bluuebunny/crossref_metadata_2025 huggingface dataset:
Brand-Name Alphabet Books and Reading the Victorian Marketplace
Authors: Hoffman A Robin
Published: October 2024

“Chapter 5: Brand-Name Alphabet Books and Reading the Victorian Marketplace” looks at alphabetical illustrations designed by Kate Greenaway and Hablot Knight Browne, or “Phiz”—Charles Dickens’s best-known illustrator—to show how branding combined with the rise of photomechanical reproduction in England during the last quarter of the nineteenth century. Greenaway’s bestselling A Apple Pie (1886) and Phiz’s Funny Alphabet (1883) disregarded both visual and textual literacy in order to commodify nostalgic ideas about childhood, glorifying domestic reading instruction over schooling. In the process, such works undermined contemporary efforts to revitalize craft and aesthetics within an increasingly text-based print culture. Literacy education was an incidental goal in the face of appeals to the heartstrings and pocketbooks of nostalgic adults.
Inevitable Literacy and the Alphabet at the Fin de Siècle
Authors: Hoffman A Robin
Published: October 2024

“Chapter 6: Inevitable Literacy and the Alphabet at the Fin de Siècle” concludes this survey of nineteenth-century works by arguing that widely circulated late Victorian representations of the alphabet tended to reinforce the alphabet’s bureaucratic and even colonizing functions rather than its visual character. After nationalized elementary education normalized textual literacy in childhood, alphabet books were less useful for promoting aesthetics or design—especially after photographic modes of representation and reproduction had saturated print culture. Rudyard Kipling’s Just So stories about “How the Alphabet Was Made” (1902) instead satirized evolutionary theory, while Hilaire Belloc’s A Moral Alphabet (1899) expressed cynicism about schooling. Both writers exploited alphabetical illustration and nostalgia in order to advocate for the survival of individualized inscription alongside industrial modes.
Integrating datasets from herbarium specimens and images to treat a Neotropical myrtle species complex
Authors: Gaem Paulo Henrique , Andrella Giovani Carlos , Maurin Olivier , Bittrich Volker , Mazine Fiorella Fernanda , Lucas Eve , Estanislau do Amaral Maria do Carmo
Published: October 2024

Background and Aims

Herbaria are the most important source of information for plant taxonomic work. Resources and technologies available today, such as digitized collections and herbarium DNA sequencing, can help accelerate taxonomic decisions in challenging plant groups. Here we employ an integrative methodology relying exclusively on herbarium specimens to investigate species boundaries in the Neotropical Myrcia neoobscura complex (Myrtaceae).

Methods

We collected morphometric data from high-resolution images of herbarium sheets and analysed them using hierarchical clustering. We posteriorly tested the obtained morpho-groups with phylogenomics using the Angiosperms353 probe kit. We also gathered phenological and geographical information from specimen labels and built phenological histograms and ecological niche models to investigate ecological differences amongst taxa.

Key Results

Current circumscriptions of Myrcia arenaria, Myrcia neoglabra and Myrcia neoregeliana are confirmed in this study. Conversely, the four pieces of evidence together support Calyptranthes langsdorffii var. grandiflora, Marlierea regeliana var. parviflora and Marlierea warmingiana as separate from Myrcia marliereana, Myrcia neoriedeliana and Myrcia neoobscura, respectively, contrary to arrangements proposed by previous authors. Integrated analyses also support separation between Myrcia excoriata and two similar, undescribed taxa.

Conclusions

Our data reveal the need for major changes in the systematics of the group, with recognition of 12 species. The successful delivery of our study aims was possible due to obtaining robust, high-quality data from museum specimens. We emphasize the importance of maintaining botanical collections physically and digitally available for taxonomic work and advocate their use to accelerate taxonomic solutions of tropical species complexes hollistically. This is urgent, given the paucity of funds for fieldwork and unprecedented rates of habitat loss in the tropics.
Laissez-Passer: Papering over the French Revolutionary Past
Authors: Taws Richard
Published: October 2024

In France, the last decade of the eighteenth century saw an explosion in papers of diverse kinds, put to new political uses. However, in the aftermath of the French Revolution, paper was also instrumentalised to articulate histories of revolutionary participation, as well as changing ideas about revolutionary identification. Some of these were coded as virtuous: paper objects found a place at the heart of sentimental accounts of personal sacrifice, such as that of prison warder Joseph Cange. Conversely, paper was central to claims for culpability or reparation—most strikingly, assorted papers were mobilised as defence against recrimination for involvement in regicide, as discussed here in relation to printmaker and politician Antoine-Louis-François Sergent-Marceau. This essay considers how the apparent abundance that characterised the period’s paper ecology, along with new attitudes toward paper’s proliferation, preservation and disposal, bore the imprint of political justification, evasion and historical revisionism—all framed by the need to ‘pass’ as post-revolutionary.
Gallstone ileus causing perforation of multiple segments of small bowel
Authors: Eiref Andrew D , Hester Karri , Glaspy Tyler , Sarkisova Anna , Anand Sohini , Zimmerman Patrick W , Nicoara Michael , Patel Krishan , Walden Heath , Eiref Simon D
Published: October 2024

Gallstone ileus results in a mechanical small bowel obstruction when an itinerant gallstone tumbles downstream and obstructs the bowel lumen. Associated proximal intestinal injury with perforation is rare, and concomitant perforation of multiple segments of bowel in the setting of gallstone ileus has never been reported in the literature. We are reporting the case of a 67-year-old female patient who had gallstone ileus causing perforation of multiple segments of small bowel. At operation, she was found to have a 3.2-cm gallstone lodged at the terminal ileum, perforation of both the mid ileum and mid jejunum, and gross enteric spillage. She underwent removal of the gallstone and small bowel resection × 2. She was initially left in discontinuity with an open abdomen. She returned to the operating room 2 days later for bowel anastomosis and abdominal closure. She recovered well after surgery and was discharged home.
Care-theoretic semantics
Authors: Ferguson Thomas Macaulay , Kadlečíková Jitka
Published: October 2024

This paper argues for two claims, one conservative and the other one less so. First is the thesis that the range of linguistic features that can be considered authentically semantic is far wider in breadth than is typically acknowledged. In particular, linguistic phenomena that are entirely orthogonal to veridical considerations—including ethical matters—are sufficiently robust to support e.g. theories of meaning and inference. Second, we aim to argue that philosophy’s prioritization of truth obscures the existence of an important prior concern for care or the reduction of harm. Specifically, we offer a topic-theoretic interpretation of the bounds consequence reading of sequents put forward by Restall and Ripley. We argue that this reading allows us to provide a rigorous semantics using the newly introduced categories of care and harm. An important objection may be that philosophy requires the centrality and priority of truth above all else insofar as truth-like features are necessary to ground theories of meaning or reasoning. Anticipating such an objection, we will argue that care not only is an authentically semantic feature but also that care is sufficient to ground such theories.
Procalcitonin-Guided Management and Duration of Antibiotic Therapy in Critically Ill Cancer Patients With Sepsis (Pro-Can Study): A Randomized Controlled Trial
Authors: Nazer Lama H. , Awad Wedad , Thawabieh Hadeel , Abusara Aseel , Abdelrahman Deema , Addassi Awad , Abuatta Osama , Sughayer Maher , Shehabi Yahya
Published: October 2024

OBJECTIVES:

To evaluate the effect of procalcitonin-guided management on the duration of antibiotic therapy in critically ill cancer patients with sepsis.

DESIGN:

Randomized, controlled, single-blinded trial.

SETTING:

A comprehensive multidisciplinary cancer hospital in Jordan.

PATIENTS:

Adults with cancer treated in the ICU who were started on antibiotics for suspected infection, met the SEPSIS-3 criteria, and were expected to stay in the ICU greater than or equal to 48 hours.

INTERVENTIONS:

Patients were randomized to the procalcitonin-guided or standard care (SC) arms. All patients had procalcitonin measured daily, up to 5 days or until ICU discharge or death. For the procalcitonin arm, a procalcitonin-guided algorithm was provided to guide antibiotic management, but clinicians were allowed to override the algorithm, if clinically indicated. In the SC arm, ICU clinicians were blinded to the procalcitonin levels.

MEASUREMENTS AND MAIN RESULTS:

Primary outcome was time to antibiotic cessation. We also evaluated the number of antibiotic-free days at 28 days, hospital discharge, or death, whichever came first, and antibiotic defined daily doses (DDDs). We enrolled 77 patients in the procalcitonin arm and 76 in the SC arm. Mean age was 58 ± 14 (sd) years, 67% were males, 74% had solid tumors, and 13% were neutropenic. Median (interquartile range [IQR]) Sequential Organ Failure Assessment scores were 7 (6–10) and 7 (5–9) and procalcitonin concentrations (ng/mL) at baseline were 3.4 (0.8–16) and 3.4 (0.5–26), in the procalcitonin and SC arms, respectively. There was no difference in the median (IQR) time to antibiotic cessation in the procalcitonin and SC arms, 8 (4–11) and 8 (5–13), respectively (p = 0.463). Median (IQR) number of antibiotic-free days were 20 (17–24) and 20 (16–23), (p = 0.484) and total DDDs were 1541.4 and 2050.4 in the procalcitonin and SC arms, respectively.

CONCLUSIONS:

In critically ill cancer patients with sepsis, procalcitonin-guided management did not reduce the duration of antibiotic treatment.
Long-term exposure to air pollution and prevalent nonalcoholic fatty liver disease
Authors: Matthiessen Clara , Glaubitz Lina , Lucht Sarah , Kälsch Julia , Luedde Tom , Erbel Raimund , Stang Andreas , Schmidt Börge , Friedman Scott L. , Canbay Ali , Bechmann Lars P. , Hoffmann Barbara
Published: October 2024

Background:

Nonalcoholic fatty liver disease (NAFLD) is a disease characterized by lipid accumulation within hepatocytes, ranging from simple steatosis to steatohepatitis, in the absence of secondary causes of hepatic fat accumulation. Although air pollution (AP) has been associated with several conditions related to NAFLD (e.g., metabolic syndrome, type 2 diabetes mellitus), few studies have explored an association between AP and NAFLD. The aim of the study was to investigate whether exposure to AP is associated with NAFLD prevalence.

Methods:

We used baseline cross-sectional data (2000–2003) of the Heinz–Nixdorf–Recall cohort study in Germany (baseline n = 4,814), a prospective population-based cohort study in the urbanized Ruhr Area. Mean annual exposure to size-fractioned particulate matter (PM10, PM2.5, PMcoarse, and PM2.5abs), nitrogen dioxide, and particle number was assessed using two different exposure models: a chemistry transport dispersion model, which captures urban background AP exposure on a 1 km2 grid at participant’s residential addresses, and a land use regression model, which captures point-specific AP exposure at participant’s residential addresses. NAFLD was assessed with the fatty liver index (n = 4,065), with NAFLD defined as fatty liver index ≥60. We estimated ORs of NAFLD per interquartile range of exposure using logistic regression, adjusted for socio-demographic and lifestyle variables.

Results:

We observed a NAFLD prevalence of 31.7% (n = 1,288). All air pollutants were positively associated with NAFLD prevalence, with an OR per interquartile range for PM2.5 of 1.11 (95% confidence interval [CI] = 1.00, 1.24) using chemistry transport model, and 1.06 (95% CI = 0.94, 1.19) using the land use regression model, respectively.

Conclusion:

There was a positive association between long-term AP exposure and NAFLD.
Postpartum Ultrasound: An Indispensable Tool in the Labor Ward
Authors: Henrich Wolfgang , Paping Alexander
Published: October 2024

Postpartum hemorrhage can occur because of different conditions. Apart from placental remnants and uterine atony, less common causes include uterine rupture, placental polyps, arteriovenous malformations, and pseudoaneurysms. Ultrasound plays a key role in the precise definition of the underlying pathology, which is necessary to initiate the appropriate therapy. It also helps to depict intraabdominal hematomas and uterine scar dehiscence, 2 conditions that do not necessarily lead to postpartum hemorrhage but are associated with increased maternal morbidity. This article presents 52 ultrasound images together with clinical and histopathologic images to give an overview of both frequent and rare pathologies in the postpartum period.
Uptake of Cascade Genetic Testing for Hereditary Breast and Ovarian Cancer: A Systematic Review and Meta-Analysis
Authors: Ahsan Muhammad Danyal , Chandler Isabelle R. , Min Samantha , Grant Benjamin , Primiano Michelle , Greenwald Jamieson , Soussana Tamar N. , Baltich Nelson Becky , Thomas Charlene , Chapman-Davis Eloise , Sharaf Ravi N. , Frey Melissa K.
Published: October 2024

This is a systematic review and meta-analysis evaluating the uptake of cascade genetic testing for hereditary breast and ovarian cancer syndrome. Among 30 studies included for meta-analysis, the uptake of cascade genetic testing was 33% (95% CI 25%-42%), with higher uptake rates among females compared with male relatives, and among first-degree compared with second-degree relatives. These findings indicate suboptimal uptake of cascade genetic testing among people at risk for hereditary breast and ovarian cancer syndrome, representing a missed opportunity for cancer prevention and early detection. There is a need for interventions to improve uptake rates.
Spinal lumbar Urocortin 3-expressing neurons are associated with both scratching and Compound 48/80-induced sensations
Authors: Franck Marina C. M. , Weman Hannah M. , Ceder Mikaela M. , Ahemaiti Aikeremu , Henriksson Katharina , Bengtsson Erica , Magnusson Kajsa A. , Koning Harmen K. , Öhman-Mägi Caroline , Lagerström Malin C.
Published: October 2024

Urocortin 3 is a neuropeptide that belongs to the corticotropin-releasing hormone family and is involved in mechanosensation and stress regulation. In this study, we show that Urocortin 3 marks a population of excitatory neurons in the mouse spinal cord, divided into 2 nonoverlapping subpopulations expressing protein kinase C gamma or calretinin/calbindin 2, populations previously associated with mechanosensation. Electrophysiological experiments demonstrated that lumbar spinal Urocortin 3 neurons receive both glycinergic and GABAergic local tonic inhibition, and monosynaptic inputs from both Aβ and C fibers, which could be confirmed by retrograde trans-synaptic rabies tracing. Furthermore, fos analyses showed that subpopulations of lumbar Urocortin 3 neurons are activated by artificial scratching or Compound 48/80-induced sensations. Chemogenetic activation of lumbar Urocortin 3-Cre neurons evoked a targeted biting/licking behavior towards the corresponding dermatome and chemogenetic inhibition decreased Compound 48/80-induced behavior. Hence, spinal lumbar Urocortin 3 neurons represent a mechanically associated population with roles in both scratching and Compound 48/80-induced sensations.
Alpha transcranial alternating current stimulation modulates pain anticipation and perception in a context-dependent manner
Authors: Li Xiaoyun , Jin Richu , Lu Xuejing , Zhan Yilin , Jiang Naifu , Peng Weiwei
Published: October 2024

Pain perception is closely tied to the brain's anticipatory processes, particularly involving the suppression of sensorimotor α-oscillations, which reflect the system's readiness for incoming pain. Higher sensorimotor α-oscillation levels are correlated with lower pain sensitivity. Alpha transcranial alternating current stimulation (α-tACS) can enhance these oscillations, potentially reducing pain perception, with effects that may be sustained and influenced by the certainty of pain expectations. Hence, this study investigated the immediate and sustained effects of α-tACS on pain anticipation and perception, focusing on how these effects are shaped by the certainty of expectations. In a double-blind, sham-controlled design, 80 healthy participants underwent a 20-minute session of real or sham α-tACS over the right sensorimotor region. Behavioral and neural responses related to pain anticipation and perception were recorded before, immediately after, and 30 minutes poststimulation under both certain and uncertain conditions. Compared with sham stimulation, real α-tACS disrupted the habituation of laser-evoked potentials (N2-P2 complex), particularly under certain expectations, with effects persisting 30 minutes poststimulation. In anticipatory brain oscillations, real α-tACS enhanced somatosensory α1-oscillations and increased midfrontal θ-oscillations in conditions of certainty, with θ-oscillation modulation showing sustained effects. Mediation analysis revealed that α-tACS reduced pain reactivity by enhancing somatosensory α1-oscillations but increased pain reactivity through the enhancement of midfrontal θ-oscillations, with the latter effect being more pronounced. These findings suggest that while α-tACS may provide pain relief through somatosensory α-oscillation augmentation, its stronger and longer-lasting impact on midfrontal θ-oscillations could lead to hyperalgesia, particularly in the context of certain pain expectations.
Diagnosis of a suspicious Spitzoid nevus
Authors: Lee Anne
Published: October 2024

The mortality rate of cutaneous melanoma in the United States continues to increase year over year. Research supports that the development of melanoma is determined by genetics, the environment, and an individual’s behavior with certain phenotypic features, such as fair skin, red hair, multiple moles, and a prior history of sunburns, placing some individuals at greater risk of developing melanoma. New treatments have improved the survival rate of individuals with melanoma; however, the proper diagnosis of this deadly cancer is imperative. Histopathology remains the gold standard for diagnosing melanoma, sometimes with the help of immunohistochemistry staining. When a clear diagnosis cannot be made, genomic testing can be a helpful tool to differentiate between a benign and malignant lesion. Here, we present the case of a 27-year-old male patient with Fitzpatrick skin type III who presented to the dermatology clinic with a growing pink bump on his left upper arm. After a shave biopsy, the dermatopathologist reported that the lesion was a suspicious-looking Spitzoid nevus, for which a wide excision by surgical oncology was recommended. The immunohistochemistry staining did not secure a diagnosis of benign or malignant. As the diagnosis was inconclusive, the specimen was sent for a gene expression profile test, which came back positive, indicating malignant melanoma. This case illustrates how diagnostic and prognostic genomic testing can be used to identify a malignant melanoma and determine the likelihood of metastasis, thus guiding the patient's follow-up plan. It also illustrates how genomic testing might help the patient avoid unnecessary and costly medical procedures with potential side effects.
Multicenter study of OPRM1 A118G and promoter-region DNA methylation associations with opioid outcomes and chronic postsurgical pain after pediatric musculoskeletal surgery
Authors: Upton Brian A. , Krolick Kristen N. , Zhang Xue , Pilipenko Valentina , Martin Lisa J. , Ji Hong , Glynn Susan , Barnett Kristi , Ganesh Arjunan , Monitto Constance L. , Einhorn Lisa M. , Ramamurthi Radhamangalam J. , Chidambaran Vidya
Published: October 2024

Introduction:

Mu opioid receptor gene (OPRM1) variant rs1799971 introduces a CpG site, which may influence DNA methylation (DNAm) and opioid/pain outcomes.

Objectives:

In this nested analysis, we investigated both OPRM1 A118G genotype and promoter/immediate downstream blood DNAm sequencing data for associations with opioid effects and chronic postsurgical pain (CPSP) in a surgical cohort.

Methods:

Prospectively recruited opioid naïve patients undergoing Nuss procedure or spinal fusion with rs1799971 genotypes (Illumina arrays), DNAm (next generation enzymatic methylation sequencing at Chr6:154,039,209-154,039,803) and outcomes—opioid analgesia (integrated opioid use + pain over postoperative days 0 and 1 normalized to surgery type), safety—respiratory depression (RD) in high opioid use groups, and CPSP (Numerical Rating Scale >3/10 2-12 months postsurgery)—were included. Linear and logistic regression were performed to test genetic and epigenetic associations, adjusted for sociodemographics, cell types, and analgesics.

Results:

In this cohort (N = 112; 15.3 ± 2.0 years, 50% female, 83% White, 55% had CPSP, 13% had RD), DNAm at Chr6:154039216-154039217 was associated with CPSP (odds ratio [OR], 1.26; 95% confidence interval [CI], 1.00-1.57; P = 0.03), Chr6:154039661-154039662 with acute integrated pain (β = −20.9, 95% CI, −40.70 to −1.10, P = 0.04), Chr6:154039520-154039521 (OR, 1.49; 95% CI, 1.09-2.03; P = 0.01), and Chr6:154039571-154039572 (OR, 1.47; 95% CI, 1.08-2.01; P = 0.02) with RD. Significant CpG sites were located in Repressed Polycomb chromatin states. Genotype was not associated with DNAm or outcomes.

Conclusion:

Our analyses support OPRM1 DNAm as predictors of acute and chronic pain/opioid outcomes in children after painful surgery. Study limitations included absent GG genotype, low sequencing coverage, and lack of correction for multiple testing.
An innovative phase 2 chronic pain master protocol design to assess novel mechanisms in multiple pain types
Authors: Knopp Kelly L. , Downing AnnCatherine M. , Anthony Leslie , Chaterjee Saptarshi , Price Karen , Sparks JonDavid
Published: October 2024

Introduction:

The phase 2 chronic pain master protocol (CPMP) presented here provides a construct to accelerate the investigation of novel analgesics, broadly referred to here as mechanisms. Designed to address historical challenges in analgesic research and development, such as the choice of indication, this protocol enables the efficient evaluation of potential therapeutics with different mechanisms of action in 3 pain types: nociceptive pain (osteoarthritis), neuropathic pain (diabetic peripheral neuropathic pain), and mixed pain (chronic low back pain).

Methods:

The study design was determined before the identification of any specific molecule. Statistical simulations were conducted to optimize the methodology and design, the culmination of which were submitted to and accepted by the Complex Innovative Trial Design Pilot Meeting Program, a unique collaboration with the United States Food and Drug Administration. Benefits of the CPMP include limiting the number of study participants exposed to placebo and reducing the total sample size over time by leveraging placebo data across studies within a pain type and efficacy data across pain types for a specific molecule. The CPMP design enables: (1) efficient evaluation of multiple novel mechanisms of action; (2) the study of multiple molecules simultaneously or serially; (3) direct statistical comparison of molecules within a pain type; and (4) efficient planning and conduct of clinical studies. ClinicalTrials.gov ID NCT05986292.

Perspective:

By evaluating novel mechanisms across different pain types, therapeutic potential can be assessed more efficiently compared with traditional individual clinical studies.
Exploring the Meta-debrief
Authors: Kumar Prashant , Collins Kathleen , Oliver Nathan , Duys Rowan , Park-Ross Jocelyn Frances , Paton Catherine , Laws-Chapman Colette , Eppich Walter , McGowan Neil
Published: October 2024

Summary Statement

Otherwise known as debriefing the debrief, meta-debriefing describes the practice of debriefing simulation facilitators after they have facilitated, or observed, a debriefing. It is a vital component of enhancing debriefing skills, irrespective of where debriefers may be in terms of their professional development journey from novice to expert. We present the following 4 fundamental pillars, which underpin the creation of an impactful meta-debriefing strategy: theoretically driven, psychologically safe, context dependent, and formative in function. Furthermore, we describe various strategies that, underpinned by these 4 key pillars, contribute to a toolbox of techniques that enable meta-debriefers to develop proficiency and flexibility in their practice. We have synthesized and critically reviewed the current evidence base, derived mostly from the debriefing literature, and highlighted gaps to address in meta-debriefing contexts. We hope this article stimulates discussion among simulation practitioners, progresses the science and art of meta-debriefing, and prompts further research so that meta-debriefing can become an integral evidence-based component of our faculty development processes.
Literature Review on the Effectiveness and Required Dosages of Cognitive Interventions for Older Adults
Authors: Winningham Robert G. , Pacheco Alexis J.
Published: October 2024

Objective:

The purpose of this article is to review interventions that have been shown to improve cognitive abilities in older adults, including aerobic training, resistance training, yoga, tai chi, dual tasking, and meditation. The purpose of this article is to identify findings that can lead to recommendations regarding optimal dosages of the above interventions.

Methods:

This literature review relied heavily on meta-analyses that combined data from randomized controlled studies in order to identify interventions that reliably produce meaningful improvements in cognition. In addition, the meta-analyses were used to find dosage recommendations that appeared when similar studies were analyzed.

Conclusions:

There is ample evidence that various physical exercise and cognitive stimulation interventions can lead to meaningful improvements in cognition. The results often vary as a function of the participants’ cognitive abilities and presence of cognitive impairment or dementia. In many cases, it is possible to begin making recommendations in terms of the length of sessions and the length of interventions for various populations.
Sorlinia euscelidii gen. nov., sp. nov., a novel acetic acid bacterium isolated from the leafhopper Euscelidius variegatus (Hemiptera: Cicadellidae)
Authors: Marasco Ramona , Michoud Grégoire , Seferji Kholoud A. , Gonella Elena , Garuglieri Elisa , Rolli Eleonora , Alma Alberto , Mapelli Francesca , Borin Sara , Daffonchio Daniele , Crotti Elena
Published: October 2024

Acetic acid bacteria – belonging to the Acetobacteraceae family – are found in the gut of many sugar-feeding insects. In this study, six strains have been isolated from the hemipteran leafhopper Euscelidius variegatus. While they exhibit high 16S rRNA gene sequence similarities to uncultured members of the Acetobacteraceae family, they could not be unequivocally assigned to any particular type species. Considering the clonality of the six isolates, the EV16PT strain was used as a representative of this group of isolates. The genome sequence of EV16PT is composed of a 2.388 Mbp chromosome, with a DNA G+C content of 57 mol%. Phylogenetic analyses based on the 16S rRNA gene sequence and whole-genome multilocus sequence analysis indicate that EV16PT forms a monophyletic clade with the uncultivated endosymbiont of Diaphorina citri, the Candidatus Kirkpatrickella diaphorinae. Such a phylogenetic clade is positioned between those of Asaia-Swaminathania and Kozakia. The genomic distance metrics based on gene and protein sequences support the proposal that EV16PT is a new species belonging to a yet-undescribed genus. It is a rod-shaped Gram-stain-negative bacterium, strictly aerobic, non-motile, non-spore-forming, showing optimal growth without salt (NaCl) at 30 °C and pH of 6–7. The major quinone is Q10, and the dominant cellular fatty acids (>10%) are C18:l
ω7c, C19 : 0 cyclo ω6c, C16 : 0 and C19 : 1 2OH. The polar lipid profile comprises diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine, along with unidentified aminophospholipids, glycophospholipids, aminolipids and lipids. Based on a polyphasic approach, including phylogenetic, phylogenomic, genome relatedness, phenotypic and chemotaxonomic characterisations, EV16PT (= KCTC 8296T, = DSM 117028T) is proposed as a representative of a novel species in a novel genus with the proposed name Sorlinia euscelidii gen. nov., sp. nov., in honour of Prof. Claudia Sorlini, an Italian environmental microbiologist at the University of Milan who inspired the research on microbial diversity, including symbiosis in plants and animals.
Applying nanopore sequencing technology in Paracoccidioides sp.: a high-quality DNA isolation method for next-generation genomic studies
Authors: Lorenzini Campos Melina Noelia , Amadio Ariel Fernando , Irazoqui José Matías , Acevedo Raúl Maximiliano , Rojas Florencia Dinorah , Corredor Sanguña Luis Hernando , Formichelli Laura Belén , Lucero Raúl Horacio , Giusiano Gustavo Emilio
Published: October 2024

Paracoccidioidomycosis is a severe systemic endemic mycosis caused by Paracoccidioides spp. which mainly affects individuals in Latin America. Progress in Paracoccidioides genomics has been slow, as evidenced by the incomplete reference databases available. Next-generation sequencing is a valuable tool for epidemiological surveillance and genomic characterization. With the ability to sequence long reads without the need for prior amplification, Oxford Nanopore Technology (ONT) offers several advantages, but high-quality and high-quantity DNA samples are required to achieve satisfactory results. Due to the low concentration of Paracoccidioides DNA in clinical samples and inefficient culture isolation methods, DNA extraction can be a significant barrier to genomic studies of this genus. This study proposes a method to obtain a high-coverage de novo genome assembly for Paracoccidioides using an improved DNA extraction method suitable for sequencing with ONT. The assembly obtained was comparable in size to those constructed from available data from Illumina technology. To our knowledge, this is the first genome assembly of Paracoccidioides sp. of such a large size constructed using ONT.
AMRColab – a user-friendly antimicrobial resistance detection and visualization tool
Authors: Lam Su Datt , Di Gregorio Sabrina , Ang Mia Yang , Griffiths Emma , Jamaluddin Tengku Zetty Maztura Tengku , Nathan Sheila , Neoh Hui-min
Published: October 2024

Antimicrobial resistance (AMR) poses a significant threat to global public health, with the potential to cause millions of deaths annually by 2050. Effective surveillance of AMR pathogens is crucial for monitoring and predicting their behaviour in response to antibiotics. However, many public health professionals lack the necessary bioinformatics skills and resources to analyse pathogen genomes effectively. To address this challenge, we developed AMRColab, an open-access bioinformatics analysis suite hosted on Google Colaboratory. AMRColab enables users with limited or no bioinformatics training to detect and visualize AMR determinants in pathogen genomes using a ‘plug-and-play’ approach. The platform integrates established bioinformatics tools such as AMRFinderPlus and hAMRonization, allowing users to analyse, compare and visualize trends in AMR pathogens easily. A trial run using methicillin-resistant Staphylococcus aureus (MRSA) strains demonstrated AMRColab’s effectiveness in identifying AMR determinants and facilitating comparative analysis across strains. A workshop was conducted and feedback from participants indicated high confidence in using AMRColab and a willingness to incorporate it into their research. AMRColab’s user-friendly interface and modular design make it accessible to a diverse audience, including medical laboratory technologists, medical doctors and public health scientists, regardless of their bioinformatics expertise. Future improvements to AMRColab will include enhanced visualization tools, multilingual support and the establishment of an online community platform. AMRColab represents a significant step towards democratizing AMR surveillance and empowering public health professionals to combat AMR effectively.
Towards the development of a management protocol for Subjective Cognitive Decline: insights from a cross-sectional and longitudinal analyses of multimodal data from a memory clinic
Authors: Mazzeo Salvatore , Lassi Michael , Padiglioni Sonia , Vergani Alberto Arturo , Moschini Valentina , Scarpino Maenia , Giacomucci Giulia , Burali Rachele , Morinelli Carmen , Fabbiani Carlo , Galdo Giulia , Amato Lorenzo Gaetano , Bagnoli Silvia , Emiliani Filippo , Ingannato Assunta , Nacmias Benedetta , Sorbi Sandro , Grippo Antonello , Mazzoni Alberto , Bessi Valentina
Published: October 2024

Structured abstract

Introduction

Subjective cognitive decline (SCD) is considered as an early symptomatic stage of Alzheimer’s disease (AD). This study aimed to develop a management protocol for SCD based on cross-sectional and longitudinal analyses.

Methods

We enrolled 440 SCD patients who underwent neurological and neuropsychological assessments, MRI scans,APOEgenotyping, and AD biomarker evaluations. Patients were followed for a median of 10 years.

Results

A link was observed between SCD severity, insomnia, and benzodiazepine use. Aβ pathology was identified in 35% of cases. During follow-up, 87 patients progressed to mild cognitive impairment or dementia. The multi-modal clinical profile of each patient was processed by a machine learning model, predicting progression with 74% accuracy and providing a hierarchy of importance of features predicting progression.

Discussion

Our findings support the development of a personalized clinical management protocol for SCD that considers demographic, clinical, cognitive and biological factors for both baseline characterization and prognostic purposes.
Based on breast CEUS parameters combined with serum CA153, a nomogram model was constructed to predict the molecular classification of breastcancer
Authors: Ji Yanlei , Han Zhen , Zhang Yong , Sun Wenwen
Published: October 2024

Objective

To analyze the role of contrast-enhanced ultrasound (CEUS) parameters combined with serum tumor marker CA153 in the prediction of Breast Cancer (BC) molecular typing.

Methods

From January 2020 to January 2023, 120 BC patients diagnosed in our hospital were studied. According to the pathological results, the patients were divided into Luminal and non-Luminal BC groups. Both groups underwent contrast-enhanced ultrasoun. The time-intensity curve (TIC) is obtained, and the relevant characteristic parameters are obtained, including peak intensity (PI), peak time (TTP), area under the curve (AUC), and mean transit time (MTT). Serum tumor marker CA153 was detected in both groups. Combined with CEUS characteristic parameters and serum CA153 of two groups of BC patients, a multiple Logistic regression model was constructed, and a nomogram prediction model was constructed based on the model. Calibration curve and receiver operating characteristic (ROC) curve were used to analyze the value of this model in the prediction of BC molecular classification.

Results

There were no significant differences between Luminal BC patients and non-Luminal BC patients in clinical parameters and qualitative parameters of contrast-enhanced ultrasound, while there were statistical differences between quantitative parameters PI, AUC and serum tumor marker CA153. The AUC of the combined diagnosis of three parameters (PI, AUC and CA153) was significantly higher than that of the single index diagnosis group. The ROC curve AUC of BC molecular typing was predicted to be 0.94 based on the three-parameter nomogram, and the fitting of the actual curve and the ideal curve in the calibration curve was close.

Conclusions

The nomogram model based on breast contrast-enhanced ultrasound (CEUS) parameters combined with serum CA153 can effectively predict the molecular classification of BC.
Evolution of plasmid domestication in plant-associatedPantoea: massive gain of genetic redundancy followed by differential gene loss
Authors: Picazo Devani Romero , Kwasigroch Paul , Hülter Nils F. , Dagan Tal
Published: October 2024

Plasmids are important drivers of evolutionary transformations and ecological adaptation in prokaryotes. Plasmids supplying the host with beneficial functions may become domesticated and gain a stable inheritance within the host lineage in the form of secondary chromosomes. Chromosomes descendent from plasmids (termed chromids) comprise core genes that are universally present in all taxon members. The origin of plasmid core genes remains poorly understood and alternative hypotheses entailing gene translocation or genetic redundancy are debated. Studying plasmid evolution in plant-associatedPantoea, we show that the largePantoeaplasmid (LPP) and plasmid pPag1 comprise core genes in the host taxa. We infer the LPP acquisition in plant-associated ancestors, while the pPag1 acquisition is traced to the ancestor of plant growth-promoting species. We show that both plasmids are vertically inherited and the LPP replication is furthermore coordinated with cell division, hence they are better described as chromids. Using phylogenomics we infer that the plasmid acquisition manifested in massive gene gain, some redundant with the chromosome, followed by differential gene loss. Our results provide an explanation for the evolution of core plasmid genes that entails plasmid-driven species divergence, which preliminarily manifests in genetic redundancy, and is followed by gradual loss of redundant genes.

Significance statement

Adaptation to host-associated lifestyle in bacteria can be promoted by the acquisition of plasmids, which are mobile extra-chromosomal genetic elements. A canonic example is the symbiosisRhizobiaplasmids, where essential traits to interact with Legumes are plasmid-encoded. Symbiosis plasmids are likely to evolve into stably inherited domesticated plasmids (termed chromids). Recent research reveals that potential chromids are widely distributed among plant-associated bacteria. Studying the origin of plasmids in the plant-associated genusPantoea, we show that the largePantoeaplasmid (LPP) and plasmid pPag1 are domesticated. Phylogenomic analyses trace back the plasmid origin to ancestral nodes in thePantoeaspecies tree. We reconstruct main events in chromid evolution, including massive gene gain, some redundant with the chromosome, and differential gene loss.
Tuberculosis Following In Vitro Fertilization: A Systematic Review of Case Reports, Case Series, and Cohort Studies
Authors: Garg Ravindra Kumar , Malhotra Hardeep Singh , Suresh Vinay , Garg Rajiv , Jain Amita , Gupta Sarika , Agrawal Smriti
Published: October 2024

Introduction

Tuberculosis (TB) remains a leading global health threat, with increasing concerns regarding post-in vitro fertilization (IVF) TB, especially in high-burden areas. Post-IVF maternal TB poses serious risks to both pregnant women and fetuses, often leading to miscarriage, fetal malformation, or mortality. Congenital TB, though rare, can result from maternal infection, with potentially devastating outcomes.

Methods

A systematic review of case reports, case series, and cohort studies was conducted following PRISMA guidelines. Databases including PubMed, Scopus, Embase, and Google Scholar were searched until October 7, 2024, for studies related to TB following in vitro fertilization. Cases were evaluated for clinical presentations, diagnostics, treatment, and outcomes. We separately reviewed 11 cohort studies due to the lack of available individual patient data and the considerable variability in their methodologies.

Results

Thirty-seven reports comprising 48 cases were analyzed, with the majority from Asia. Post-IVF TB is commonly presented as miliary TB in mothers, with systemic involvement including pulmonary, central nervous system (CNS), and genitourinary manifestations. Newborns frequently develop congenital TB, presenting with respiratory distress and neurological issues. The diagnosis was confirmed through techniques such as sputum polymerase chain reaction (PCR), endometrial biopsies, and imaging. Maternal outcomes improved with anti-TB therapy, while neonatal outcomes varied, with high mortality rates.

Conclusion

Post-IVF TB manifests in mothers as miliary TB with systemic involvement; congenital TB in newborns often leads to respiratory distress, neurological complications, and high mortality. TB screening before IVF is critical in high-risk regions to prevent severe maternal and neonatal complications.
Harnessing GPT-4 for Automated Curation of E3-Substrate Relationships in the Ubiquitin-Proteasome System
Authors: Zhang Zhiqian , Elledge Stephen J.
Published: October 2024

The ubiquitin-proteasome system (UPS) is a complex regulatory network involving around 600 E3 ligases that collectively govern the stability of the human proteome by targeting thousands of proteins for degradation. Understanding this network requires integrating vast amounts of information on gene and protein interactions scattered across unstructured literature. Historically, manual curation has been the gold standard for transforming such data into structured databases, but this process is time-consuming, prone to error, and unable to keep up with the rapid growth of scientific publications. To address these limitations, we developed a scalable, cost-effective workflow using GPT-4, a large language model (LLM), to automate the curation of degradative E3-substrate relationships from the literature. By mining approximately two million PubMed papers, we identified 7,829 degradation-related abstracts and curated a structured database of 3,294 unique E3-substrate pairs using GPT-4, achieving an annotation accuracy rate approaching that of human experts. The resulting database of E3-substrate pairs offers valuable insights into the ubiquitin-proteasome system by highlighting understudied E3s and previously unknown UPS substrates in proteome-wide stability experiments. This automated approach represents substantial increase in productivity compared to manual curation and stands as the largest effort to date utilizing LLMs for the automated curation of protein-protein regulatory relationships. We further showed that our approach is generalizable to other enzyme-substrate families, such as deubiquitinases, kinases, and phosphatases. Overall, our study demonstrates the potential of LLMs as a scalable technology for large-scale curation of signalling relationships, substituting and complementing manual curation to accelerate biological research.
The window of opportunity: a case study of the battery electric vehicle in Thailand
Authors: Intarakumnerd Patarapong , Charoenporn Peera
Published: October 2024

Purpose

Thailand, although a late entrant, has emerged as a significant center for the production and export of internal combustion engine (ICE) vehicles in Asia. With the arrival of a disruptive battery-electric vehicle (BEV), this study aims to investigate whether Thailand can exploit this window of opportunity to leapfrog.

Design/methodology/approach

This paper uses data sourced from Thailand’s Department of Intellectual Property to analyze electric vehicle (EV) patent applications. This paper collected qualitative data and conducted interviews with several EV manufacturers.

Findings

Although Japanese automakers dominate essential EV technology patents, they trail behind Chinese automakers, which benefited from the Free Trade Agreement (FTA) in EV sales. The incumbents, Japanese and Western, choose to expand their production of hybrid electric vehicles (HEVs) and plug-in hybrid vehicles. ICE technology does not constrain new entrants, such as Chinese automakers, Japanese newcomers and Thai newcomers. Compared to Japanese carmakers stuck with ICE and HEV technologies, they have been transitioning to BEVs at a faster pace. BEV has opened the door for large Thai indigenous energy corporations to enter the automotive industry by focusing on niche areas (nonfour-wheel vehicles) and supporting businesses like charging stations. In summary, Thailand has successfully attracted foreign direct investment (FDI) into the EV sector, but it has not yet succeeded in developing indigenous technologies related to EVs. The Thai automobile sector fails to leapfrog because it is too tied up with Japanese automotive production networks and has an unfavorable FTA with China.

Originality/value

This study sheds light on the limitations of an industrial development strategy relying on openness to trade and FDI without adequately strengthening indigenous technologies and firms, as the country adopting the strategy fails to leapfrog when the window of opportunities created by disruptive technologies arrives.
Unleashing the missing link between work-family conflict and affective commitment: implications for health professionals
Authors: Iqbal Juman , Shagirbasha Shameem , Kumar Madhan , Mufeed S.A.
Published: October 2024

Purpose

Elucidating on the theoretical framework of conservation of resource and social identity theories, we aim to explore the association between work-family conflict (bidirectional, i.e. work-to-family conflict (WFC) and family-to-work conflict (FWC)) and affective commitment (AC) via emotional exhaustion (EE). Besides, the buffering effect of organizational identification (OI) in the bi-directional work-family conflict and EE relationship and perceived interactional justice (PIJ) between EE and AC were also tested.

Design/methodology/approach

A multi-time study was conducted in which data from 675 doctors working in different public hospitals across India were gathered at three-time intervals (T1, T2 and T3). The collected data were then analyzed using statistical software tools, namely AMOS 24 and SPSS v23.

Findings

It was indicated that WFC and FWC have a significant negative association with AC. EE was shown to mediate the relationship between bi-directional work-family conflict and AC. Additionally, OI buffered the relationship between WFC, FWC and EE. Moreover, PIJ was established as a moderating factor in the relationship between EE and AC.

Originality/value

This paper provides a new insight into the work-family conflict-AC relationship by examining it through the mediating role of EE. It offers a nuanced understanding by establishing the buffering effects of OI in the bi-directional WFC and EE. To our knowledge, this research represents the inaugural attempt to investigate the moderating influence of PIJ in the relationship between EE and AC.