The lipomatous tumour was successfully excised during surgery, with the subclavian vein and surrounding structures being preserved. Histopathological analysis confirmed the diagnosis of a benign lipoma. This case highlights the significance of early diagnosis, meticulous surgical planning and multidisciplinary collaboration to achieve the best possible outcomes.
RidStress 2 randomised controlled trial protocol: an Australian phase III clinical trial of intrapartum sildenafil citrate or placebo to reduce emergency caesarean birth for fetal distress in women with small or suboptimally grown infants at term (≥37 weeks)
Authors: Triggs Tegan , Badawi Nadia , Crawford Kylie , Liley Helen , Lehner Christoph , Nugent Rachael , Kristensen Karl , da Silva Costa Fabrício , Tarnow-Mordi William , Kumar Sailesh 
Published: September 2024

IntroductionSmall for gestational age (SGA) infants are at increased risk of fetal distress in labour requiring emergency operative birth (by caesarean section (CS), vacuum or forceps). We have previously shown that maternal oral sildenafil citrate (SC) in labour halves the need for operative birth for suspected fetal distress in women with appropriately grown term infants.Methods and analysisRidStress 2 is a phase III randomised, double-blinded, placebo-controlled trial of 660 women with an SGA or suboptimally grown fetus (estimated fetal weight or abdominal circumference<10th centile for gestational age) planning a vaginal birth at term. The trial will determine whether oral intrapartum SC (50 mg eight hourly) reduces the relative risk of emergency CS for fetal distress compared with placebo. The primary outcome is CS for fetal distress, and the secondary outcomes are any operative birth for fetal distress, cost-effectiveness of SC treatment and 2-year childhood neurodevelopmental outcomes. To detect a 33% reduction in the primary outcome from 30% to 20% for an alpha of 0.05 and power of 80% with 10% dropout, requires approximately 660 women (330 in each arm). This sample size will also yield >90% power to detect a similar reduction for the secondary outcome of any operative birth (CS or instrumental vaginal birth) for fetal distress.Ethics and disseminationEthics approval was granted by the Mater Misericordiae Limited Human Research Ethics Committee (EC00332) on 11 September 2020. We plan to disseminate the results of this randomised controlled trial through presentations at scientific meetings and peer-reviewed journals, adhering to all relevant reporting guidelines.Trial registration numberRidStress 2 is registered with the Australian New Zealand Clinical Trials Registry (ACTRN12621000354886, 29/03/2021) and the Therapeutic Goods Association of Australia (date registered: 16 March 2021).
Developmental characteristics and control effects of myopia and eye diseases in children and adolescents: a school-based retrospective cohort study in Southwest China
Authors: Tang Wenyi , Tan Tao , Lin Jiang , Wang Xin , Ye Bo , Zhou Lina , Zhao Danni , Liu Ling , Zou Lingyun 
Published: September 2024

ObjectivesTo characterise the prevalence of myopia and eye diseases among school adolescents and children in Southwest China, and to evaluate the effectiveness of myopia control tools.DesignRetrospective cohort study.SettingAcross 95 basic education institutions in Southwest China.Participants96 146 children aged 3–17 years from a school-based survey conducted between 2019 and 2021.Primary outcome measuresThe data of vision assessment and eye disease examination of school students were analysed, including a total of four surveys once per semester. The prevalence of myopia categorised as low (−0.5D to −3.0D), moderate (−3.0D to −6.0D) and high (≥−6.0D), along with the prevalence of significant ocular diseases, was assessed. Stratified analyses were conducted to investigate the impact of correction time on visual acuity (VA) and biological parameters. Subsequently, the subjects across the groups were matched using the nearest neighbour method, followed by multidimensional statistical analysis.ResultsThe prevalence of myopia among the surveyed students was 38.39%. After controlling for confounding variables, the statistical analysis revealed a 0.1 increase in mean VA within the orthokeratology group and a 0.1 decrease in VA within the spectacle group (p<0.001), with statistically significant differences in corneal radius, corneal curvature and equivalent spherical lens (p<0.05). Multivariate analysis indicated a statistically significant reduction in VA in the ophthalmopathy group compared with the control group (p=0.031). Furthermore, it was demonstrated that the risk of eye disease during vision correction was greater among older students than their younger counterparts (OR>1), and that female students exhibited a higher risk than male students (OR=1.5).ConclusionsThe current high prevalence of myopia and eye diseases among Southwest China’s school youths demands public health attention. Minors wearing orthokeratology lenses at night, especially in primary school, exhibit significantly improved naked-eye vision. However, vigilant eye healthcare during the correction period is crucial, especially for girls.
Enhancing patient participation in discharge medication communication: a feasibility pilot trial
Authors: Tobiano Georgia , Manias Elizabeth , Chaboyer Wendy , Latimer Sharon L , Teasdale Trudy , Wren Kellie , Jenkinson Kim , Marshall Andrea P 
Published: September 2024

ObjectivesTo pilot test a co-designed intervention that enhances patient participation in hospital discharge medication communication.DesignPilot randomised controlled trial.SettingOne tertiary hospital.ParticipantsPatients who were ≥45 years of age; ≥1 chronic illness and ≥1 regularly prescribed medication that they manage at home were recruited between October 2022 and May 2023. Healthcare professionals on participating units completed surveys.InterventionThe co-designed intervention included three websites: a medication search engine, a medication question builder and tools to facilitate medication management at home. Inpatient posters contained QR codes to provide access to these websites.Primary and secondary outcome measuresThe primary outcomes were the feasibility of study processes and intervention acceptability. Feasibility of study processes was measured in terms of recruitment, fidelity, retention, missing data and contamination. Patients in the intervention group and healthcare professionals on the wards self-reported intervention acceptability. Secondary outcomes were medication understanding, use, self-efficacy and healthcare utilisation.Results60 patients were recruited and randomised; half in each study group. The intervention was largely delivered as intended, and 99.7% of data collected was complete. In total, 16/59 (27.1%) patients were lost to follow-up 28 days after hospital discharge, and 3 patients in the usual care group reported that they saw the intervention poster prior to hospital discharge. 21 of 24 intervention group patients (87.5%) deemed the intervention acceptable, while half of the healthcare professionals (n=5, 50%) thought it was acceptable.ConclusionsWe demonstrated that in a future definitive trial, intervention fidelity would be high with little missing data, and patients would likely find the intervention acceptable. Thus, a larger trial may be warranted, as the intervention is implementable and approved by patients. However, additional strategies to increase recruitment and retention of eligible participants are needed. Healthcare professionals may require more preparation for the intervention to enhance their perceptions of intervention acceptability.Trial registration numberACTRN12622001028796.
Healthcare service utilisation among adults with coronary artery disease in rural Aluva, South India: a community-based cross-sectional study
Authors: Mohandas Neeraj Vinod , Vijayakumar Krishnapillai , Sreedevi Aswathy , George Neethu , Menon Jaideep , Dinesh Avani , Mohandas Vinod 
Published: September 2024

ObjectivesTo assess the pattern and determinants of healthcare service utilisation among adults with coronary artery disease (CAD) in a rural setting in Kerala, India.DesignA community-based cross-sectional analysis conducted within a study cohort.SettingThe study was conducted from January 2022 to March 2022 within the ENDIRA Cohort (Epidemiology of Non-communicable Diseases In Rural Areas) in the rural part of Aluva municipality of Ernakulam district, Kerala, India, which comprises five adjacent panchayats with a population of approximately 100, 000 individuals.ParticipantsPatients with CAD aged 35–80 years from the ENDIRA cohort with a history of at least one event of myocardial infarction in the past decade.Outcome measuresThe main outcome measured was the inadequacy of healthcare service utilisation among patients with CAD. The factors evaluated included age, gender, socioeconomic status, insurance, out of pocket expenses, choice of health care facility for follow up, distance from health centre as well as reported alcohol use, tobacco use and healthcare satisfactionResultsThe study encompassed 623 participants with a mean age of 65.12 (±8.55) years, of whom 71% were males. The prevalence of inadequate utilisation of health services was 58.7%. The independent predictors of underutilisation included reported alcohol consumption (adjusted OR (AOR) 2.36; 95% CI 1.41 to 3.95), living more than 20 km from healthcare facilities (AOR 1.96; 95% CI 1.14 to 3.37) as well as the preferences for specific doctors and adequate services at healthcare facilities (AOR 3.43; 95% CI 1.46 to 8.04). The patients with monthly CAD medication expenses exceeding Rs4000 had 0.26 times lesser odds to underuse healthcare services (AOR 0.26; 95% CI 0.10 to 0.65).ConclusionThe study reveals a suboptimal pattern of healthcare service utilisation among patients with CAD. Ensuring community access to standardised, high-quality follow-up care is crucial for enhancing healthcare utilisation following CAD.
Cohort profile: the ADAPT study, a prospective study of pregnancy preferences, pregnancy, and health and well-being in the southwestern USA
Authors: Rocca Corinne H , Gould Heather , Gonzalez Elizabeth , Foster Diana G , Muñoz Isabel , Parra Miriam , Ralph Lauren J 
Published: September 2024

Purpose
Significant methodological shortcomings limit the validity of prior research on pregnancy decision-making and the effects of ‘unintended’ pregnancies on people’s health and well-being. The Attitudes and Decisions After Pregnancy Testing (ADAPT) study investigates the consequences for individuals unable to attain their pregnancy and childbearing preferences using an innovative nested prospective cohort design and novel conceptualisation and measurement of pregnancy preferences.

Participants
This paper describes the characteristics of the ADAPT Study Cohort, comprised of 2015 individuals aged 15–34 years, assigned female at birth, recruited between 2019 and 2022 from 23 health facilities in the southwestern USA.

Findings to date
The cohort was on average 25 years old. About 59% identified as Hispanic/Latine, 21% as white, and 8% as black, 13% multiracial or another race. Over half (56%) were nulliparous. About 32% lived in a household with income <100% of the federal poverty level. A significant minority (37%) reported a history of a depressive, anxiety or other mental health disorder diagnosis, and 30% reported currently experiencing moderate or severe depressive symptoms. Over one-quarter (27%) had ever experienced physical intimate partner violence, and almost half (49%) had ever experienced emotional abuse. About half (49%) had been diagnosed with a chronic health condition, and 37% rated their physical health as fair or poor. The 335 (17%) participants who experienced incident pregnancy over 1 year were similar to selected non-pregnant matched comparison participants in terms of age, racial and ethnic identity, and parity but were more likely to live with a main partner than comparison participants.

Future plans
We will continue to follow participants who experienced incident pregnancy and non-pregnant comparison participants until 2026. Analyses will examine pregnancy decision-making and investigate differences in health and well-being by prepregnancy pregnancy desires and feelings after the discovery of pregnancy, offering new insights into the consequences of not attaining one’s reproductive preferences.

Trial registration number

NCT03888404
.