bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chronic pulmonary aspergillosis incidence in newly detected pulmonary tuberculosis cases during follow‐up
Authors: Jha Dhouli , Kumar Umesh , Meena Ved Prakash , Sethi Prayas , Singh Amandeep , Nischal Neeraj , Jorwal Pankaj , Vyas Surabhi , Singh Gagandeep , Xess Immaculata , Singh Urvashi B. , Sinha Sanjeev , Mohan Anant , Wig Naveet , Kabra Sushil Kumar , Ray Animesh 
Published: May 2024

AbstractBackgroundChronic pulmonary aspergillosis (CPA) is known to complicate patients with post‐tubercular lung disease. However, some evidence suggests that CPA might co‐exist in patients with newly‐diagnosed pulmonary tuberculosis (P.TB) at diagnosis and also develop during therapy. The objective of this study was to confirm the presence of CPA in newly diagnosed P.TB at baseline and at the end‐of‐TB‐therapy.Materials and MethodsThis prospective longitudinal study included newly diagnosed P.TB patients, followed up at third month and end‐of‐TB‐therapy with symptom assessment, anti‐Aspergillus IgG antibody and imaging of chest for diagnosing CPA.ResultsWe recruited 255 patients at baseline out of which 158 (62%) completed their follow‐up. Anti‐Aspergillus IgG was positive in 11.1% at baseline and 27.8% at end‐of‐TB‐therapy. Overall, proven CPA was diagnosed in 7% at baseline and 14.5% at the end‐of‐TB‐therapy. Around 6% patients had evidence of aspergilloma in CT chest at the end‐of‐TB‐therapy.ConclusionsCPA can be present in newly diagnosed P.TB patients at diagnosis and also develop during anti‐tubercular treatment. Patients with persistent symptoms or developing new symptoms during treatment for P.TB should be evaluated for CPA. Whether patients with concomitant P.TB and CPA, while receiving antitubercular therapy, need additional antifungal therapy, needs to be evaluated in future studies.
Antifungal activity of aminopyrrolnitrin against Trichophyton verrucosum in a guinea pig model of dermatophytosis
Authors: Lee Han Gyu , Bok Eun‐Yeong , Jung Young‐Hun , Hur Tai‐Young , Kim Young‐Ok , Kong Hee Jeong , Kim Dong‐Gyun , Kim Young‐Sam , Oem Jae Ku 
Published: May 2024

AbstractBackgroundDermatophytosis is a common and major public health concern worldwide. Despite the increasing availability of antifungal drugs, relapses and untreated cases of dermatophyte infections are reported. Therefore, novel antifungal agents are required. Aminopyrrolnitrin (APRN) shows promise for dermatophytosis treatment because of its antifungal activity.ObjectivesThis study aimed to assess the antifungal properties of APRN against Trichophyton verrucosum (T. verrucosum), in both laboratory settings and a guinea pig model.MethodsThe minimum inhibitory concentrations (MICs) of APRN and enilconazole against T. verrucosum were determined according to the CLSI M38 method. The skins of 16 male guinea pigs were infected with 1.0 × 108 conidia of T. verrucosum and the animals were grouped into sets of four: negative control group (NC) received normal saline; positive control group (PC) received 2 μg/mL of enilconazole; and APRN4 and APRN8 received 4 and 8 μg/mL of APRN, respectively. Clinical, mycological and histological efficacies were measured after 10 days.ResultsThe MIC90 of APRN and enilconazole against T. verrucosum was 4 and 2 μg/mL, respectively. The clinical scores of PC, APRN4, and APRN8 were significantly lower than those of NC. Clinical and mycological efficacies were higher for APRN8, APRN4 and PC. No fungi were observed in the skin tissues of APRN4 and APRN8, while fungi were observed in 50% of the PC.ConclusionAPRN showed antifungal activity against T. verrucosum in vitro and in vivo and is a potential candidate for the treatment of dermatophytosis.
Accurate and comprehensive evaluation of O6‐methylguanine‐DNA methyltransferase promoter methylation by nanopore sequencing
Authors: Halldorsson Skarphedinn , Nagymihaly Richard Mark , Patel Areeba , Brandal Petter , Panagopoulos Ioannis , Leske Henning , Lund‐Iversen Marius , Sahm Felix , Vik‐Mo Einar O. 
Published: May 2024

AbstractAimsThe methylation status of the O6‐methylguanine‐DNA methyltransferase (MGMT) promoter region is essential in evaluating the prognosis and predicting the drug response in patients with glioblastoma. In this study, we evaluated the utility of using nanopore long‐read sequencing as a method for assessing methylation levels throughout the MGMT CpG‐island, compared its performance to established techniques and demonstrated its clinical applicability.MethodsWe analysed 165 samples from CNS tumours, focusing on the MGMT CpG‐island using nanopore sequencing. Oxford Nanopore Technologies (ONT) MinION and PromethION flow cells were employed for single sample or barcoded assays, guided by a CRISPR/Cas9 protocol, adaptive sampling or as part of a whole genome sequencing assay. Methylation data obtained through nanopore sequencing were compared to results obtained via pyrosequencing and methylation bead arrays. Hierarchical clustering was applied to nanopore sequencing data for patient stratification.ResultsNanopore sequencing displayed a strong correlation (R2 = 0.91) with pyrosequencing results for the four CpGs of MGMT analysed by both methods. The MGMT‐STP27 algorithm's classification was effectively reproduced using nanopore data. Unsupervised hierarchical clustering revealed distinct patterns in methylated and unmethylated samples, providing comparable survival prediction capabilities. Nanopore sequencing yielded high‐confidence results in a rapid timeframe, typically within hours of sequencing, and extended the analysis to all 98 CpGs of the MGMT CpG‐island.ConclusionsThis study presents nanopore sequencing as a valid and efficient method for determining MGMT promotor methylation status. It offers a comprehensive view of the MGMT promoter methylation landscape, which enables the identification of potentially clinically relevant subgroups of patients. Further exploration of the clinical implications of patient stratification using nanopore sequencing of MGMT is warranted.
Validity of dietary assessment methods compared with doubly labeled water in children: A systematic review and meta‐analysis
Authors: Mehranfar Sanaz , Jalilpiran Yahya , Jafari Alireza , Jayedi Ahmad , Shab‐bidar Sakineh , Speakman John R. , Djafarian Kurosh 
Published: May 2024

SummaryObjectivesWe aimed to validate dietary assessment methods against the gold standard, doubly labeled water (DLW), for estimating total energy intake (TEI).MethodsPubMed, Scopus, Web of Science, and Google Scholar databases were searched until May 2023. Inclusion criteria encompassed studies involving participants aged 1–18 years, employing dietary assessment methods like food records, dietary histories, food frequency questionnaire (FFQ), or 24‐h recalls estimating TEI alongside DLW to measure total energy expenditure (TEE). Data were pooled using random‐effects meta‐analysis models.ResultsThirty‐three studies were identified, with sample sizes ranging from 9 to 118 participants. Meta‐analysis of 22 studies identified underestimation of TEI (mean difference [MD] = −262.9 kcal/day [95% CI: −380.0, −145.8]; I2 = 93.55%) for food records compared with TEE estimated by DLW. Other dietary assessment methods, including food recalls (n = 9) (MD = 54.2 kcal/day [95% CI: −19.8, 128.1]; I2 = 49.62%), FFQ (n = 7) (MD = 44.5 kcal/day [95% CI: −317.8, 406.8]; I2 = 94.94%), and diet history (n = 3) (MD = −130.8 kcal/day [95% CI: −455.8, 194.1]; I2 = 77.48%), showed no significant differences in TEI compared with DLW‐estimated TEE. All studies were of high quality.ConclusionFood records may underestimate TEI, yet additional research is needed to identify the most accurate methods for assessing children's dietary intake.
A Novel Internal Fixation Design for the Treatment of AO/OTA‐31A3.3 Intertrochanteric Fractures: Finite Element Analysis
Authors: Chen Xiaofeng , Tang Miaotian , Zhang Xiaomeng , Zhang Yichong , Wang Yilin , Xiong Chen , Ji Yun , Wang Yanhua , Zhang Dianying 
Published: May 2024

ObjectiveAO/OTA 31‐A3.3 intertrochanteric fracture is the most unstable type of intertrochanteric fracture, with a high rate of postoperative complications and implant failure. We have designed a new intramedullary fixation, proximal femoral totally bionic nail (PFTBN), for the treatment of A3.3 intertrochanteric fracture. To test its biomechanical performance, we adopted the method of finite element analysis and compared PFTBN with proximal femoral nail antirotation (PFNA) and proximal femoral bionic nail (PFBN, another internal fixation we previously designed for stable intertrochanteric fractures).MethodsMimics, 3‐matic, ANSYS, and other software were used to construct a highly precise and realistic 3D digital model of the human femur. An AO/OTA 31‐A3.3 intertrochanteric fracture of the femur was constructed according to the 2018 classification of AO/OTA, and then assembled with PFNA, PFBN and PFTBN models, respectively. The stress distribution and displacement distribution of the three groups of constructs were tested under three times the body weight load and one‐foot standing configuration.ResultsIn terms of maximum stress and maximum displacement, the PFTBN group outperforms the PFBN group, and the PFBN group, in turn, surpasses the PFNA group. The maximum stress of PFTBN group was 408.5 Mpa, that of PFBN group was 525.4 MPa, and that of PFNA group was 764.3 Mpa. Comparatively, the maximum stress in the PFTBN group was reduced by 46.6% when contrasted with the PFNA group. Moreover, the stress dispersion within the PFTBN group was more evenly distributed than PFNA group. Regarding maximum displacement, the PFTBN group displayed the least displacement at 5.15 mm, followed by the PFBN group at 7.32 mm, and the PFNA group at 7.73 mm. Notably, the maximum displacement of the PFTBN group was 33.4% less than that observed in the PFNA group. Additionally, the relative displacement between the fragment and implant at the tip of pressure screw or helical blade was 0.22 mm in the PFTBN group, 0.34 mm in the PFBN group, and substantially higher 0.51 mm in the PFNA group.ConclusionThe “lever‐reconstruction‐balance” theory provides a new perspective for us to understand the mechanical conduction of the proximal femur. Compared with PFNA, in treating A3.3 intertrochanteric fractures PFTBN can better reconstruct the function of lateral wall, restore physiological mechanical conduction, increase postoperative stability, and finally reduce the risk of postoperative cut‐out and implant failure. It might be a better alternative for the treatment of A3.3 intertrochanteric fracture.
Pleiotropic phenotypic effects of the TaCYP78A family on multiple yield‐related traits in wheat
Authors: Ma Meng , Wu Linnan , Li Mengyao , Li Long , Guo Lijian , Ka Deyan , Zhang Tianxing , Zhou Mengdie , Wu Baowei , Peng Haixia , Hu Zhaoxin , Liu Xiangli , Jing Ruilian , Zhao Huixian 
Published: May 2024

SummaryIncreasing crop yield depends on selecting and utilizing pleiotropic genes/alleles to improve multiple yield‐related traits (YRTs) during crop breeding. However, synergistic improvement of YRTs is challenging due to the trade‐offs between YRTs in breeding practices. Here, the favourable haplotypes of the TaCYP78A family are identified by analysing allelic variations in 1571 wheat accessions worldwide, demonstrating the selection and utilization of pleiotropic genes to improve yield and related traits during wheat breeding. The TaCYP78A family members, including TaCYP78A3, TaCYP78A5, TaCYP78A16, and TaCYP78A17, are organ size regulators expressed in multiple organs, and their allelic variations associated with various YRTs. However, due to the trade‐offs between YRTs, knockdown or overexpression of TaCYP78A family members does not directly increase yield. Favourable haplotypes of the TaCYP78A family, namely A3/5/16/17Ap‐Hap II, optimize the expression levels of TaCYP78A3/5/16/17‐A across different wheat organs to overcome trade‐offs and improve multiple YRTs. Different favourable haplotypes have both complementary and specific functions in improving YRTs, and their aggregation in cultivars under strong artificial selection greatly increase yield, even under various planting environments and densities. These findings provide new support and valuable genetic resources for molecular breeding of wheat and other crops in the era of Breeding 4.0.
Organisational teleology 2.0: Grounding biological purposiveness in regulatory control
Authors: Bich Leonardo 
Published: May 2024

AbstractThis paper critically revises the organisational account of teleology, which argues that living systems are first and foremost oriented towards a goal: maintaining their own conditions of existence. It points out some limitations of this account, mainly in the capability to account for the richness and complexity of biological systems and their purposeful behaviours. It identifies the reason of these limitations in the theoretical grounding of this account, specifically in the too narrow notion of closure of constraints, focused on self‐production. It proposes to ground an organisational account of biological teleology in the capability of living system not just to produce and replace their parts, but to control their own internal dynamics and behaviours in such a way as to maintain themselves. This theoretical framework has two advantages. It better captures the distinctive features of biological organisations and consequently the richness and active nature of their purposeful behaviours. By doing so, it makes it possible to apply this framework beyond minimal theoretical models to real biological cases.
Dualism about undercutting defeat
Authors: Tiozzo Marco 
Published: May 2024

AbstractMost philosophers agree that the distinction between rebutting and undercutting defeaters is sound. Recently, however, there has been much debate over the nature of and relationship between rebutting and undercutting defeaters. Among the things that have been argued about is whether undercutting defeat, in contrast to rebutting defeat, require higher‐order commitment, i.e., a belief regarding the link between the source of justification and the target proposition. This paper examines the debate and argues that whether or not undercutting defeaters require higher‐order commitments to this effect depends on the relevant defeatee at issue. A belief might fail to be rational in at least two ways—either by failing to correctly respond to one's reasons or by failing to be coherent with one's other attitudes. According to dualism about rationality these failings reflect two genuine and distinct kinds of rationality: substantive and structural rationality. In line with this view, the paper suggests that we should make a parallel distinction between substantive and structural undercutting defeaters. An advantage of classifying undercutting defeaters in this way is that it helps to disentangle the current debate. Another interesting result is that the proposed distinction lends further support to dualism about rationality.
Early Family Formation, Selective Migration, and Childhood Conditions in Rural America☆
Authors: Brooks Matthew M. , Clark Shelley 
Published: May 2024

AbstractThirty years ago, rural Americans got married and had children at significantly younger ages than urban Americans. More recent data indicate that these differences persist today, but our understanding of what drives these differences remains limited. To address this gap, we (1) generate Kaplan–Meier estimates of the ages of the first marriage, first union, and first birth among those who lived in rural and urban areas in 2019, (2) evaluate the extent to which rural–urban differences in the timing of family formation reflect selective migration, (3) assess whether rural–urban differences in childhood SES and demographic characteristics further explain differences in timing, and (4) explore rural–urban differences by gender. We find substantial 4.3, 3.8, and 5.1‐year gaps in the ages at which rural and urban women marry, start unions, and become parents, respectively. These gaps largely do not reflect selective migration. Differences in women's age of first birth are attributable to differences in childhood conditions, yet differences in marital and union timing remain unexplained. Rural–urban gaps in the timing of family formation are much larger among women than among men. These patterns of early family formation in rural America have critical implications for families' and children's well‐being as well as rural depopulation.
The reach of decentralized poverty governance: Race, politics, and framing poverty in community action agency mission statements
Authors: Kane Emily W. 
Published: May 2024

AbstractThe literature on decentralized public assistance programs in the United States documents racialized, partisan poverty governance founded on paternalism and individualistic frameworks. This article extends that literature to consider such frameworks in a unique site of poverty governance, Community Action Agencies (CAAs). Established during the War on Poverty in the 1960's, CAAs emphasized “maximum feasible participation” from low‐income citizens, aspiring to participatory models and funding structures that some believed could block systemically racist and politicized resource allocation. Drawing on a novel dataset of mission statements for CAAs across the US, I test how three distinct dimensions of the framing of poverty vary by the racial and partisan context of each agency's geographic location. Individualist, passive framings are common, and significantly more so in geographic areas with more residents of color and greater support for Republican political candidates. But some of the inclusive and participatory aspirations of CAA structures remain evident too, with race and politics predicting these even more strongly. Thus, my analyses provide new evidence for the way decentralization allows the deep reach of racialized and partisan approaches to addressing poverty, even with new measures and even in an arena in which inclusive participation was a central founding aspiration.
Tonal Phonotactics in Southern Min
Authors: Huang Yishan 
Published: May 2024

AbstractThis paper is the first to explore tonal phonotactics in the world's natural languages. Zhangzhou Southern Min is theoretically assumed to have 7320 possible syllables but more than 71% of them are not empirically attested. Each lexical tone is logically possible to generate 915 syllables; however, the attested number only ranges from 98 syllables under tone 8 to 392 under tone 1. This study bases on a large corpus to explore how individual tones behave in the formation of attestable syllables, in what way tonal phonotactics occur and what mechanisms have trigged phonotactic constraints from both synchronic and diachronic factors. This study substantially stretches and advances our knowledge of tonal phonotactics as an important phonology phenomenon in this language. The exploration is supposed to serve as a model for thorough investigations of tonal phonotactics in Sinitic languages, shedding important light on the generalization of areal characteristics in Asia that possess rich and complex tonal contrasts. The study also contributes vital linguistics data to the typology of phonotactics in human languages, while enlightening a research direction of using experimental methods to model phonotactic restrictions in speakers' mental grammar and language practice.
An exception-reporting approach for wound swab culture: effect on post-report antibiotic initiation
Authors: Bloomfield Max , van der Werff Koen , Todd Sue , Bocacao Marjel , Reed Hamish , Balm Michelle , Blackmore Tim 
Published: May 2024

ABSTRACT

A prior analysis suggested that wound swab culture (WSC) results were driving unnecessary antibiotic use in patients who were not already receiving treatment. As a quality-improvement initiative, our laboratory introduced an “exception-reporting” protocol on 1 March 2023, whereby typical wound pathogens susceptible to recommended empiric therapy (flucloxacillin/cefalexin) were not reported, and a comment was provided, stating no significant resistant organisms had been detected. Full results were available to clinicians on request. Cultures falling outside protocol criteria were reported in the standard fashion. This analysis sought to assess the effect of exception-reporting on post-report antibiotic initiation (PRAI). All community WSC results were matched to antibiotic dispensing records from October 2021 to December 2023. Sampling without treatment pre-report was termed “test and wait” (TaW). Following TaW, PRAI was identified if antibiotics were started within 5 days post-report. There were 1,819 and 764 WSCs received in the pre-change and post-change periods, respectively, where an initial TaW approach had been taken and an organism eligible for exception-reporting had been isolated. In the post-change period, 407 (53.3%) met the criteria and were exception-reported. PRAI occurred in 901 (49.5%) pre-change samples, compared to 102 (25.1%,
P
< 0.01) with exception-reporting. There was no detectable increase in hospitalization or repeat WSC collection in the 30 days following exception-reporting. Exception-reporting was associated with a markedly reduced proportion of patients being initiated on antibiotics following WSC where an organism had been isolated. The naming of organisms in reports appears to drive unnecessary antibiotic prescribing in many patients. These results require confirmation in other jurisdictions.

IMPORTANCE
Wound swab culture is a high-volume test performed in clinical microbiology laboratories. In this analysis, we have shown that an alternative approach to reporting positive wound swab cultures has resulted in a large reduction in post-report antibiotic initiation, suggesting that the current standard method of reporting generates considerable unnecessary antibiotic use. If these findings are replicated elsewhere, wider adoption of this reporting would represent an opportunity for many clinical microbiology laboratories to have a significant impact on community antimicrobial stewardship.
Diversity, evolution, and emergence of fish viruses
Authors: Costa Vincenzo A. , Holmes Edward C. 
Published: May 2024

ABSTRACT

The production of aquatic animals has more than doubled over the last 50 years and is anticipated to continually increase. While fish are recognized as a valuable and sustainable source of nutrition, particularly in the context of human population growth and climate change, the rapid expansion of aquaculture coincides with the emergence of highly pathogenic viruses that often spread globally through aquacultural practices. Here, we provide an overview of the fish virome and its relevance for disease emergence, with a focus on the insights gained through metagenomic sequencing, noting potential areas for future study. In particular, we describe the diversity and evolution of fish viruses, for which the majority have no known disease associations, and demonstrate how viruses emerge in fish populations, most notably at an expanding domestic-wild interface. We also show how wild fish are a powerful and tractable model system to study virus ecology and evolution more broadly and can be used to identify the major factors that shape vertebrate viromes. Central to this is a process of virus-host co-divergence that proceeds over many millions of years, combined with ongoing cross-species virus transmission.