bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct estimation and inference of higher-level correlations from lower-level measurements with applications in gene-pathway and proteomics studies
Authors: Wang Yue , Shi Haoran 
Published: August 2024

Abstract
This paper tackles the challenge of estimating correlations between higher-level biological variables (e.g. proteins and gene pathways) when only lower-level measurements are directly observed (e.g. peptides and individual genes). Existing methods typically aggregate lower-level data into higher-level variables and then estimate correlations based on the aggregated data. However, different data aggregation methods can yield varying correlation estimates as they target different higher-level quantities. Our solution is a latent factor model that directly estimates these higher-level correlations from lower-level data without the need for data aggregation. We further introduce a shrinkage estimator to ensure the positive definiteness and improve the accuracy of the estimated correlation matrix. Furthermore, we establish the asymptotic normality of our estimator, enabling efficient computation of P-values for the identification of significant correlations. The effectiveness of our approach is demonstrated through comprehensive simulations and the analysis of proteomics and gene expression datasets. We develop the R package highcor for implementing our method.
Sensing Toxic Injustice: Exploring the Polluting Touch of Colonialism
Authors: Lam Anita , Kohm Steven 
Published: August 2024

AbstractThe bodies of missing and murdered Indigenous women and girls are often discovered at polluted sites in Winnipeg, Canada, including the Red River. Left at toxic sites that authorities deem environmentally dangerous, these women became untouchable in death, mired in sociocultural representations of disposability and wasting practices. We link murdered and missing Indigenous women and girls to the polluting effects of white settler colonialism especially pertaining to the degradation of Winnipeg’s waterways. As a means for enacting slow, environmental violence, current waste allocation practices remain tied to colonial systems that continue to harm Indigenous peoples. To foreground overlapping devaluations of Indigenous lands and people, we argue for a sensory criminology that is sensitized to the ongoing damage of colonial violence.
Post-Disaster Social Connectedness in Parent–Child Dyads: A Qualitative Investigation of Changes in Coping and Social Capital of Rural Australian Families Following Bushfires
Authors: Stribley Lisa , Krishnamoorthy Govind , Dallinger Vicki , Ma Jennifer , Nielsen Thomas , Bryce India , Rees Bronwyn , Morse Alyssa , Rogers Marg , Burton Lorelle 
Published: August 2024

Abstract
The increasing frequency of natural disasters, such as bushfires, pose significant challenges for countries like Australia. This research investigates the changes in social connectedness following a bushfire disaster in 2019 in the rural community of Cudlee Creek, South Australia, Australia. Research has repeatedly highlighted the importance of social connectedness, social capital and secure attachment relationships in mitigating post-disaster mental health concerns. This study utilised semi-structured interviews with eight parent–child dyads twenty months post-disaster to understand changes in parent–child relationships, the quality of extended family ties and the role of the broader community in recovery and coping. Reflexive thematic analysis revealed three themes: (i) differences in children and parents in preferred forms of social support; (ii) a thinning of previously available support and (iii) altered patterns of communication in the parent–child relationships. The findings highlight the complex interactions of multi-systemic and intersectional disadvantages on social isolation and loss of social capital following disasters. The results also highlight the influence of stoic beliefs on patterns of miscommunication in parent–child dyads in rural contexts. Implications for the implementation of community-wide post-disaster supports, sociometric approaches to mental health screening and assessment, and targeted interventions for rural families.
Myxodiaspory inAdenostemma brasilianum(Asteraceae): morphological and histochemical strategies for diaspore dispersion
Authors: Dosil Hiriart Florencia D , Hernández Marcelo P , Segura Luciano N , Katinas Liliana 
Published: August 2024

AbstractMyxodiaspory, the extrusion of sticky substances by the diaspores (seeds, fruits, anthocarps, and parts of infrutescences), has several selective advantages, one of which is aiding the adherence of diaspores between feathers/fur of animals that transport them over short or long distances. The diaspores of Asteraceae have three structures that can contain sticky substances: exocarp epidermal cells, exocarp trichomes, and viscid pappus. The South American species Adenostemma brasilianum (Asteraceae) has all three features. We examined the anatomy, secreted substances, and mode of adhesion of the diaspores of A. brasilianum to understand its strategies for dispersion. The fruit comprises an exocarp with glandular trichomes arranged spirally and scarce nonglandular trichomes, two layers of mesocarp separated by phytomelanin, and an endocarp. The pappus has a basal ring, a stalk, and a head with glandular trichomes. The mucilage, secreted by the glandular trichomes of fruit and pappus, reacted positively to tests for pectins, essential oils, lipophilic substances, and gums. The test for tannins gave a homogeneous positive reaction in the phytomelanin area, and as droplets, in the outer mesocarp layer and in the exocarp. The whole capitulum of A. brasilianum is adapted for successful transportation of its diaspores via diaspore release, secretion, and positioning. We discuss the idea that the dispersal adaptive traits found here evolved as phylogenetic parallelisms in the family.
Machine learning based on biological context facilitates the identification of microvascular invasion in intrahepatic cholangiocarcinoma
Authors: Xu Shuaishuai , Wan Mingyu , Ye Chanqi , Chen Ruyin , Li Qiong , Zhang Xiaochen , Ruan Jian 
Published: August 2024

Abstract
Intrahepatic cholangiocarcinoma is a rare disease associated with a poor prognosis, primarily due to early recurrence and metastasis. An important feature of this condition is microvascular invasion (MVI). However, current predictive models based on imaging have limited efficacy in this regard. This study employed a random forest model to construct a predictive model for MVI identification and uncover its biological basis. Single-cell transcriptome sequencing, whole exome sequencing, and proteome sequencing were performed. The area under the curve of the prediction model in the validation set was 0.93. Further analysis indicated that MVI-associated tumor cells exhibited functional changes related to epithelial–mesenchymal transition and lipid metabolism due to alterations in the nuclear factor-kappa B and mitogen-activated protein kinase signaling pathways. Tumor cells were also differentially enriched for the interleukin-17 signaling pathway. There was less infiltration of SLC30A1+ CD8+ T cells expressing cytotoxic genes in MVI-associated intrahepatic cholangiocarcinoma, whereas there was more infiltration of myeloid cells with attenuated expression of the major histocompatibility complex II pathway. Additionally, MVI-associated intercellular communication was closely related to the SPP1–CD44 and ANXA1–FPR1 pathways. These findings resulted in a brilliant predictive model and fresh insights into MVI.
Case report: severe hypertrophic cardiomyopathy in a female neonate caused by de novo variant in NDUFB11
Authors: Tariq Javeria , Townsend Madeleine , Parikh Sumit , Bennett Jeffrey 
Published: August 2024

Abstract

Background
Hypertrophic cardiomyopathy in the neonate has a diverse genetic background, and non-sarcomeric variants may not be identified on commercial genetic testing panels. NDUFB11 is an X-linked mitochondrial Complex I protein and is known to cause histiocytoid cardiomyopathy but has not been described in female infants with hypertrophic cardiomyopathy. We present this first reported case of obstructive hypertrophic cardiomyopathy in a female neonate secondary to a pathogenic variant in NDUFB11.

Case summary
A term female neonate presented following a prenatal diagnosis of biventricular hypertrophy and growth restriction. She developed lactic acidosis after birth and whole-genome sequencing identified a de novo variant in the mitochondrial Complex I gene, NDUFB11 (c.391G&gt;A, p.Glu131Lys). There was progression of left ventricular hypertrophy and obstruction, with rapid development of heart failure symptoms. She was unresponsive to beta-blocker medical therapy and was not suitable for advanced mechanical support. There was subsequent clinical deterioration resulting in death by 3 months of age.

Discussion
Hemizygous variants in NDUFB11 have been associated with hypertrophic cardiomyopathy in male infants previously, and skewed X-linked inactivation likely resulted in the presentation described here in a female infant. This variant was not identifiable by commercial cardiomyopathy panels. We highlight the importance of rapid whole-genome sequencing in cases of infantile hypertrophic cardiomyopathy and the importance of genetic diagnosis in guiding prognosis and care for these individuals.
Two-station Lg wave attenuation tomography in Eastern Asia
Authors: Chen Youlin , Xu Xiwei , Xie Jiakang , Ghalib Hafidh A A , Liang Shanshan 
Published: August 2024

SUMMARY
Utilizing over 31 000 Lg waveforms from 136 crustal earthquakes recorded at 346 regional stations, we conduct detailed tomographic mappings of the Lg Q structure across Eastern Asia in a frequency range from 0.5 to 4.0 Hz. By improving the standard two-station (TS) method, we effectively correct non-unity site response ratios using site responses estimated at individual stations. This innovative approach combines the flexible recording geometry of the TS method with the precision of reversed two-station (RTS) and reversed two-event (RTE) methods, producing a comprehensive data set devoid of source and site effects for Q tomography. To address unsolvable 3-D structural effects in the Lg spectral amplitude modelling, we justify these as modelling errors with a Gaussian distribution. This approach supports our SVD-based tomographic method, allowing for effective inversion of attenuation parameters and quantitative assessment of model resolution and errors. Our results reveal a complex relationship between Lg Q and the tectonic characteristics of Eastern Asia. In well-resolved regions, low Qo (1-Hz Q) values correspond to areas with high heat flow, partial melt, thick sediment and recent tectonic-thermal activities, in contrast to high Qo values in stable, ancient crusts lacking recent tectonic activity. Rift basins are characterized by low Lg Qo, whereas flexural basins generally have high Qo basements. We also note that post-formation factors, such as sedimentation and crustal flow intrusion, significantly impact Qo values. Furthermore, Lg Q shows a complex frequency relationship, though the power-law approximation with positive power η remains useful. The frequency dependence power η is inversely related to Qo: the regions with low Qo typically have high η and vice versa. This study provides reliable attenuation tomographic and relative site response models for Lg waves in Eastern Asia, pertinent for relative geophysical studies.
Jacobian Schemes Arising From Hypersurface Arrangements in ℙn
Authors: Migliore Juan , Nagel Uwe 
Published: August 2024

Abstract
Freeness is an important property of a hypersurface arrangement, although its presence is not well understood. A hypersurface arrangement in ${\mathbb{P}}^{n}$ is free if $S/J$ is Cohen–Macaulay (CM), where $S = K[x_{0},\ldots ,x_{n}]$ and $J$ is the Jacobian ideal. We study three related unmixed ideals: $J^{top}$, the intersection of height two primary components, $\sqrt{J^{top}}$, the radical of $J^{top}$, and when the $f_{i}$ are smooth we also study $\sqrt{J}$. Under mild hypotheses, we show that these ideals are CM. This establishes a full generalization of an earlier result with Schenck from hyperplane arrangements to hypersurface arrangements. If the hypotheses fail for an arrangement in projective $3$-space, the Hartshorne–Rao module measures the failure of CMness. We establish consequences for the even liaison classes of $J^{top}$ and $\sqrt{J}$.
Bridging the Gap Between Labour Law and Company Law: Wedderburn’s Legacy: An Appreciation
Authors: Villiers Charlotte 
Published: August 2024

Abstract
The paper surveys the extensive writings of the late Professor Lord Wedderburn and explores the interactions between company law and labour law. A set of case studies illustrates labour law’s relative weakness in the contemporary corporate law context. Whilst it does change over time, company law has largely remained consistent with its two fundamental principles of separate legal personality and limited liability and its complementary prioritisation of the shareholders’ interests. These stable features provide a foundation that grants powerful corporate actors considerable freedom to pursue their interests and to organise their corporations however they please with little regard for those providing labour. Labour law finds itself constantly having to adapt to changing economic (and connected political) realities, fraying further the already threadbare protections for workers, especially in the context of global trade. With modern globalisation and financialization, a variety of “shareholders” and increasingly byzantine corporate structural arrangements have emerged presenting few opportunities to mitigate the impacts of their harmful activities. Investors and managers extract value with exploitative and detrimental consequences for the workers and other stakeholders. Fundamental reforms to company law are required for more effective workers’ voice and protection. Key words Lord Wedderburn, company law, labour law, employment law.
Bacteroidia and Clostridia are equipped to degrade a cascade of polysaccharides along the hindgut of the herbivorous fish Kyphosus sydneyanus
Authors: Facimoto Cesar T , Clements Kendall D , White W Lindsey , Handley Kim M 
Published: August 2024

Abstract
The gut microbiota of the marine herbivorous fish Kyphosus sydneyanus are thought to play an important role in host nutrition by supplying short-chain fatty acids (SCFAs) through fermentation of dietary red and brown macroalgae. Here, using 645 metagenome-assembled genomes (MAGs) from wild fish, we determined the capacity of different bacterial taxa to degrade seaweed carbohydrates along the gut. Most bacteria (99%) were unclassified at the species level. Gut communities and CAZyme-related transcriptional activity were dominated by Bacteroidia and Clostridia. Both classes possess genes CAZymes acting on internal polysaccharide bonds, suggesting their role initiating glycan depolymerization, followed by rarer Gammaproteobacteria and Verrucomicrobiae. Results indicate that Bacteroidia utilize substrates in both brown and red algae, whereas other taxa, namely, Clostridia, Bacilli, and Verrucomicrobiae, utilize mainly brown algae. Bacteroidia had the highest CAZyme gene densities overall, and Alistipes were especially enriched in CAZyme gene clusters (n = 73 versus just 62 distributed across all other taxa), pointing to an enhanced capacity for macroalgal polysaccharide utilization (e.g., alginate, laminarin, and sulfated polysaccharides). Pairwise correlations of MAG relative abundances and encoded CAZyme compositions provide evidence of potential inter-species collaborations. Co-abundant MAGs exhibited complementary degradative capacities for specific substrates, and flexibility in their capacity to source carbon (e.g., glucose- or galactose-rich glycans), possibly facilitating coexistence via niche partitioning. Results indicate the potential for collaborative microbial carbohydrate metabolism in the K. sydneyanus gut, that a greater variety of taxa contribute to the breakdown of brown versus red dietary algae, and that Bacteroidia encompass specialized macroalgae degraders.
A pharmacometric multistate model for predicting long-term treatment outcomes of patients with pulmonary TB
Authors: Lin Yu-Jou , Zou Yuanxi , Karlsson Mats O , Svensson Elin M 
Published: August 2024

Abstract

Background
Studying long-term treatment outcomes of TB is time-consuming and impractical. Early and reliable biomarkers reflecting treatment response and capable of predicting long-term outcomes are urgently needed.

Objectives
To develop a pharmacometric multistate model to evaluate the link between potential predictors and long-term outcomes.

Methods
Data were obtained from two Phase II clinical trials (TMC207-C208 and TMC207-C209) with bedaquiline on top of a multidrug background regimen. Patients were typically followed throughout a 24 week investigational treatment period plus a 96 week follow-up period. A five-state multistate model (active TB, converted, recurrent TB, dropout, and death) was developed to describe observed transitions. Evaluated predictors included patient characteristics, baseline TB disease severity and on-treatment biomarkers.

Results
A fast bacterial clearance in the first 2 weeks and low TB bacterial burden at baseline increased probability to achieve conversion, whereas patients with XDR-TB were less likely to reach conversion. Higher estimated mycobacterial load at the end of 24 week treatment increased the probability of recurrence. At 120 weeks, the model predicted 55% (95% prediction interval, 50%–60%), 6.5% (4.2%–9.0%) and 7.5% (5.2%–10%) of patients in converted, recurrent TB and death states, respectively. Simulations predicted a substantial increase of recurrence after 24 weeks in patients with slow bacterial clearance regardless of baseline bacterial burden.

Conclusions
The developed multistate model successfully described TB treatment outcomes. The multistate modelling framework enables prediction of several outcomes simultaneously, and allows mechanistically sound investigation of novel promising predictors. This may help support future biomarker evaluation, clinical trial design and analysis.
Antimicrobial prescribing in referral hospitals in Timor-Leste: results of the first two national point prevalence surveys, 2020–21
Authors: Ximenes Guilherme , Saha Sajal K , Guterres Helio , Vieira Adriano , Harris Lisa , Mahony Michelle , Dos Santos Agata , Toto Lucia , Amaral Elfiana , Spargo Jessie C , Tay Sze Yen , Amaral Salvador , Champlin Karen , Draper Anthony D K , Francis Joshua R , Yan Jennifer , Lynar Sarah A 
Published: August 2024

Abstract

Objectives
To describe antimicrobial use (AMU) in patients admitted to hospitals in Timor-Leste.

Methods
In 2020 and 2021, we undertook antimicrobial prescribing point prevalence surveys across all six hospitals in Timor-Leste (one national and five municipal) to describe AMU and appropriateness in admitted patients.

Results
In 2020, 291/394 (73.9%) surveyed patients had been prescribed antimicrobials, compared with 260/403 (64.5%) in 2021 (P = 0.004). Most (309/551; 56.1%) were prescribed one antimicrobial, and 179/551 (32.5%) were prescribed two. The most commonly prescribed antibiotics were ceftriaxone (38.5% in 2020, 41.5% in 2021) and ampicillin (35.7% in 2020, 32.3% in 2021), followed by gentamicin, metronidazole and cloxacillin. Reserve antibiotics like meropenem and vancomycin were minimally used. Of all antimicrobial prescriptions, 70.8% were deemed appropriate in 2020 and 69.1% in 2021. Antimicrobial prescriptions for surgical and post-partum prophylaxis were frequently deemed inappropriate [37/50 (74.0%) and 39/44 (88.6%) prescriptions, respectively].

Conclusions
Most patients admitted to hospital in Timor-Leste are prescribed antimicrobials, and approximately one-third of these prescriptions are inappropriate. However, this was in the context of limited local guideline availability at the time of surveys and limited microbiological culture capacity outside of the capital, Dili. Improved microbiological guidance, iterative guideline revisions based on local antimicrobial resistance (AMR) surveillance data, and enhanced stewardship activities including further point prevalence studies, could improve antimicrobial use, optimize patient outcomes and reduce AMR in Timor-Leste.
Glycated Albumin to Predict Adverse Neonatal Outcomes among Women with Diabetes and Overweight or Obese Body Mass Index
Authors: Powers Carson Jennifer , Arora Jyoti , Carter Ebony 
Published: August 2024

Abstract

Background
Glycated albumin (GA) has shown promise in predicting risk of adverse neonatal outcomes (ANO) in pregnant women with type 2 diabetes (T2DM) and gestational diabetes (GDM). However, previous studies showing a negative correlation between GA and body mass index (BMI) suggest that lower predictive cutoffs may be needed in populations with elevated BMI.

Methods
We performed a case-control study of prospectively enrolled pregnant women with T2DM or GDM and BMI ≥25 kg/m2 matched to biobanked controls without diabetes. Serum collected during the second and/or third trimesters was used to measure the percentage of GA (% GA). Receiver operating characteristic (ROC) curves were used to examine % GA to predict an ANO composite, including macrosomia, hypoglycemia, respiratory distress syndrome, and/or hyperbilirubinemia for the second and third trimesters.

Results
The median BMIs for cases and controls were 34.0 and 31.0 kg/m2, respectively. The area under the ROC curve to predict the ANO composite was significant for second trimester values but ambiguous for third trimester due to its wide 95% CI. A cutoff of 12.3% GA during second trimester showed 100% sensitivity and 73% specificity. Transference of previously published reference ranges did not validate, suggesting lower ranges are needed for women with overweight/obesity.

Conclusions
In this pilot study, % GA shows promise to stratify pregnant patients with diabetes and obesity into risk categories for ANO with excellent predictive ability in the second trimester. If this holds in larger studies, using second trimester % GA could allow additional intervention to improve blood glucose control and minimize ANO.