bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinicopathological characteristics and diagnostic accuracy of BRAF mutations in ameloblastoma: A Bayesian network analysis
Authors: Zhang Ao‐Bo , Zhang Jian‐Yun , Liu Yu‐Ping , Wang Shuo , Bai Jia‐Ying , Sun Li‐Sha , Li Tie‐Jun
Published: May 2024

Objective

This Bayesian network meta‐analysis was performed to analyze the associations between clinicopathological characteristics and BRAF mutations in ameloblastoma (AM) patients and to evaluate the diagnostic accuracy.

Materials and Methods

Four electronic databases were searched from 2010 to 2024. The search terms used were specific to BRAF and AM. Observational studies or randomized controlled trials were considered eligible. The incidence of BRAF mutation and corresponding clinicopathological features in AM patients were subjected to Bayesian network analyses and diagnostic accuracy evaluation.

Results

A total of 937 AM patients from 20 studies were included. The pooled prevalence of BRAF mutations in AM patients was 72%. According to the Bayesian network analysis, BRAF mutations are more likely to occur in younger (odds ratio [OR], 2.3; credible interval [CrI]: 1.2–4.5), mandible site (OR, 3.6; 95% CrI: 2.7–5.2), and unicystic (OR, 1.6; 95% CrI: 1.1–2.4) AM patients. Similarly, higher diagnostic accuracy was found in the younger, mandible, and unicystic AM groups.

Conclusions

The incidence, risk, and diagnostic accuracy of BRAF mutation in AM were greater in younger patients, those with mandible involvement, and those with unicystic AM than in patients with other clinicopathological features. In addition, there was a strong concordance in the diagnostic accuracy between molecular tests and immunohistochemical analysis.
Introduction to the special issue “Productivity revolutions: Past and future”
Authors: Palma Nuno
Published: May 2024

We may be living at the dawn of a productivity revolution era brought about by modern science and technological improvements. The six research papers published in this special issue of The Manchester School, titled “Productivity Revolutions: Past and Future,” provide us with lessons on how economies and societies have dealt with the challenges posed by such revolutions.
Premature agglomeration?: Two phases of development with spatial sorting
Authors: Forslid Rikard , Okubo Toshihiro
Published: May 2024

Clusters in the developing world do, to a large extent, attract low‐educated individuals, and these clusters are in some cases, characterized by urbanization without industrialization. This contrasts starkly to clusters in advanced economies that attract high‐skilled individuals and entrepreneurs. In this paper, we develop a model of agglomeration and spatial sorting that is consistent with these two types of different agglomeration processes in developed and developing countries. We show that a poor country that has an agglomeration with low skilled individuals, may get stuck in this equilibrium, but that free mobility of human capital from the outset nevertheless is superior from the perspective of total social welfare.
The effects of Lr34 and Lr67 on Fusarium head blight resistance and deoxynivalenol accumulation in wheat
Authors: McCallum Brent D. , Hiebert Colin W. , McCartney Curt A. , Henriquez Maria Antonia
Published: May 2024

The resistance gene Lr34 conditions durable disease resistance to many biotrophic wheat pathogens and has been incorporated into many wheat cultivars throughout the world. Lr67 is a similar adult plant resistance gene that also conditions resistance to multiple wheat diseases. Both genes significantly reduce disease severity and work in an additive manner with other rust resistance genes. To determine the effect of Lr34 and Lr67 on Fusarium head blight (FHB), two doubled haploid populations, segregating for each of these genes, were developed in the Thatcher wheat background by crossing near‐isogenic lines. Progeny from these populations were tested in five Fusarium graminearum‐inoculated disease nurseries and assessed for FHB symptoms, using a visual rating index (VRI), and deoxynivalenol (DON) accumulation. Both Lr34 and Lr67 significantly reduced visual symptoms of FHB and DON overall, though those effects were not significant in all environments. The overall reduction in the group of progeny with the resistant allele compared to the group with the susceptible allele for VRI was 9.4% for Lr34 and 6.8% for Lr67, while for DON it was 16.4% for Lr34 and 14.9% for Lr67. These genes represent important tools for improving resistance to FHB and many other diseases in wheat.
Microbiome dynamics during malting of barley grains infested by Fusarium graminearum strains
Authors: Bakker Matthew G. , Jayathissa Anuradha U. , Fernando W. G. Dilantha , Badea Ana , Tucker James R.
Published: May 2024

Barley grain harvested for malting poses an interesting case study for the impacts of plant‐associated microbiomes because the conditions created during malting favour continued vigorous microbial activity after grain harvest. Suppression of pathogens is among the key functions performed by microbiomes, and it would be beneficial if we could harness this function. Over a 3‐year field trial, we micro‐malted barley that had been experimentally infested with each of seven different strains of the fungal pathogen Fusarium graminearum, and profiled bacterial microbiomes at key stages in the malting process (grain, post‐steeping, post‐germination and final dried malt). The greatest impacts on bacterial microbiomes were observed to be from the year and stage of malting, with comparatively fewer impacts of barley cultivar or pathogen strain. Relatively limited impacts of the presence and strain identity of fungal pathogen on the bacterial microbiome of malting barley probably reflects the colonization by other fungi, as our inoculation took place under field conditions with supplemental irrigation. Both community level shifts and significant responses by individual taxa were evident. Microbiome characteristics or the relative abundances of specific bacterial taxa helped to explain pathogen biomass, mycotoxin production and beer gushing. Manipulative experiments will be required to test hypotheses suggested by these microbiome profiles.
End‐of‐life conversations for the older person: A concept analysis
Authors: Yip Wing Ki Agnes , Chung Pui Man Betty , Christensen Martin
Published: May 2024

Aim

The aim of this concept analysis is to seek clarity as to what end‐of‐life conversations involve by developing a clear working definition and using model cases to conceptualise the defining attributes of an end‐of‐life conversations with the older person.

Design

Walker and Avant's eight step approach to Concept Analysis.

Data Sources

Four databases were searched, including PubMed, CINAHL, PsycINFO, and Scopus. A total of 339 publications were identified with 30 papers meeting the inclusion criteria and put forward for the final conceptual analysis.

Results

The defining attributes associated with end‐of life conversations included (1) an ongoing process of older person empowerment, (2) discussion's concerning values and preferences concerning end‐of‐life issues, and (3) maintaining an open dialogue between all concerned individuals. Antecedents were associated with the older person is their readiness to talk openly about death and dying. Consequences were identified as having a better understanding of what death and dying may mean to the older person in a more specific manner.

Conclusions

End‐of‐life conversations are vital in understanding an individual's values and preferences at the end of life, and yet, the concept of the end‐of‐life conversation has not been well defined in the literature. End‐of‐life conversations with the older person encompass ongoing discussions and maintaining open dialogue around end‐of‐life care while developing strategies to promote individual empowerment in making informed choices. Using a conceptual model, aides in addressing aspects of end‐of‐life conversations and an acknowledgment of the dynamic process of end‐of‐life conversations.
Collecting pieces for the ‘puzzle’: Nurses' intraprofessional collaboration in the hospital‐to‐home transition of older patients
Authors: Hansen Mette Frier , Martinsen Bente , Galvin Kathleen , Thomasen Bjørn Porup , Norlyk Annelise
Published: May 2024

Background and aim

Communication is a key factor in intraprofessional collaboration between hospital nurses and homecare nurses in hospital‐to‐home transitions of older patients with complex care needs. Gaining knowledge of the nature of cross‐sectoral communication is crucial for understanding how nurses collaborate to ensure a seamless patient trajectory. This study explores how cross‐sectoral electronic health records communication influences collaboration between hospital nurses and homecare nurses when discharging older patients with complex care needs.

Method

The study is based on qualitative group interviews with six hospital nurses and 14 homecare nurses working at different hospitals and municipalities across Denmark. Data were analysed using reflexive thematic analysis, as described by Braun and Clark.

Findings

The themes Collecting pieces for the ‘puzzle’: Losing the holistic picture of the patient; Working blindfolded: limited provision of and access to critical information; and Bypassing the ‘invisible wall’: dialogue supports cohesion illustrate the impact of organisational structures within electronic health records have on hospital nurses' and homecare nurses' intraprofessional collaboration across sectors. Challenges with predefined and word‐limited elements in digital communication, and inadequate and limited access to significant medical information were identified. To compensate for the inadequacy of the electronic health records, direct contact and dialogue were emphasised as ways of fostering successful collaboration and overcoming the barriers created by electronic health records.

Conclusion

Despite hospital nurses' and homecare nurses' desire to conduct holistic patient assessments, their ability to collaborate was hindered by failures in electronic health record communication resulting from restrictive organisational structures across sectors. Thus, it became necessary for hospital nurses and homecare nurses to bypass the electronic health record system and engage in dialogue to provide holistic care when discharging older patients with complex care needs. However, by hospital nurses and homecare nurses compensating for counter‐productive organisational structures, problems brought about by the electronic health record system paradoxically remain invisible.
Functional vertical connectivity of microbial communities in the ocean
Authors: Chen Shi , Xie Zhang-Xian , Yan Ke-Qiang , Chen Jian-Wei , Li Dong-Xu , Wu Peng-Fei , Peng Ling , Lin Lin , Dong Chun-Ming , Zhao Zihao , Fan Guang-Yi , Liu Si-Qi , Herndl Gerhard J. , Wang Da-Zhi
Published: May 2024

Sinking particles are a critical conduit for the transport of surface microbes to the ocean’s interior. Vertical connectivity of phylogenetic composition has been shown; however, the functional vertical connectivity of microbial communities has not yet been explored in detail. We investigated protein and taxa profiles of both free-living and particle-attached microbial communities from the surface to 3000 m depth using a combined metaproteomic and 16
S
rRNA amplicon sequencing approach. A clear compositional and functional vertical connectivity of microbial communities was observed throughout the water column with Oceanospirillales, Alteromonadales, and Rhodobacterales as key taxa. The surface-derived particle-associated microbes increased the expression of proteins involved in basic metabolism, organic matter processing, and environmental stress response in deep waters. This study highlights the functional vertical connectivity between surface and deep-sea microbial communities via sinking particles and reveals that a considerable proportion of the deep-sea microbes might originate from surface waters and have a major impact on the biogeochemical cycles in the deep sea.
Predicting the pathways of string-like motions in metallic glasses via path-featurizing graph neural networks
Authors: Wang Qi , Zhang Long-Fei , Zhou Zhen-Ya , Yu Hai-Bin
Published: May 2024

String-like motions (SLMs)—cooperative, “snake”-like movements of particles—are crucial for dynamics in diverse glass formers. Despite their ubiquity, questions persist: Do SLMs prefer specific paths? If so, can we predict these paths? Here, in Al-Sm glasses, our isoconfigurational ensemble simulations reveal that SLMs do follow certain paths. By designing a graph neural network (GNN) to featurize the environment around directional paths, we achieve a high-fidelity prediction of likely SLM pathways, solely based on the static structure. GNN gauges a structural measure to assess each path’s propensity to engage in SLMs, akin to a “softness” metric, but for paths rather than for atoms. Our GNN interpretation reveals the critical role of the bottleneck zone along a path in steering SLMs. By monitoring “path softness,” we elucidate that SLM-favored paths transit from fragmented to interconnected upon glass transition. Our findings reveal that, beyond atoms or clusters, glasses have another dimension of structural heterogeneity: “paths.”
A pattern recognition artificial olfactory system based on human olfactory receptors and organic synaptic devices
Authors: Song Hyun Woo , Moon Dongseok , Won Yousang , Cha Yeon Kyung , Yoo Jin , Park Tai Hyun , Oh Joon Hak
Published: May 2024

Neuromorphic sensors, designed to emulate natural sensory systems, hold the promise of revolutionizing data extraction by facilitating rapid and energy-efficient analysis of extensive datasets. However, a challenge lies in accurately distinguishing specific analytes within mixtures of chemically similar compounds using existing neuromorphic chemical sensors. In this study, we present an artificial olfactory system (AOS), developed through the integration of human olfactory receptors (hORs) and artificial synapses. This AOS is engineered by interfacing an hOR-functionalized extended gate with an organic synaptic device. The AOS generates distinct patterns for odorants and mixtures thereof, at the molecular chain length level, attributed to specific hOR-odorant binding affinities. This approach enables precise pattern recognition via training and inference simulations. These findings establish a foundation for the development of high-performance sensor platforms and artificial sensory systems, which are ideal for applications in wearable and implantable devices.
Single-sample image-fusion upsampling of fluorescence lifetime images
Authors: Kapitany Valentin , Fatima Areeba , Zickus Vytautas , Whitelaw Jamie , McGhee Ewan , Insall Robert , Machesky Laura , Faccio Daniele
Published: May 2024

Fluorescence lifetime imaging microscopy (FLIM) provides detailed information about molecular interactions and biological processes. A major bottleneck for FLIM is image resolution at high acquisition speeds due to the engineering and signal-processing limitations of time-resolved imaging technology. Here, we present single-sample image-fusion upsampling, a data-fusion approach to computational FLIM super-resolution that combines measurements from a low-resolution time-resolved detector (that measures photon arrival time) and a high-resolution camera (that measures intensity only). To solve this otherwise ill-posed inverse retrieval problem, we introduce statistically informed priors that encode local and global correlations between the two “single-sample” measurements. This bypasses the risk of out-of-distribution hallucination as in traditional data-driven approaches and delivers enhanced images compared, for example, to standard bilinear interpolation. The general approach laid out by single-sample image-fusion upsampling can be applied to other image super-resolution problems where two different datasets are available.
Machine learning–enhanced molecular network reveals global exposure to hundreds of unknown PFAS
Authors: Wang Xuebing , Yu Nanyang , Jiao Zhaoyu , Li Laihui , Yu Hongxia , Wei Si
Published: May 2024

Unknown forever chemicals like per- and polyfluoroalkyl substances (PFASs) are difficult to identify. Current platforms designed for metabolites and natural products cannot capture the diverse structural characteristics of PFAS. Here, we report an automatic PFAS identification platform (APP-ID) that screens for PFAS in environmental samples using an enhanced molecular network and identifies unknown PFAS structures using machine learning. Our networking algorithm, which enhances characteristic fragment matches, has lower false-positive rate (0.7%) than current algorithms (2.4 to 46%). Our support vector machine model identified unknown PFAS in test set with 58.3% accuracy, surpassing current software. Further, APP-ID detected 733 PFASs in real fluorochemical wastewater, 39 of which are previously unreported in environmental media. Retrospective screening of 126 PFASs against public data repository from 20 countries show PFAS substitutes are prevalent worldwide.
In Science Journals
Authors: Vignieri Sacha , Lavine Marc S. , Szuromi Phil , Lopez Bianca , Jiang Di , Wong Wei , Matsiko Amos , Nusinovich Yevgeniya , Maroso Mattia , Smith Keith T. , Olingy Claire , Malo Courtney
Published: May 2024

Highlights from the
Science
family of journals
Archaeologists accused of theft, bullying, abuse of power
Authors: Enserink Martin
Published: May 2024

Couple at Leiden University broke norms for 3 decades, investigators say
How the German cockroach conquered the world
Authors: Incorvaia Darren
Published: May 2024

DNA study implicates medieval warfare and colonial trade
Patient outcomes by baseline pathogen resistance phenotype and genotype in CERTAIN-1, a Phase 3 study of cefepime-taniborbactam versus meropenem in adults with complicated urinary tract infection
Authors: Moeck Greg , Gasink Leanne B. , Mendes Rodrigo E. , Woosley Leah N. , Dorr MaryBeth , Chen Hongzi , Wagenlehner Florian M. , Henkel Tim , McGovern Paul C.
Published: May 2024

CERTAIN-1 was a Phase 3, double-blind, randomized, parallel group study of the efficacy and safety of cefepime-taniborbactam versus meropenem in the treatment of adults with complicated urinary tract infection (cUTI), including acute pyelonephritis. We determined susceptibility of Enterobacterales and
Pseudomonas aeruginosa
baseline pathogens to cefepime-taniborbactam and comparators and characterized β-lactam resistance mechanisms. Microbiologic response and clinical response were assessed in patient subsets defined by baseline pathogens that were of cefepime-, multidrug-, or carbapenem-resistant phenotype or that carried β-lactamase genes. Among Enterobacterales baseline pathogens, 26.8%, 4.1%, and 3.0% carried genes for extended-spectrum β-lactamases (ESBLs), AmpC, and carbapenemases, respectively. Within each treatment group, while composite success rates at Test of Cure in resistant subsets by pathogen species were similar to those by pathogen overall, composite success rates in meropenem patients were numerically lower for cefepime-resistant
Escherichia coli
(9/19; 47.4%) and ESBL
E. coli
(13/25; 52.0%) compared with
E. coli
overall (62/100; 62.0%). Cefepime-taniborbactam achieved composite success in 7/8 (87.5%) patients with carbapenem-resistant Enterobacterales and 8/9 (88.9%) patients with Enterobacterales with a carbapenemase gene (5 OXA-48-group; 2 KPC-3; 2 NDM-1). Cefepime-taniborbactam also achieved composite success in 8/16 (50.0%) patients and clinical success in 13/16 (81.3%) patients with
P. aeruginosa
; corresponding rates were 4/7 (57.1%) and 6/7 (85.7%) for meropenem. Cefepime-taniborbactam demonstrated efficacy in adult cUTI patients with cefepime-, multidrug-, and carbapenem-resistant pathogens including pathogens with ESBL, AmpC, and carbapenemase genes.

CLINICAL TRIALS

This study is registered with

ClinicalTrials.gov
as
NCT03840148

.
Dissemination of influenza B virus to the lower respiratory tract of mice is restricted by the interferon response
Authors: Schwab Lara S. U. , Do Thi H. T. , Pilapitiya Devaki , Koutsakos Marios
Published: May 2024

The global burden of disease caused by influenza B virus (IBV) is substantial; however, IBVs remain overlooked. Understanding host–pathogen interactions and establishing physiologically relevant models of infection are important for the development and assessment of therapeutics and vaccines against IBV. In this study, we assessed an upper respiratory tract (URT)-restricted model of mouse IBV infection, comparing it to the conventional administration of the virus to the total respiratory tract (TRT). We found that URT infections caused by different strains of IBV disseminate to the trachea but resulted in limited dissemination of IBV to the lungs. Infection of the URT did not result in weight loss or systemic inflammation even at high inoculum doses and despite robust viral replication in the nose. Dissemination of IBV to the lungs was enhanced in mice lacking functional type I IFN receptor (IFNAR2), but not IFNγ. Conversely, in mice expressing the IFN-inducible gene Mx1, we found reduced IBV replication in the lungs and reduced dissemination of IBV from the URT to the lungs. Inoculation of IBV in both the URT and TRT resulted in seroconversion against IBV. However, priming at the TRT conferred superior protection from a heterologous lethal IBV challenge compared to URT priming, as determined by improved survival rates and reduced viral replication throughout the respiratory tract. Overall, our study establishes a URT-restricted IBV infection model, highlights the critical role of IFNs in limiting dissemination of IBV to the lungs, and also demonstrates that the lack of viral replication in the lungs may impact protection from subsequent infections.

IMPORTANCE

Our study investigated how influenza B virus (IBV) spreads from the nose to the lungs of mice and the impact this has on disease and protection from re-infection. We found that when applied to the nose only, IBV does not spread very efficiently to the lungs in a process controlled by the interferon response. Priming immunity at the nose only resulted in less protection from re-infection than priming immunity at both the nose and lungs. These insights can guide the development of potential therapies targeting the interferon response as well as of intranasal vaccines against IBV.
An indigenously developed tele-ICU model to treat severe cases of envenomation in remote regions in India
Authors: MB Lokesh , Parmar Dileep Singh , Singh Sukhdev , Britto Carl
Published: May 2024

In cases of severe envenomation due to snakebites, patients require antivenom, intensive care management, including respiratory support, haemodynamic monitoring and renal replacement therapy. Early recognition and treatment of complications such as acute kidney injury, rhabdomyolysis and coagulopathy are important to improve outcomes.

Tele-ICU models can play a critical role in providing access to critical care expertise and nuanced support to remote healthcare facilities that may not have the necessary resources or expertise to manage complex cases of envenomation. With the help of telemedicine technology, remote intensivists can provide timely guidance on diagnosis and ongoing management, improving the quality of care and outcomes for patients. We discuss two patients in resource-constrained regions of India with severe envenomation who were managed with tele-ICU support.
Immunotherapy in the neoadjuvant treatment of gastrointestinal tumors: is the time ripe?
Authors: Gervaso Lorenzo , Ciardiello Davide , Oliveira Rivadavio Antunes , Borghesani Michele , Guidi Lorenzo , Benini Lavinia , Algeri Laura , Spada Francesca , Zampino Maria Giulia , Cella Chiara Alessandra , Fazio Nicola
Published: May 2024

Immune checkpoint inhibitors (ICIs) revolutionized the management of mismatch repair-deficient (dMMR)/microsatellite instability-high (MSI-H) gastrointestinal (GI) cancers. Based on notable results observed in the metastatic setting, several clinical trials investigated ICIs as neoadjuvant treatment (NAT) for localized dMMR/MSI-H GI cancers, achieving striking results in terms of clinical and pathological responses and creating the opportunity to spare patients from neoadjuvant chemotherapy and/or radiotherapy and even surgical resection. Nevertheless, these impressive findings are mainly derived from small proof of concept phase II studies and there are still several open questions to address. Moreover, dMMR/MSI-H represents a limited subgroup accounting for less than 10% of GI cancers. Consequently, many efforts have been produced to investigate neoadjuvant ICIs also in mismatch repair-proficient/microsatellite stable (MSS) cancers, considering the potential synergistic effect in combining immune-targeted agents with standard therapies such as chemo and/or radiotherapy. However, results for combining ICIs to the standard of care in the unselected population are still unsatisfactory, without improvements in event-free survival in esophago-gastric adenocarcinoma for the addition of pembrolizumab to chemotherapy, and sometimes limited benefit in patients with locally advanced rectal cancer. Therefore, a major challenge will be to identify among the heterogenous spectrum of this disease, those patients that could take advantage of neoadjuvant immunotherapy and deliver the most effective treatment. In this review we discuss the rationale of NAT in GI malignancies, summarize the available evidence regarding the completed trials that evaluated this treatment strategy in both MSI-H and MSS tumors. Finally, we discuss ongoing studies and future perspectives to render neoadjuvant immunotherapy another arrow in the quiver for the treatment of locally advanced GI tumors.
Shaping the Outlook for the Autonomy Economy
Authors: Liu Shaoshan
Published: May 2024

In each issue of
Communications
, we publish selected posts or excerpts from the many blogs on our website. The views expressed by bloggers are their own and not necessarily held by
Communications
or the Association for Computing Machinery.

Read more blogs and join the discussion at https://cacm.acm.org/blog.

https://cacm.acm.org/blog

Shaoshan Liu examines the role of autonomous machine computing in fostering the autonomy economy.
Supplementary Table S3 from Use of Deep Learning to Evaluate Tumor Microenvironmental Features for Prediction of Colon Cancer Recurrence
Authors: Sinicrope Frank A. , Nelson Garth D. , Saberzadeh-Ardestani Bahar , Segovia Diana I. , Graham Rondell P. , Wu Christina , Hagen Catherine E. , Shivji Sameer , Savage Paul , Buchanan Dan D. , Jenkins Mark A. , Phipps Amanda I. , Swallow Carol , LeMarchand Loic , Gallinger Steven , Grant Robert C. , Pai Reetesh K. , Sinicrope Stephen N. , Yan Dongyao , Shanmugam Kandavel , Conner James , Cyr David P. , Kirsch Richard , Banerjee Imon , Alberts Steve R. , Shi Qian , Pai Rish K.
Published: May 2024

Supplementary Table S3
Supplementary Table S2 from Use of Deep Learning to Evaluate Tumor Microenvironmental Features for Prediction of Colon Cancer Recurrence
Authors: Sinicrope Frank A. , Nelson Garth D. , Saberzadeh-Ardestani Bahar , Segovia Diana I. , Graham Rondell P. , Wu Christina , Hagen Catherine E. , Shivji Sameer , Savage Paul , Buchanan Dan D. , Jenkins Mark A. , Phipps Amanda I. , Swallow Carol , LeMarchand Loic , Gallinger Steven , Grant Robert C. , Pai Reetesh K. , Sinicrope Stephen N. , Yan Dongyao , Shanmugam Kandavel , Conner James , Cyr David P. , Kirsch Richard , Banerjee Imon , Alberts Steve R. , Shi Qian , Pai Rish K.
Published: May 2024

Supplementary Table S2
Supplementary Table S1 from Use of Deep Learning to Evaluate Tumor Microenvironmental Features for Prediction of Colon Cancer Recurrence
Authors: Sinicrope Frank A. , Nelson Garth D. , Saberzadeh-Ardestani Bahar , Segovia Diana I. , Graham Rondell P. , Wu Christina , Hagen Catherine E. , Shivji Sameer , Savage Paul , Buchanan Dan D. , Jenkins Mark A. , Phipps Amanda I. , Swallow Carol , LeMarchand Loic , Gallinger Steven , Grant Robert C. , Pai Reetesh K. , Sinicrope Stephen N. , Yan Dongyao , Shanmugam Kandavel , Conner James , Cyr David P. , Kirsch Richard , Banerjee Imon , Alberts Steve R. , Shi Qian , Pai Rish K.
Published: May 2024

Supplementary Table S1
Data from Use of Deep Learning to Evaluate Tumor Microenvironmental Features for Prediction of Colon Cancer Recurrence
Authors: Sinicrope Frank A. , Nelson Garth D. , Saberzadeh-Ardestani Bahar , Segovia Diana I. , Graham Rondell P. , Wu Christina , Hagen Catherine E. , Shivji Sameer , Savage Paul , Buchanan Dan D. , Jenkins Mark A. , Phipps Amanda I. , Swallow Carol , LeMarchand Loic , Gallinger Steven , Grant Robert C. , Pai Reetesh K. , Sinicrope Stephen N. , Yan Dongyao , Shanmugam Kandavel , Conner James , Cyr David P. , Kirsch Richard , Banerjee Imon , Alberts Steve R. , Shi Qian , Pai Rish K.
Published: May 2024

Abstract
Deep learning may detect biologically important signals embedded in tumor morphologic features that confer distinct prognoses. Tumor morphologic features were quantified to enhance patient risk stratification within DNA mismatch repair (MMR) groups using deep learning. Using a quantitative segmentation algorithm (QuantCRC) that identifies 15 distinct morphologic features, we analyzed 402 resected stage III colon carcinomas [191 deficient (d)-MMR; 189 proficient (p)-MMR] from participants in a phase III trial of FOLFOX-based adjuvant chemotherapy. Results were validated in an independent cohort (176 d-MMR; 1,094 p-MMR). Association of morphologic features with clinicopathologic variables, MMR, KRAS, BRAFV600E, and time-to-recurrence (TTR) was determined. Multivariable Cox proportional hazards models were developed to predict TTR. Tumor morphologic features differed significantly by MMR status. Cancers with p-MMR had more immature desmoplastic stroma. Tumors with d-MMR had increased inflammatory stroma, epithelial tumor-infiltrating lymphocytes (TIL), high-grade histology, mucin, and signet ring cells. Stromal subtype did not differ by BRAFV600E or KRAS status. In p-MMR tumors, multivariable analysis identified tumor-stroma ratio (TSR) as the strongest feature associated with TTR [HRadj 2.02; 95% confidence interval (CI), 1.14–3.57; P = 0.018; 3-year recurrence: 40.2% vs. 20.4%; Q1 vs. Q2–4]. Among d-MMR tumors, extent of inflammatory stroma (continuous HRadj 0.98; 95% CI, 0.96–0.99; P = 0.028; 3-year recurrence: 13.3% vs. 33.4%, Q4 vs. Q1) and N stage were the most robust prognostically. Association of TSR with TTR was independently validated. In conclusion, QuantCRC can quantify morphologic differences within MMR groups in routine tumor sections to determine their relative contributions to patient prognosis, and may elucidate relevant pathophysiologic mechanisms driving prognosis.
Significance:
A deep learning algorithm can quantify tumor morphologic features that may reflect underlying mechanisms driving prognosis within MMR groups. TSR was the most robust morphologic feature associated with TTR in p-MMR colon cancers. Extent of inflammatory stroma and N stage were the strongest prognostic features in d-MMR tumors. TIL density was not independently prognostic in either MMR group.
A representação dos povos quilombolas na obra Torto arado, de Itamar Vieira Junior (2019): o racismo estrutural sob o olhar feminino
Authors: Santiago João Lucas , Oliveira Vanderléia da Silva
Published: May 2024

Analysis of Torto arado (2019), by Itamar Vieira Junior with attention to the point of view of narration, since the narrators of the novel, three quilombola women, reveal in the work the marks left by slavery in Brazil, which consequently helps in the understanding of structural and institutional racism in Brazilian society. As a result, it appears that the novel expresses the relationship between the slavery past and the current portrait of blacks, quilombola communities and social inequality in Brazil.
A problematização da raça na produção literária de Mia Couto: uma breve análise de O Outro Pé da Sereia em comparação com a produção de Miriam Alves
Authors: Rocha Cintia Ribeiro
Published: May 2024

This article proposes an analytical and comparative reading of black African civilizational values ​​in the works of Mia Couto and Miriam Alves. Issues of race will be problematized to analyze the approximations and distances in the works of the two authors regarding the representations of the black people on the African continent and from a diasporic perspective. In this sense, it will be observed how the black enunciation in the work of the writer Miriam Alves dialogues with principles of Afro-centered community life.
Torto arado: a literatura de resistência na narrativa de Itamar Vieira Júnior
Authors: Gouveia Juanna Beatriz de Brito , Almeida Matheus Lucas de
Published: May 2024

O presente artigo analisa o dialogismo entre a literatura e a resistência que se relacionam para apresentar um cenário que trabalha as dicotomias entre medo e coragem, voz e silêncio, fertilidade e infertilidade, cidade e campo na obra Torto arado (VIEIRA JÚNIOR, 2018). Com base nas análises realizadas, percebe-se que a obra mantém relação com a realidade social e traz luz a voz de mulheres resistentes, protetoras e provedoras que atravessaram tudo, suportando a crueldade que lhes foi imposta.
Itamar Vieira Junior e as heranças da escravidão no Brasil: os explorados deste tempo
Authors: Andrade Patrícia Helena Baialuna de
Published: May 2024

This paper aims to analyze two short stories by Itamar Vieira Junior— “Alma” and “Doramar ou a Odisseia”, as well as his heralded novel Torto arado — as literary problematizations of a social issue that remains invisible to most Brazilians: the contemporary forms of slavery that claim victims among the most economically vulnerable workers, who are often the descendants of those enslaved during Brazil’s colonial times.
"Mas há algo de contorno ou travessia no dia": entrevista com Francesca Cricelli
Authors: Silva Sandro Adriano da , Luz Cleber da Silva
Published: May 2024

Interview with poet, translator and researcher Francesca Cricelli.
Reflexões sobre a literatura brasileira contemporânea
Authors: Pietroforte Antonio Vicente Seraphim
Published: May 2024

Quem estuda a literatura brasileira contemporânea, antes de tudo, depara-se com a pluralidade de autores, estilos e temáticas. No meio da quantidade, porém, algumas regularidades podem ser encontradas; com vistas a determiná-las, no trabalho seguinte opta-se por encaminhar algumas reflexões a propósito da poesia brasileira contemporânea em dois níveis de análise literária: primeiramente, propõem-se uma sistematização das formas prosódico-fonológicas, semânticas e narrativas, enfim, das formas semióticas gerais e abstratas da poesia brasileira contemporânea; em seguida, enumeram-se e são analisadas brevemente algumas de suas temáticas mais recorrentes.
Microstructure and mechanical properties of wire-arc directed energy deposited Al-Mg-Sc aluminum alloy: As-deposited and aging heat treated
Authors: Cui Jiayuan , Guo Xinpeng , Hao Shuai , Zhao Yuanzheng , Guo Xuming
Published: May 2024

In this study, Al-Mg-Sc aluminum alloys were fabricated using wire-arc directed energy deposition. The focus of the study was to analyze the microstructure and mechanical properties of these alloys. Comparative analysis was conducted on the samples obtained from the as-deposited and aging treated, respectively. Furthermore, the precipitation process of the second phases and the associated strengthening mechanism were elucidated. The findings revealed that the presence of precipitated Al3(Sc,Zr) particles acted as heterogeneous nucleation nuclei of α-Al, facilitating the formation of equiaxial grains. During the subsequent aging treatment, the secondary Al3(Sc,Zr) particles precipitated directly without transitioning through intermediate phases. Additionally, the experimental results demonstrated that these secondary Al3(Sc,Zr) phases hindered the dislocation movement, leading to enhanced mechanical properties in Al-Mg-Sc alloys through precipitation strengthening. In the horizontal direction, the average ultimate tensile strength (UTS) and yield strength (YS) were measured as 361 ± 5 MPa, 251 ± 4 MPa, and 281 ± 6 MPa, 179 ± 6 MPa in the vertical direction, respectively. The elongations were found to be 15.8 ± 0.8% and 4.0 ± 0.5% in the horizontal and vertical directions, respectively. The observed variations in mechanical properties were attributed to the presence of interlayer pores.
OsEXPA7 Encoding an Expansin Affects Grain Size and Quality Traits in Rice (Oryza sativa L.)
Authors: Zhang Xinwei , Wang Ying , Liu Mingyu , Yan Peiwen , Niu Fuan , Ma Fuying , Hu Jian , He Shicong , Cui Jinhao , Yuan Xinyu , Yang Jinshui , Cao Liming , Luo Xiaojin
Published: May 2024

Background

Yield and quality are the two most important traits in crop breeding. Exploring the regulatory mechanisms that affect both yield and quality traits is of great significance for understanding the molecular genetic networks controlling these key crop attributes. Expansins are cell wall loosening proteins that play important roles in regulating rice grain size.

Results

We investigated the effect of OsEXPA7, encoding an expansin, on rice grain size and quality. OsEXPA7 overexpression resulted in increased plant height, panicle length, grain length, and thousand-grain weight in rice. OsEXPA7 overexpression also affected gel consistency and amylose content in rice grains, thus affecting rice quality. Subcellular localization and tissue expression analyses showed that OsEXPA7 is localized on the cell wall and is highly expressed in the panicle. Hormone treatment experiments revealed that OsEXPA7 expression mainly responds to methyl jasmonate, brassinolide, and gibberellin. Transcriptome analysis and RT-qPCR experiments showed that overexpression of OsEXPA7 affects the expression of OsJAZs in the jasmonic acid pathway and BZR1 and GE in the brassinosteroid pathway. In addition, OsEXPA7 regulates the expression of key quantitative trait loci related to yield traits, as well as regulates the expression levels of BIP1 and bZIP50 involved in the seed storage protein biosynthesis pathway.

Conclusions

These results reveal that OsEXPA7 positively regulates rice yield traits and negatively regulates grain quality traits by involving plant hormone pathways and other trait-related pathway genes. These findings increase our understanding of the potential mechanism of expansins in regulating rice yield and quality traits and will be useful for breeding high-yielding and high-quality rice cultivars.
Comparing the in vitro efficacy of chlorhexidine and povidone-iodine in the prevention of post-surgical endophthalmitis
Authors: Batista Celso Soares Pereira , Loscos-Giménez Irene , Gámez María , Altaba Raul , de Miniac Daniela , Martí Neus , Bassaganyas Francisca , Juanes Elena , Rivera Alba , Navarro Ferran
Published: May 2024

Background

Intravitreal injections are a common ophthalmologic procedure. While infections following these injections are rare, they can lead to endophthalmitis, with potentially serious consequences. Various methods have been proposed to prevent endophthalmitis, including the use of antisepsis and antibiotics in patient preparation.

Purpose

To evaluate the antiseptic efficacy of aqueous chlorhexidine (CHX) and povidone-iodine (PI) when used alone and in combination with lidocaine gel (LG) in vitro.

Methods

Two independent experimental trials were conducted. The first trial determined the minimum inhibitory concentrations (MICs) and the minimum bactericidal concentrations (MBCs) of CHX and PI against six bacterial strains. The second trial evaluated the bactericidal efficacy of the antiseptic agents (CHX 0.1% and PI 5%) and their combination with LG against the same bacterial strains.

Results

CHX was more effective than PI in reducing the number of colonies forming units (cfus) of the tested bacteria. The order in which the antiseptic and LG were administered affected their effectiveness, with CHX administered before LG resulting in greater reduction of bacterial growth.

Conclusions

CHX 0.1% is more effective than PI 5% as an antiseptic agent. Application of CHX and PI prior to the use of lidocaine gel results in a more effective reduction of microorganisms.
The Carthamus tinctorius L. genome sequence provides insights into synthesis of unsaturated fatty acids
Authors: Dong Yuanyuan , Wang Xiaojie , Ahmad Naveed , Sun Yepeng , Wang Yuanxin , Liu Xiuming , Yao Na , Jing Yang , Du Linna , Li Xiaowei , Wang Nan , Liu Weican , Wang Fawei , Li Xiaokun , Li Haiyan
Published: May 2024

Domesticated safflower (Carthamus tinctorius L.) is a widely cultivated edible oil crop. However, despite its economic importance, the genetic basis underlying key traits such as oil content, resistance to biotic and abiotic stresses, and flowering time remains poorly understood. Here, we present the genome assembly for C. tinctorius variety Jihong01, which was obtained by integrating Oxford Nanopore Technologies (ONT) and BGI-SEQ500 sequencing results. The assembled genome was 1,061.1 Mb, and consisted of 32,379 protein-coding genes, 97.71% of which were functionally annotated. Safflower had a recent whole genome duplication (WGD) event in evolution history and diverged from sunflower approximately 37.3 million years ago. Through comparative genomic analysis at five seed development stages, we unveiled the pivotal roles of fatty acid desaturase 2 (FAD2) and fatty acid desaturase 6 (FAD6) in linoleic acid (LA) biosynthesis. Similarly, the differential gene expression analysis further reinforced the significance of these genes in regulating LA accumulation. Moreover, our investigation of seed fatty acid composition at different seed developmental stages unveiled the crucial roles of FAD2 and FAD6 in LA biosynthesis. These findings offer important insights into enhancing breeding programs for the improvement of quality traits and provide reference resource for further research on the natural properties of safflower.
Toxin genotypes, antibiotic resistance and their correlations in Clostridioides difficile isolated from hospitals in Xi’an, China
Authors: Zhang Sukai , Ma Chen , Zhang Haiyue , Zhao Congcong , Guo Ruibing , Liu Jiahao , Wang Jing , Yuan Jing , Jia Kai , Wu Airong , Chen Yanjiong , Lei Jin’e
Published: May 2024

Background

Clostridioides difficile is the main pathogen of antimicrobial-associated diarrhoea and health care facility-associated infectious diarrhoea. This study aimed to investigate the prevalence, toxin genotypes, and antibiotic resistance of C. difficile among hospitalized patients in Xi’an, China.

Results

We isolated and cultured 156 strains of C. difficile, representing 12.67% of the 1231 inpatient stool samples collected. Among the isolates, tcdA + B + strains were predominant, accounting for 78.2% (122/156), followed by 27 tcdA-B + strains (27/156, 17.3%) and 6 binary toxin gene-positive strains. The positive rates of three regulatory genes, tcdC, tcdR, and tcdE, were 89.1% (139/156), 96.8% (151/156), and 100%, respectively. All isolates were sensitive to metronidazole, and the resistance rates to clindamycin and cephalosporins were also high. Six strains were found to be resistant to vancomycin.

Conclusion

Currently, the prevalence rate of C. difficile infection (CDI) in Xi’an is 12.67% (156/1231), with the major toxin genotype of the isolates being tcdA + tcdB + cdtA-/B-. Metronidazole and vancomycin were still effective drugs for the treatment of CDI, but we should pay attention to antibiotic management and epidemiological surveillance of CDI.
Carbapenem-resistant gram-negative bacterial infections and risk factors for acquisition in a Kenyan intensive care unit
Authors: Maina Jane Wairimu , Mutua Jeniffer Munyiva , Musyoki Abednego Moki
Published: May 2024

Background

Carbapenem-resistant Gram-negative bacteria (CR-GNB) are a critical public health threat globally; however, there are inadequate surveillance data, especially in intensive care units (ICU), to inform infection prevention and control in many resource-constrained settings. Here, we assessed the prevalence of CR-GNB infections and risk factors for acquisition in a Kenyan ICU.

Methods

A hospital-based cross-sectional study design was adopted, recruiting 162 patients clinically presenting with bacterial infection after 48 h of ICU admission, from January to October 2022 at the Nairobi West Hospital, Kenya. Demographics and clinical data were collected by case report form. The type of sample collected, including blood, tracheal aspirate, ascitic tap, urine, stool, and sputum depended on the patient’s clinical presentation and were transported to the hospital Microbiology laboratory in a cool box for processing within 2 h. The samples were analyzed by cultured and BD Phoenix system used for isolates’ identity and antimicrobial susceptibility.

Results

CR-GNB infections prevalence was 25.9% (42/162), with Klebsiella pneumoniae (35.7%, 15/42) and Pseudomonas aeruginosa (26.2%, 11/42) predominating. All isolates were multidrug-resistant (MDR). P. aeruginosa and A. baumannii were 100% colistin-resistant, while K. pneumoniae (33.3%) was tigecycline-resistant. History of antibiotics (aOR = 3.40, p = 0.005) and nasogastric tube (NGT) use (aOR = 5.84, p = < 0.001) were the risk factors for infection.

Conclusion

Our study highlights high MDR- and CR-GNB infections in ICU, with prior antibiotic exposure and NGT use as risk factors, and diminishing clinical value of colistin and tigecycline. In this study setting and beyond, strict implementation of antimicrobial stewardship programs and adherence to infection prevention and control through monitoring, evaluation and feedback are warranted to curb CR-GNB infections, especially among the risk groups.
Cutaneous Lagenidium deciduum infection in a patient with relapsed acute myeloid leukemia
Authors: Theophilopoulos Joanna , King Rebekah , Citta Autumn , Alford Constance , Dotson Natalie , Cañete-Gibas Connie , Sanders Carmita , Wiederhold Nathan , Ligon John A. , Trieu Connie
Published: May 2024

Background

Lagenidium deciduum is an oomycete that can cause infections in mammals that present similarly to pythiosis and mucormycosis. Most of the existing case reports have occurred in canines and have been fatal. In animals, medical therapy has not been successful, so surgical excision is the mainstay of treatment. Lagenidium sp. infections in humans are rare. There is only one case of a human Lagenidium sp. infection in the literature, and it presented as an ocular infection. The human ocular infection was resistant to medical therapy and required a penetrating keratoplasty for cure. Additional reports of effective therapy are needed to guide management of this emerging pathogen. We present the first case of a cutaneous Lagenidium deciduum infection in a human patient, which is also the first documented case of a Lagenidium deciduum infection in an immunocompromised host of any species.

Case presentation

An 18-year-old female with relapsed acute myeloid leukemia, awaiting a haploidentical stem cell transplant, presented with erythematous cutaneous lesions on her left hip and bilateral buttocks that enlarged and blackened over several days. About 1 week later, boil-like lesions appeared on her bilateral buttocks. The skin lesions were initially presumed to be bacterial in origin, so the patient was treated with clindamycin and cefepime with little improvement. Upon further investigation, fungal cultures and skin biopsies revealed aseptate hyphae, so the patient was switched to isavuconazole and amphotericin B due to concern for mucormycosis. Phenotypic characterization and DNA sequencing were performed by the Fungus Testing Laboratory, University of Texas Health Science Center at San Antonio, which identified the causal fungal organism as Lagenidium deciduum. All of her cutaneous lesions were surgically excised, and the patient was treated with micafungin, terbinafine, doxycycline, and azithromycin. Micafungin and terbinafine were continued until she achieved engraftment post-transplant.

Conclusions

We report the first successful treatment of a human Lagenidium infection in an immunocompromised host through a combination of aggressive surgical excision and prolonged antifungal therapy during the prolonged neutropenia associated with allogeneic stem cell transplant. Prompt diagnosis and management may prevent disseminated oomycosis.