bluuebunny/crossref_metadata_2025 huggingface dataset:
Reevaluation of ovarian cyst fine-needle aspiration cytology: A 10-year institutional experience
Authors: Takeda Kotaro , Cai Guoping , Adeniran Adebowale J , Sun Tong
Published: June 2024

Objectives

Fine-needle aspiration (FNA) of ovarian cyst fluid remains useful for certain clinical circumstances despite low sensitivity and potential safety concerns. The current study aimed to reevaluate the performance of ovarian cystic fluid cytology following American College of Obstetricians and Gynecologists guidelines using a single-institution cohort.

Methods

A total of 507 ovarian cyst FNA cases from 2013 to 2023 were reviewed. Patients’ demographics and clinical and radiologic information were collected through the electronic database. The performance was calculated using corresponding surgical pathology diagnosis as the gold standard.

Results

Overall, cytologic diagnoses were nondiagnostic (ND), negative for malignancy (NFM), atypical (ATY), suspicious for malignancy (SFM), and malignant (M) in 5 (1.0%), 478 (94.3%), 14 (2.7%), 2 (0.4%), and 8 (1.6%) cases, respectively. Among 349 specimens (68.8%) that had a corresponding surgical pathology, the rate of malignancy (including borderline tumors) was 1.2% (4 of 325) in NFM, 72.7% in ATY (8 of 11), and 100% in both SFM (2 of 2) and M (8 of 8) specimens. Considering NFM and ATY as negative results and SFM and M as positive results, overall, the sensitivity of ovarian cystic fluid cytology was 45.4% and the specificity was 100%.

Conclusions

As an uncommon test, ovarian cystic fluid cytology has moderate sensitivity and high specificity. Despite limitations, ovarian cystic FNA cytology remains a valuable diagnostic tool in certain aspects.
The curious case of selenium hyperaccumulation in Coelospermum decipiens from the Cape York Peninsula (Queensland, Australia)
Authors: Harvey Maggie-Anne , Pinto Irish Katherine , Harris Hugh H , Erskine Peter D , van der Ent Antony
Published: June 2024

Background and Aims

The tropical shrub Coelospermum decipiens (Rubiaceae) is an extreme selenium (Se) hyperaccumulator, reported to accumulate up to 1140 µg Se g−1 when found growing on soils with levels of Se below the limit of detection (i.e. <0.01 mg Se kg−1) leading to a bioconcentration factor of >100 000.

Methods

Coelospermum decipiens plants were sampled from different populations in far north Queensland and analysed for Se concentrations. Plant material was subjected to synchrotron X-ray fluorescence microscopy (XFM) and synchrotron X-ray absorption spectroscopy (XAS) investigations to gain insights into the elemental distribution and chemical speciation of Se.

Results

The foliar Se concentrations ranged from 100 to 1000 µg Se g−1, except for the seeds, which had up to 28 000 µg Se g−1. The soils from the Hope Vale area were locally Se-enriched up to 48 mg Se kg−1, but there was no relationship between soil and plant Se concentrations. Synchrotron XFM analysis revealed that Se was localized in the blade margin tissue of the younger leaves, whilst the XAS analysis determined that Se occurs as an organo-Se compound.

Conclusions

We report the occurrence of seleniferous soils in the Cape York Peninsula soils for the first time, which may partly explain the evolution of Se hyperaccumulation in C. decipiens. The extremely high concentrations of Se in the seeds is suggestive of a herbivory protection function. The capacity of this species to accumulate and hyperaccumulate Se from non-seleniferous soils is akin to that of other ‘seed’-based accumulators, such as some members of the Lecythidaceae family.
Inference of gene regulatory networks based on directed graph convolutional networks
Authors: Wei Pi-Jing , Guo Ziqiang , Gao Zhen , Ding Zheng , Cao Rui-Fen , Su Yansen , Zheng Chun-Hou
Published: June 2024

Inferring gene regulatory network (GRN) is one of the important challenges in systems biology, and many outstanding computational methods have been proposed; however there remains some challenges especially in real datasets. In this study, we propose Directed Graph Convolutional neural network-based method for GRN inference (DGCGRN). To better understand and process the directed graph structure data of GRN, a directed graph convolutional neural network is conducted which retains the structural information of the directed graph while also making full use of neighbor node features. The local augmentation strategy is adopted in graph neural network to solve the problem of poor prediction accuracy caused by a large number of low-degree nodes in GRN. In addition, for real data such as E.coli, sequence features are obtained by extracting hidden features using Bi-GRU and calculating the statistical physicochemical characteristics of gene sequence. At the training stage, a dynamic update strategy is used to convert the obtained edge prediction scores into edge weights to guide the subsequent training process of the model. The results on synthetic benchmark datasets and real datasets show that the prediction performance of DGCGRN is significantly better than existing models. Furthermore, the case studies on bladder uroepithelial carcinoma and lung cancer cells also illustrate the performance of the proposed model.
Optimal linear ensemble of binary classifiers
Authors: Ahsen Mehmet Eren , Vogel Robert , Stolovitzky Gustavo
Published: June 2024

Motivation

The integration of vast, complex biological data with computational models offers profound insights and predictive accuracy. Yet, such models face challenges: poor generalization and limited labeled data.

Results

To overcome these difficulties in binary classification tasks, we developed the Method for Optimal Classification by Aggregation (MOCA) algorithm, which addresses the problem of generalization by virtue of being an ensemble learning method and can be used in problems with limited or no labeled data. We developed both an unsupervised (uMOCA) and a supervised (sMOCA) variant of MOCA. For uMOCA, we show how to infer the MOCA weights in an unsupervised way, which are optimal under the assumption of class-conditioned independent classifier predictions. When it is possible to use labels, sMOCA uses empirically computed MOCA weights. We demonstrate the performance of uMOCA and sMOCA using simulated data as well as actual data previously used in Dialogue on Reverse Engineering and Methods (DREAM) challenges. We also propose an application of sMOCA for transfer learning where we use pre-trained computational models from a domain where labeled data are abundant and apply them to a different domain with less abundant labeled data.

Availability and implementation

GitHub repository, https://github.com/robert-vogel/moca.
Document-level biomedical relation extraction via hierarchical tree graph and relation segmentation module
Authors: Yuan Jianyuan , Zhang Fengyu , Qiu Yimeng , Lin Hongfei , Zhang Yijia
Published: June 2024

Motivation

Biomedical relation extraction at the document level (Bio-DocRE) involves extracting relation instances from biomedical texts that span multiple sentences, often containing various entity concepts such as genes, diseases, chemicals, variants, etc. Currently, this task is usually implemented based on graphs or transformers. However, most work directly models entity features to relation prediction, ignoring the effectiveness of entity pair information as an intermediate state for relation prediction. In this article, we decouple this task into a three-stage process to capture sufficient information for improving relation prediction.

Results

We propose an innovative framework HTGRS for Bio-DocRE, which constructs a hierarchical tree graph (HTG) to integrate key information sources in the document, achieving relation reasoning based on entity. In addition, inspired by the idea of semantic segmentation, we conceptualize the task as a table-filling problem and develop a relation segmentation (RS) module to enhance relation reasoning based on the entity pair. Extensive experiments on three datasets show that the proposed framework outperforms the state-of-the-art methods and achieves superior performance.

Availability and implementation

Our source code is available at https://github.com/passengeryjy/HTGRS.
Multimodal subtypes identified in Alzheimer’s Disease Neuroimaging Initiative participants by missing-data-enabled subtype and stage inference
Authors: Estarellas Mar , Oxtoby Neil P , Schott Jonathan M , Alexander Daniel C , Young Alexandra L
Published: June 2024

Alzheimer’s disease is a highly heterogeneous disease in which different biomarkers are dynamic over different windows of the decades-long pathophysiological processes, and potentially have distinct involvement in different subgroups. Subtype and Stage Inference is an unsupervised learning algorithm that disentangles the phenotypic heterogeneity and temporal progression of disease biomarkers, providing disease insight and quantitative estimates of individual subtype and stage. However, a key limitation of Subtype and Stage Inference is that it requires a complete set of biomarkers for each subject, reducing the number of datapoints available for model fitting and limiting applications of Subtype and Stage Inference to modalities that are widely collected, e.g. volumetric biomarkers derived from structural MRI. In this study, we adapted the Subtype and Stage Inference algorithm to handle missing data, enabling the application of Subtype and Stage Inference to multimodal data (magnetic resonance imaging, positron emission tomography, cerebrospinal fluid and cognitive tests) from 789 participants in the Alzheimer’s Disease Neuroimaging Initiative. Missing-data Subtype and Stage Inference identified five subtypes having distinct progression patterns, which we describe by the earliest unique abnormality as ‘Typical AD with Early Tau’, ‘Typical AD with Late Tau’, ‘Cortical’, ‘Cognitive’ and ‘Subcortical’. These new multimodal subtypes were differentially associated with age, years of education, Apolipoprotein E (APOE4) status, white matter hyperintensity burden and the rate of conversion from mild cognitive impairment to Alzheimer’s disease, with the ‘Cognitive’ subtype showing the fastest clinical progression, and the ‘Subcortical’ subtype the slowest. Overall, we demonstrate that missing-data Subtype and Stage Inference reveals a finer landscape of Alzheimer’s disease subtypes, each of which are associated with different risk factors. Missing-data Subtype and Stage Inference has broad utility, enabling the prediction of progression in a much wider set of individuals, rather than being restricted to those with complete data.
UCP1 expression in human brown adipose tissue is inversely associated with cardiometabolic risk factors
Authors: Kwok T’ng Choong , Ramage Lynne E , Kelman Alexandra , Suchacki Karla J , Gray Calum , Boyle Luke D , Semple Scott I , MacGillivray Tom , MacNaught Gillian , Patel Dilip , van Beek Edwin J R , Semple Robert K , Wakelin Sonia J , Stimson Roland H
Published: June 2024

Objective

Brown adipose tissue (BAT) is a therapeutic target for obesity. 18F-fluorodeoxyglucose positron emission tomography (18F-FDG PET) is commonly used to quantify human BAT mass and activity. Detectable 18F-FDG uptake by BAT is associated with reduced prevalence of cardiometabolic disease. However, 18F-FDG uptake may not always be a reliable marker of BAT thermogenesis, for example, insulin resistance may reduce glucose uptake. Uncoupling protein 1 (UCP1) is the key thermogenic protein in BAT. Therefore, we hypothesised that UCP1 expression may be altered in individuals with cardiometabolic risk factors.

Methods

We quantified UCP1 expression as an alternative marker of thermogenic capacity in BAT and white adipose tissue (WAT) samples (n = 53) and in differentiated brown and white pre-adipocytes (n = 85).

Results

UCP1 expression in BAT, but not in WAT or brown/white differentiated pre-adipocytes, was reduced with increasing age, obesity, and adverse cardiometabolic risk factors such as fasting glucose, insulin, and blood pressure. However, UCP1 expression in BAT was preserved in obese subjects of <40 years of age. To determine if BAT activity was also preserved in vivo, we undertook a case-control study, performing 18F-FDG scanning during mild cold exposure in young (mean age ∼22 years) normal weight and obese volunteers. 18F-FDG uptake by BAT and BAT volume were similar between groups, despite increased insulin resistance.

Conclusion

18F-FDG uptake by BAT and UCP1 expression are preserved in young obese adults. Older subjects retain precursor cells with the capacity to form new thermogenic adipocytes. These data highlight the therapeutic potential of BAT mass expansion and activation in obesity.
HLA investigation in ICI-induced T1D and isolated ACTH deficiency including meta-analysis
Authors: Ono Mayo , Nagao Mototsugu , Takeuchi Haruki , Fukunaga Etsuya , Nagamine Tomoko , Inagaki Kyoko , Fukuda Izumi , Iwabu Masato
Published: June 2024

Objective

Widespread use of immune checkpoint inhibitors (ICIs) in cancer treatment has led to an increase in the number of reported cases of immunotherapy-related endocrinopathies. This study aimed to analyze and compare human leukocyte antigen (HLA) signatures associated with ICI-induced type 1 diabetes (ICI-T1D) and isolated adrenocorticotropic hormone deficiency (ICI-IAD) in patients with both conditions.

Methods

HLA signatures were examined for their frequencies of occurrence in 22 patients with ICI-T1D without concurrent IAD, including 16 patients from nationwide reports (ICI-T1D group) and 14 patients with ICI-IAD without concurrent T1D (ICI-IAD group). The HLA signatures were also compared for their respective frequencies in 11 patients with ICI-T1D and ICI-IAD, including eight from nationwide reports (ICI-T1D/IAD group).

Results

In the ICI-T1D group, HLA-DRB1*09:01-DQB1*03:03 and DQA1*03:02, which are in linkage disequilibrium with DRB1*09:01-DQB1*03:03 and DRB1*13:02-DQB1*06:04, were susceptible to ICI-T1D, whereas DRB1*15:02-DQB1*06:01 was protective against ICI-T1D. In the ICI-IAD group, DPB1*09:01, C*12:02-B*52:01, and DRB1*15:02-DRB1*06:01, which are in strong linkage disequilibrium, were associated with susceptibility to ICI-IAD. Moreover, DRB1*15:02-DRB1*06:01 was not detected in the ICI-T1D/IAD group.

Conclusions

This study revealed specific HLA signatures associated with ICI-T1D and ICI-IAD. Moreover, HLA-DRB1*15:02-DRB1*06:01, an ICI-IAD-susceptible HLA haplotype, coincides with the ICI-T1D-protective HLA haplotype, suggesting that the presence of DRB1*15:02-DRB1*06:01 may protect against the co-occurrence of T1D in patients with ICI-IAD.
Digest: Individual- and population-level effects of SARS-CoV-2 evolution and changing preventative measures
Authors: Punchihewa Sehan
Published: June 2024

Although COVID-19 is no longer classified as a pandemic, variants of SARS-CoV-2 continue to arise. It is critical to understand how changes in viral characteristics, public policy, and behavior affect disease load and mortality. An analysis by Otto et al. (2024) shows that changes in transmission rate and immunological properties have differing effects on disease load, even among variants with similar selective advantages. The impact of various strategies aimed at countering disease spread is also analyzed.
Evolution of species recognition when ecology and sexual selection favor signal stasis
Authors: Singh Pratap , Price Trevor D
Published: June 2024

The process of reproductive character displacement involves divergence and/or the narrowing of variance in traits involved in species recognition, driven by interactions between taxa. However, stabilizing sexual selection may favor stasis and species similarity in these same traits if signals are optimized for transmission through the prevailing environment. Further, sexual selection may promote increased variability within species to facilitate individual recognition. Here we ask how the conflicting selection pressures of species recognition and sexual selection are resolved in a genus of Himalayan birds that sing exceptionally similar songs. We experimentally show that small differences in two traits (note shape and peak frequency) are both necessary and sufficient for species recognition. Song frequency shows remarkable clinal variation along the Himalayan elevational gradient, being most divergent where species co-occur, the classic signature of reproductive character displacement. Note shape shows no such clinal variation but varies more between individuals of an allopatric species than it does among individuals within species that co-occur. We argue that the different note shapes experience similar transmission constraints, and differences produced through species interactions spread back through the entire species range. Our results imply that reproductive character displacement is likely to be common.
Effect of different degumming methods on the chemical composition and physicochemical properties of tiger nut (Cyperus esculentus L.) oil
Authors: Zhang Runyang , Li Jiake , Zhu Wenxue , Chen Pengxiao , Jiang Mengmeng , Liu Huamin
Published: June 2024

Objectives

Tiger nut (Cyperus esculentus L.) oil is a promising edible oil that is rich in oleic acid. This study aimed to clarify the impact of different degumming methods on the chemical composition and physicochemical properties of crude tiger nut oil (CTO).

Materials and Methods

Five degummed tiger nut oils were prepared by high-temperature water (HWDO), medium-temperature water (MWDO), sodium chloride solution (SDO), acidic solution (ADO), and enzymatic method (EDO), respectively.

Results

Compared to that of CTO, the phospholipid contents of HWDO, MWDO, SDO, ADO, and EDO were reduced by 99.39%, 97.18%, 69.95%, 63.77%, and 65.60%, respectively. For CTO and all degummed oils, the fatty acid and endogenous antioxidant (i.e. tocopherols, sterols, flavonoids, total phenolics, and carotenoids) contents showed only small differences, but showed significant differences in quality parameters. Both the oxidative stability index and ferric ion-reducing antioxidant power decreased significantly after degumming; the former decreased from 52.26 to 15.55–19.80 h, and the latter decreased from 5818.91 to 4348.73–4524.34 μmol Trolox (TE)/kg.

Conclusions

These changes are highly related to the removal of hydratable phospholipids. In short, EDO exhibited the lowest turbidity, whereas MWDO showed the best oxidative stability (19.80 h) and highest smoke point (230.0 °C). This information can be utilized to improve the industrial production of tiger nut oil.
A nested reciprocal experimental design to map the genetic architecture of transgenerational phenotypic plasticity
Authors: Che Jincan , Wang Yu , Dong Ang , Cao Yige , Wu Shuang , Wu Rongling
Published: June 2024

Extensive studies have revealed the ecological and evolutionary significance of phenotypic plasticity, but little is known about how it is inherited between generations and the genetic architecture of its transgenerational inheritance. To address these issues, we design a mapping study by growing Arabidopsis thaliana RILs in high- and low-light environments and further growing their offspring RILs from each maternal light environment in the same contrasting environments. This tree-like design of the controlled ecological experiment provides a framework for analysing the genetic regulation of phenotypic plasticity and its non-genetic inheritance. We implement the computational approach of functional mapping to identify specific QTLs for transgenerational phenotypic plasticity. By estimating and comparing the plastic response of leaf-number growth trajectories to light environment between generations, we find that the maternal environment affects phenotypic plasticity, whereas transgenerational plasticity is shaped by the offspring environment. The genetic architecture underlying the light-induced change of leaf number not only changes from parental to offspring generations, but also depends on the maternal environment the parental generation experienced and the offspring environment the offspring generation is experiencing. Most plasticity QTLs are annotated to the genomic regions of candidate genes for specific biological functions. Our computational-experimental design provides a unique insight into dissecting the non-genetic and genetic mechanisms of phenotypic plasticity shaping plant adaptation and evolution in various forms.
Single-cell Transcriptomic Studies Unveil Potential Nodes of the Notochord Gene Regulatory Network
Authors: Negrón-Piñeiro Lenny J , Di Gregorio Anna
Published: June 2024

Synopsis

Transcription factors (TFs) are DNA-binding proteins able to modulate the timing, location, and levels of gene expression by binding to regulatory DNA regions. Therefore, the repertoire of TFs present in the genome of a multicellular organism and the expression of variable constellations of TFs in different cellular cohorts determine the distinctive characteristics of developing tissues and organs. The information on tissue-specific assortments of TFs, their cross-regulatory interactions, and the genes/regulatory regions targeted by each TF is summarized in gene regulatory networks (GRNs), which provide genetic blueprints for the specification, development, and differentiation of multicellular structures. In this study, we review recent transcriptomic studies focused on the complement of TFs expressed in the notochord, a distinctive feature of all chordates. We analyzed notochord-specific datasets available from organisms representative of the three chordate subphyla, and highlighted lineage-specific variations in the suite of TFs expressed in their notochord. We framed the resulting findings within a provisional evolutionary scenario, which allows the formulation of hypotheses on the genetic/genomic changes that sculpted the structure and function of the notochord on an evolutionary scale.
Comparing clinical and echocardiographic outcomes following valve-sparing versus transannular patch repair of tetralogy of Fallot: a systematic review and meta-analysis
Authors: Martins Russell Seth , Fatimi Asad Saulat , Mahmud Omar , Qureshi Saleha , Nasim Muhammad Taha , Virani Sehar Salim , Tameezuddin Aimen , Yasin Fatima , Malik Mahim Akmal
Published: June 2024

OBJECTIVES

Transannular patch (TAP) repair of tetralogy of Fallot (ToF)relieves right ventricular tract obstruction but may lead to pulmonary regurgitation. Valve-sparing (VS) procedures can avoid this situation, but there is a potential for residual pulmonary stenosis. Our goal was to evaluate clinical and echocardiographic outcomes of TAP and VS repair for ToF.

METHODS

A systematic search of the PubMed, Embase, Scopus, Cochrane Central Register of Controlled Trials and Web of Science databases was carried out to identify articles comparing conventional TAP repair and VS repair for ToF. Random-effects models were used to perform meta-analyses of the clinical and echocardiographic outcomes.

RESULTS

Forty studies were included in this meta-analysis with data on 11 723 participants (TAP: 6171; VS: 5045). Participants who underwent a VS procedure experienced a significantly lower cardiopulmonary bypass time [mean difference (MD): −14.97; 95% confidence interval (CI): −22.54, −7.41], shorter ventilation duration (MD: −15.33; 95% CI: −30.20, −0.46) and shorter lengths of both intensive care unit (ICU) (MD: −0.67; 95% CI: −1.29, −0.06) and hospital stays (MD: −2.30; 95% CI: [−4.08, −0.52). There was also a lower risk of mortality [risk ratio: 0.40; 95% CI: (0.27, 0.60) and pulmonary regurgitation [risk ratio: 0.35; 95% CI: (0.26, 0.46)] associated with the VS group. Most other clinical and echocardiographic outcomes were comparable in the 2 groups.

CONCLUSIONS

This meta-analysis confirms the well-established increased risk of pulmonary insufficiency following TAP repair while also demonstrating that VS repairs are associated with several improved clinical outcomes. Continued research can identify the criteria for adopting a VS approach as opposed to a traditional TAP repair.
Cellular interactions and evolutionary origins of endosymbiotic relationships with ciliates
Authors: Song Qi , Zhao Fangqing , Hou Lina , Miao Miao
Published: June 2024

As unicellular predators, ciliates engage in close associations with diverse microbes, laying the foundation for the establishment of endosymbiosis. Originally heterotrophic, ciliates demonstrate the ability to acquire phototrophy by phagocytizing unicellular algae or by sequestering algal plastids. This adaptation enables them to gain photosynthate and develop resistance to unfavorable environmental conditions. The integration of acquired phototrophy with intrinsic phagotrophy results in a trophic mode known as mixotrophy. Additionally, ciliates can harbor thousands of bacteria in various intracellular regions, including the cytoplasm and nucleus, exhibiting species specificity. Under prolonged and specific selective pressure within hosts, bacterial endosymbionts evolve unique lifestyles and undergo particular reductions in metabolic activities. Investigating the research advancements in various endosymbiotic cases within ciliates will contribute to elucidate patterns in cellular interaction and unravel the evolutionary origins of complex traits.
Interspecies ecological competition rejuvenates decayed Geobacter electroactive biofilm
Authors: Ye Yin , Zhang Lu , Hong Xiaohui , Chen Man , Liu Xing , Zhou Shungui
Published: June 2024

Bioelectrochemical systems (BESs) exploit electroactive biofilms (EABs) for promising applications in biosensing, wastewater treatment, energy production, and chemical biosynthesis. However, during the operation of BESs, EABs inevitably decay. Seeking approaches to rejuvenate decayed EABs is critical for the sustainability and practical application of BESs. Prophage induction has been recognized as the primary reason for EAB decay. Herein, we report that introducing a competitive species of Geobacter uraniireducens suspended prophage induction in Geobacter sulfurreducens and thereby rejuvenated the decayed G. sulfurreducens EAB. The transcriptomic profile of G. sulfurreducens demonstrated that the addition of G. uraniireducens significantly affected the expression of metabolism- and stress response system-related genes and in particular suppressed the induction of phage-related genes. Mechanistic analyses revealed that interspecies ecological competition exerted by G. uraniireducens suppressed prophage induction. Our findings not only reveal a novel strategy to rejuvenate decayed EABs, which is significant for the sustainability of BESs, but also provide new knowledge for understanding phage–host interactions from an ecological perspective, with implications for developing therapies to defend against phage attack.
An Alternative Microbiological Validation for an Online Water Bioburden Analyzer
Authors: Venhuizen Olivia L , Martindale Cynthia E , Liew Feng Jin , Cannon James , Samanta Arundhati , Scaramozzino Mike J
Published: June 2024

Background

The Mettler-Toledo 7000RMS analyzer is a bio-fluorescent particle counter (BFPC) used to monitor real-time bioburden results from purified water (PW).

Objective

Validation of the analyzer using 13 microorganisms and a low-intensity, fluorescent, polystyrene bead.

Methods

During the execution of the validation, a laboratory water system that met PW quality standards was connected to the 7000RMS, and a syringe pump was used to introduce various concentrations of microorganisms and fluorescent polystyrene beads to the analyzer. Samples were collected and tested via the traditional membrane filtration (MF) method and the colony-forming unit (CFU) plate count results were compared to the auto-fluorescent unit (AFU) of the 7000RMS analyzer. The validation study was designed to follow the guidance in United States Pharmacopeia (USP) Chapter <1223>, European Pharmacopeia (EP) Chapter 5.1.6, and parenteral drug association (PDA) Technical Report 33. Concepts and strategies were adapted from EP Chapter 2.6.12 Microbiological Examination of Non-Sterile Products: Microbial Enumeration Tests, EP Chapter 10.2, EP Chapter 2.6.1 Sterility, USP Chapter <61> Microbiological Examination of Non-Sterile Products: Microbial Enumeration Tests, USP Chapter <71> Sterility Tests, and Japanese Pharmacopoeia (JP) General Information Chapter G8 Water: Quality Control of Water for Pharmaceutical Use.

Results

All pre-determined validation acceptance criteria for accuracy, specificity, precision, LOD, LOQ, linearity, and range were met.

Conclusions

The 7000RMS demonstrated performance equivalence to the MF method per USP <1223> but characteristically lacked correlation to the CFU.

Highlights

This validation approach highlights the superior capabilities of the 7000RMS when compared against the traditional compendial MF testing method for PW.
Mucormycosis Superinfection of a Chemical Burn
Authors: Cochran-Caggiano Nicholas C , Paolo William , Dolinak Joan
Published: June 2024

Mucormycosis is an uncommon infection but is increasing in prevalence. Cutaneous disease is associated with burns and traumatic injuries. Cutaneous mucormycosis is the least deadly form but mortality is still approximately 36%. Burn superinfection with mucormycosis is increasingly common and can be an insidious process that may not present until the disease disseminates. We present the case of a 30-year-old male who presented to the emergency department for a rash. A rash with yellow crusting was noted to involve his scalp, face, ear, right shoulder, and parts of both feet. He had been placed on antibiotics by an urgent care a few days prior to presenting. He denied systemic symptoms, chemical exposure, change in detergent, autoimmune diseases, or travel. The patient has a history of intravenous opioid and dissociative abuse and had multiple episodes of syncope—including at his work in a factory where there were hot metals, refrigerants, and numerous corrosive chemicals. Surgical debridement revealed mucormycosis on pathology. The patient was treated with isavuconazole, surgical debridement, and skin grafting. He experienced complete recovery.
A new species of the bathyal yeti crab genus Kiwa Macpherson, Jones & Segonzac, 2005 (Decapoda: Anomura: Kiwaidae) from a hydrothermal vent field in the Eastern Pacific Ocean, with a key to the genus
Authors: Liu Xinming , Lin Jinlan , Mendoza Jose C E
Published: June 2024

A new species of yeti crab is described from a hydrothermal vent field near the equatorial Eastern Pacific Rise (EPR)-Galapagos Microplate at a depth of 1,628 m. Kiwa gemman. sp. is the fifth species of the family Kiwaidae Macpherson, Jones & Segonzac, 2005 to be described thus far. The new species can be distinguished from other congeners by having the lateral margin of chelipeds without spines, slender and mostly straight chelar fingers, and the spinose mesial margin of the endopod of the uropod. Also notable are the unique short, stiff, scaly-tipped setae on the antennal peduncles and chelipeds, which have not been reported to occur in congeners. A key to the species of the genus KiwaMacpherson, Jones & Segonzac, 2005 is provided.
The Making of Social Democracy: the Economic and Electoral Consequences of Norway’s 1936 Folk School Reform
Authors: Acemoglu Daron , Pekkarinen Tuomas , Salvanes Kjell G , Sarvimäki Matti
Published: June 2024

Upon assuming power for the first time in 1935, the Norwegian Labour Party delivered on its promise for a major schooling reform. The reform raised minimum instruction time in less-developed rural areas and boosted the resources available to rural schools, reducing class size, and raising teacher salaries. We show that cohorts more intensively affected by the reform increased their education and experienced higher labor income. Our main result is that the schooling reform also boosted support for the Norwegian Labour Party in subsequent elections. This additional support persisted for several decades and was pivotal in maintaining support for the social democratic coalition in Norway. These results are not driven by the direct impact of education and are not explained by higher turnout, or greater attention or resources from the Labour Party targeted toward the municipalities most affected by the reform. Rather, our evidence suggests that cohorts that benefited from the schooling reform, and their parents, rewarded the party for delivering a major reform that was beneficial to them.
Parameter Optimization in Cluster Identification Algorithms for Characterizing Nanoclusters in Al–Mg–Si–Cu Alloys
Authors: Song MinYoung , Kobayashi Equo , Kim JaeHwang
Published: June 2024

Optimization of user-defined parameters (Dmax, Nmin, order (K)) in the Density-based Spatial Clustering of Applications with Noise (DBSCAN) algorithm, used to characterize nanoclusters in Al–0.9% Mg–1.0% Si–0.3% Cu (mass %), was conducted. Ten combinations of parameters with a given K were considered for samples naturally aged (NA) and preaged (PA) at 100°C. We confirmed four types of unphysical clusters, artificially formed, by analyzing composition with size, atomic density, and atomic arrangement inside clusters. The optimum combinations minimizing those unphysical clusters were obtained for both NA and PA samples. Meanwhile, to evaluate the reliability of the optimum combination, volume rendering and isosurfacing were performed. As a result, regions of high solute concentration were confirmed, and those regions are in good agreement with the position of the clusters obtained by applying the optimum combination in DBSCAN. Furthermore, by comparing the optimum combinations with the fixed parameters widely used until now, we showed that for each dataset, considering independent parameters obtained in the same method is desirable rather than using fixed parameters. Consequently, an idea of determining the algorithm parameters for characterizing the nanoclusters in Al–Mg–Si(–Cu) alloys was introduced.
The Prevalence of Bullying
Authors: Srabstein Jorge C.
Published: June 2024

Because bullying is ubiquitous, we need to be aware of its occurrence, sometimes concurrently, across different social settings, including the home, school, workplace, neighborhood, cyberspace, and dating relationships. This chapter provides data, derived from cross-national surveys, highlighting the wide range of prevalence of bullying across nations. Furthermore, it offers a glimpse of some sociodemographic characteristics found to be linked to bullying. Because current epidemiologic data on bullying is limited, future surveys will need to be implemented periodically to track trends in national and regional occurrence of youth participation in bullying, as well as to determine the national frequency and characteristics of workplace victimization. Research should be developed to investigate the prevalence of bullying and other forms of victimization among individuals of all ages being evaluated in medical settings.
Morbidity Associated with Bullying and Other Forms of Victimization
Authors: Srabstein Jorge C.
Published: June 2024

A substantial body of research has highlighted a significant link between bullying (and other forms of victimization) and a wide range of health problems. Almost three-quarters of the studies are based on cross-sectional surveys conducted on nonclinical populations of children and adolescents. This line of investigation has found that participation in victimization, as a target and/or as a perpetrator, can be significantly associated with an array of physical and emotional expressions of morbidity, including headaches, irritability, depression, anxiety, insomnia, nightmares, backache, stomachache, musculoskeletal pain, inflammation, abnormal weight gain, diabetes, cardiovascular disease, inattention, dissociation, intrusive memories, psychotic symptoms, and injuries. There is a need for future studies, based on clinical populations, to further assess the scope and prevalence of symptoms and other expressions of morbidity associated with exposure to different forms of bullying and other types of victimization. Furthermore, it is important to medical and public health that future clinical research determines the prevalence of diagnostic entities that may precede or be the outcome of exposure to, or participation in, victimization, either by serving as a moderating factor or by being the expression of toxicity.
Victimization in Competitive Sports
Authors: Srabstein Jorge C.
Published: June 2024

This chapter examines the nature, frequency, and risks associated with maltreatment occurring in competitive sports. The maltreatment affects high school and college students, professional players/athletes, coaches, sports officials, and spectators. The chapter reviews what is known about bullying and other types of victimization, focusing on physical aggression in foul play, brawls, violence against sport officials, and spectator violence, especially football hooliganism. It also looks at published studies addressing sexual violence, emotional abuse, hazing, discrimination, and neglect in competitive sports. Future research should aim to ascertain the prevalence of all forms of maltreatment affecting high school and college students participating in competitive sports. Furthermore, there is a need to ascertain the health risks linked to exposure to victimization in sports, as well as to advance strategies for its prevention and detection.
Witnessing Bullying and Other Forms of Maltreatment
Authors: Srabstein Jorge C.
Published: June 2024

This chapter examines the public health significance of witnessing incidents of bullying and other forms of maltreatment beyond what has been advocated on behalf of the role of the bystander in prevention strategies. In this context, this last segment of the book reviews what is known about the prevalence and health risks of direct witnessing of bullying occurring in school, internet, or workplace; victimization in the family or community as well as indirect exposure to victimization through the victim’s narrative or while watching television news. There is a need for future efforts to be taken to develop longitudinal studies to further the understanding of the health impact of witnessing victimization, while controlling for the effects of the witness having been previously victimized. Also, we should investigate the effects of indirect exposure to victimization through the victim’s account during friends’ conversations or during a narrative by a group therapy member. Furthermore, we ought to consider including the notion of witnessing bullying or other forms maltreatment in the spectrum of poly-victimization; incorporating anamnesis about witnessing victimization as part of the clinical detection of morbidity related to bullying and other forms of victimization as well as preventing witnessing victimization during treatment of bullying related morbidity, to avoid re-victimization
Brain Gene Regulatory Networks Coordinate Nest Construction in Birds
Authors: Fang Yi-Ting , Kuo Hao-Chih , Chen Cheng-Yu , Chou Shen-Ju , Lu Chia-Wei , Hung Chih-Ming
Published: June 2024

Nest building is a vital behavior exhibited during breeding in birds, and is possibly induced by environmental and social cues. Although such behavioral plasticity has been hypothesized to be controlled by adult neuronal plasticity, empirical evidence, especially at the neurogenomic level, remains limited. Here, we aim to uncover the gene regulatory networks that govern avian nest construction and examine whether they are associated with circuit rewiring. We designed an experiment to dissect this complex behavior into components in response to pair bonding and nest material acquisition by manipulating the presence of mates and nest materials in 30 pairs of zebra finches. Whole-transcriptome analysis of 300 samples from five brain regions linked to avian nesting behaviors revealed nesting-associated gene expression enriched with neural rewiring functions, including neurogenesis and neuron projection. The enriched expression was observed in the motor/sensorimotor and social behavior networks of female finches, and in the dopaminergic reward system of males. Female birds exhibited predominant neurotranscriptomic changes to initiate the nesting stage, while males showed major changes after entering this stage, underscoring sex-specific roles in nesting behavior. Notably, major neurotranscriptomic changes occurred during pair bonding, with minor changes during nest material acquisition, emphasizing social interactions in nest construction. We also revealed gene expression associated with reproductive behaviors and tactile sensing for nesting behavior. This study presents novel neurogenomic evidence supporting the hypothesis of adult neural plasticity underlying avian nest-construction behavior. By uncovering the genetic toolkits involved, we offer novel insights into the evolution of animals’ innate ability to construct nests.
Exploring the Accuracy and Limits of Algorithms for Localizing Recombination Breakpoints
Authors: Cen Shi , Rasmussen David A
Published: June 2024

Phylogenetic methods are widely used to reconstruct the evolutionary relationships among species and individuals. However, recombination can obscure ancestral relationships as individuals may inherit different regions of their genome from different ancestors. It is, therefore, often necessary to detect recombination events, locate recombination breakpoints, and select recombination-free alignments prior to reconstructing phylogenetic trees. While many earlier studies have examined the power of different methods to detect recombination, very few have examined the ability of these methods to accurately locate recombination breakpoints. In this study, we simulated genome sequences based on ancestral recombination graphs and explored the accuracy of three popular recombination detection methods: MaxChi, 3SEQ, and Genetic Algorithm Recombination Detection. The accuracy of inferred breakpoint locations was evaluated along with the key factors contributing to variation in accuracy across datasets. While many different genomic features contribute to the variation in performance across methods, the number of informative sites consistent with the pattern of inheritance between parent and recombinant child sequences always has the greatest contribution to accuracy. While partitioning sequence alignments based on identified recombination breakpoints can greatly decrease phylogenetic error, the quality of phylogenetic reconstructions depends very little on how breakpoints are chosen to partition the alignment. Our work sheds light on how different features of recombinant genomes affect the performance of recombination detection methods and suggests best practices for reconstructing phylogenies based on recombination-free alignments.
MRNIP limits ssDNA gaps during replication stress
Authors: Bennett Laura G , Vernon Ellen G , Thanendran Vithursha , Jones Caryl M , Gamble Amelia , Staples Christopher J
Published: June 2024

Replication repriming by the specialized primase-polymerase PRIMPOL ensures the continuity of DNA synthesis during replication stress. PRIMPOL activity generates residual post-replicative single-stranded nascent DNA gaps, which are linked with mutagenesis and chemosensitivity in BRCA1/2-deficient models, and which are suppressed by replication fork reversal mediated by the DNA translocases SMARCAL1 and ZRANB3. Here, we report that the MRE11 regulator MRNIP limits the prevalence of PRIMPOL and MRE11-dependent ssDNA gaps in cells in which fork reversal is perturbed either by treatment with the PARP inhibitor Olaparib, or by depletion of SMARCAL1 or ZRANB3. MRNIP-deficient cells are sensitive to PARP inhibition and accumulate PRIMPOL-dependent DNA damage, supportive of a pro-survival role for MRNIP linked to the regulation of gap prevalence. In MRNIP-deficient cells, post-replicative gap filling is driven in S-phase by UBC13-mediated template switching involving REV1 and the TLS polymerase Pol-ζ. Our findings represent the first report of modulation of post-replicative ssDNA gap dynamics by a direct MRE11 regulator.
Maternal Smoking Prevalence in Brazil in 2013 and 2019: Not What We Expected When They Were Expecting!
Authors: Szklo André Salem , Grilo Graziele , Drope Jeffrey
Published: June 2024

Introduction

Monitoring tobacco use during pregnancy is critical for achieving the United Nations Sustainable Development Goals. We examined changes between 2013 and 2019 in the relative differences in smoking prevalence rates between pregnant and nonpregnant women aged 18–49 years.

Aims and Methods

We used data from a nationally representative health survey conducted in Brazil in 2013 and 2019. A generalized linear model with binomial family and logarithmic link function was used to estimate, for each year of analysis, the crude and adjusted (by age group, educational attainment, place of residence, and status of protection from passive smoking at home) relative differences.

Results

In 2013, the proportion point estimate of tobacco use among pregnant women was lower than that observed among nonpregnant women (4.7% vs. 9.6%). However, in 2019 proportion point estimates were virtually the same (8.5% vs. 8.4%). After adjustment for selected variables, in 2013, smoking prevalence among pregnant women was 42% (p-value ≤ .05) lower than that observed among nonpregnant women. On the other hand, in 2019, maternal smoking prevalence was 13% (p-value > .05) higher than that found among nonpregnant women.

Conclusions

Ongoing tobacco industry interference and the marketing of tobacco products to vulnerable populations pose serious threats to public health and likely contribute to increasing maternal smoking prevalence. The fact that women smoke in such an important phase of their and their unborn children’s lives reinforces the need to strengthen the implementation of concurrent tobacco control actions, including tobacco excise tax policy and prenatal tobacco prevention and cessation interventions as part of health professionals’ routine consultation.

Implications

The decline in smoking prevalence among nonpregnant women between 2013 and 2019 was accompanied by an increase in maternal smoking prevalence. Monitoring tobacco use during pregnancy is critical for achieving the United Nations Sustainable Development Goals. Ongoing tobacco industry interference and the marketing of tobacco products to vulnerable populations in Brazil pose serious threats to public health. The fact that women smoke in such an important phase of their and their unborn children’s lives reinforces the need to strengthen the implementation of concurrent tobacco control actions, including tobacco excise tax policy and primary healthcare professionals´ tobacco-related assistance during interaction with their patients.