bluuebunny/crossref_metadata_2025_split huggingface dataset:
Males differ more between developmental stages than females and plasticity to light is stage-dependent in the tropical plant, Marchantia inflexa
Authors: Moore Jonathan D , McLetchie D Nicholas 
Published: February 2025

Abstract

Background and Aims
Plants have evolved strategies to maintain photosynthesis and mitigate tissue-damaging high light. Sometimes, in separate sex seed plants, these strategies are sexually dimorphic and link to spatial segregation of the sexes (SSS) along light gradients. In vascular tissue-free plants (bryophytes) with separate sexes, SSS is common, but how light gradients, sexual dimorphisms, and SSS correlate is not well-understood. To test if sexual dimorphisms in vegetative or sexual stages lead to light-associated SSS in bryophytes, we used Marchantia inflexa whose males occupy a wider range of light conditions, including higher light conditions, than females. We also tested if changes in development differed between sexes.

Methods
We grew 25 males and 25 females in a glasshouse with clones in low and high light and assessed pigment and biomass allocation traits in vegetative and sexual thalli (analogous to leaves), representing non-sexual and sexually reproductive stages. We expected males to exhibit traits consistent with high light acclimation more than females and greater sex-differences in sexual thalli due to specialisation. Further, we reasoned that males would change more between stages than females.

Key Results
For sexual thalli, males had higher carotenoid/chlorophyll ratios (consistent with expectation) while females had higher chlorophyll a/b ratios and dry matter content (opposite from expectations). Vegetative thalli were not sexually dimorphic, but were more plastic to light than sexual thalli. Overall, the stages differed more for males than females, but without regard for light. However, female stages differed more for dry matter content.

Conclusions
Males generally need greater change in pigmentation and biomass allocation than females between stages, and we posit links for individual traits to sex function. Specialisation in sexual thalli constrains their plasticity to light compared to vegetative thalli. Yet, neither sexual dimorphism in sexual thalli nor greater change between stages for males than females clearly leads to light-associated SSS.
Duplex Study of the Nipple–Areola Complex Blood Supply in the Female Breast
Authors: Hosny Husam , Mansour Sahar , El-Essawy Nadeen M 
Published: February 2025

Abstract

Background
Although breast blood supply comes from the internal mammary, lateral thoracic, and intercostal artery perforators, the nipple–areola complex (NAC) blood supply was usually depicted as a direct continuation of those vessels rather than a true description based on anatomical research. Studies focusing on NAC vascularity are few in number, done on a limited number of subject based on microdissection, computed tomography, or MRI. The results are inconsistent and may be perplexing. Hence, the need for studies on a large number of living subject is still warranted. Because duplex proved efficient at detecting perforators, we used it to assess NAC vascularity.

Objectives
In vivo delineation of NAC blood supply by comparing this to the nipple-to-suprasternal notch (N-SN) distance and individual variation between both sides.

Methods
Female subject presenting to the Breast Imaging Unit of the institute (229 subject; 458 breasts, BIRADS I and II) were assessed by duplex for the presence of significant NAC blood supply (≥1 mm), regarding their number, source vessel, perforator level, relation to N-SN distance, and similarity between both sides.

Results
The third and fourth internal mammary artery (IMA) perforators accounted for 54.8% and 31.3%, respectively. The second IMA, lateral thoracic artery, and direct axillary branch were found in 9.2%, 3.3%, and 1.3%, respectively. The longer the N-SN distance is, the lower the supplying perforator. NAC vascularity was symmetric in 143 subject (62.4%) and asymmetric in 86 subject (37.5%).

Conclusions
The third and fourth internal mammary perforators are the main source of NAC blood supply. Right and left sides’ asymmetry is not uncommon. Finally, the longer the N-SN distance is, the lower the perforator level is anticipated.

Level of Evidence: 1 (Diagnostic)
MiNEApy: Enhancing Enrichment Network Analysis in Metabolic Networks
Authors: Pandey Vikash 
Published: February 2025

Abstract

Motivation
Modeling genome-scale metabolic networks (GEMs) helps understand metabolic fluxes in cells at a specific state under defined environmental conditions or perturbations. Elementary Flux Modes (EFMs) are powerful tools for simplifying complex metabolic networks into smaller, more manageable pathways. However, the enumeration of all EFMs, especially within GEMs, poses significant challenges due to computational complexity. Additionally, traditional EFM approaches often fail to capture essential aspects of metabolism, such as co-factor balancing and by-product generation.
The previously developed Minimum Network Enrichment Analysis (MiNEA) method addresses these limitations by enumerating alternative minimal networks for given biomass building blocks and metabolic tasks. MiNEA facilitates a deeper understanding of metabolic task flexibility and context-specific metabolic routes by integrating condition-specific transcriptomics, proteomics, and metabolomics data. This approach offers significant improvements in the analysis of metabolic pathways, providing more comprehensive insights into cellular metabolism.

Results
Here, I present MiNEApy, a Python package reimplementation of MiNEA, which computes minimal networks and performs enrichment analysis. I demonstrate the application of MiNEApy on both a small-scale and a genome-scale model of the bacterium E. coli, showcasing its ability to conduct minimal network enrichment analysis using minimal networks and context-specific data.

Availability
MiNEApy can be accessed at: https://github.com/vpandey-om/mineapy

Supplementary information
Supplementary data are available at Bioinformatics online.
SpectroPipeR—a streamlining post Spectronaut® DIA-MS data analysis R package
Authors: Michalik Stephan , Hammer Elke , Steil Leif , Salazar Manuela Gesell , Hentschker Christian , Surmann Kristin , Busch Larissa M , Sura Thomas , Völker Uwe 
Published: February 2025

Abstract

Summary
Proteome studies frequently encounter challenges in down-stream data analysis due to limited bioinformatics resources, rapid data generation, and variations in analytical methods. To address these issues, we developed SpectroPipeR, an R package designed to streamline data analysis tasks and provide a comprehensive, standardized pipeline for Spectronaut® DIA-MS data. This novel package automates various analytical processes, including XIC plots, ID rate summary, normalization, batch and covariate adjustment, relative protein quantification, multivariate analysis, and statistical analysis, while generating interactive HTML reports for e.g. ELN systems.

Availability
The SpectroPipeR package (manual: https://stemicha.github.io/SpectroPipeR/) was written in R, and is freely available on GitHub (https://github.com/stemicha/SpectroPipeR ).

Supplementary information
Supplementary data are available at Bioinformatics online.
Anchors Through Change: Exploring Identity Work in the Unified Probation Service for England & Wales
Authors: Robinson Gwen , Annison Harry , Burke Lawrence , Carr Nicola , Millings Matthew , Surridge Eleanor 
Published: February 2025

Abstract
The Probation Service for England & Wales offers an important case study for those who are interested in the impact(s) of organizational change on workers in criminal justice and, in particular, the identity work that they engage in as they move through frequent iterations of change. In this article, we draw on data from an ongoing longitudinal study of probation reform to explore identity work among a mixed sample of practitioner and management grade staff in one of 12 probation regions. Our analysis reveals the significance of both occupational and organizational sources of identification to workers of all grades, but also evidence of dis-identification with aspects of the current organization. It further reveals the importance of anchors through change in workers’ identities as they navigate paths through successive reforms. These anchors include values, places and structures that are part of probation’s legacy but which offer a sense of continuity and meaning to workers as they adapt within a turbulent field.
The Dialectics of Migration: Social Bulimia and the Deportation Pipeline in New York City
Authors: Brotherton David C , Tosh Sarah 
Published: February 2025

Abstract
Following the Illegal Immigration Reform and Immigrant Responsibility Act of 1996 New York City has undergone challenges to its status as a refuge to the teeming masses of the globe. Based on recent research in New York City, we trace the policing of its migrant communities as the US state has resorted to punitive measures to regulate non-citizens regarded as deportable aliens. While the city has resisted the exclusionary pressures of the security state, its criminalized black and migrant communities still produce the highest rates of removal, described as the deportation pipeline. We argue that the city, while presented as a model of immigrant integration, is a contested space caught between the forces of exclusion and inclusion and overdetermined by processes of crimmigration (Stumpf 2006). Such processes expand the criminological concept of ‘social bulimia’ (Young (1999a), a characteristic of late modern capitalistic society—examining how a broader dialectic between cultural assimilation and structural punitiveness is navigated by multilayered networks of contradicting actors, processes, and policies at the municipal level.
Work with People in Mental Distress Who Access Spirituality/Religion
Authors: Smith Stewart J , Read Julia 
Published: February 2025

Abstract
When social workers assist people in mental distress, complexity is added if clients self-identify as spiritual/religious. It can be challenging to know how to proceed in a helpful manner. Issues related to understanding what people are going through and how best to assist are centrally important for social workers to consider. To explore these concerns, we examine key social work ideas of social justice and holistic practice as related to spiritual/religious clients’ well-being. Following that analysis, main stream assumptions about mental illness from the medical model are reviewed. Mad Studies is then investigated with an emphasis on the term ‘mental distress’ which we have found to be a useful consideration to effectively work with people. This understanding is in harmony with holistic practice and social justice. From the insights gained from the literature, and our own experiences as counsellors, we explore constructive principles related to work with people in mental distress who are accessing spiritual/religious resources. To do this, we present a case study to review and propose strategies in working with spiritual/religious people experiencing mental distress.
‘I don’t think they look at this as an issue’. Exploring the training and development needs of practice educators in social work field education
Authors: Pascoe Katheryn Margaret 
Published: February 2025

Abstract
Social work field education is central to qualifying social work degrees, whereby placements support students to explore the connection between theory and practice, gain frontline experience before entering the workforce, and socialize into the profession. While research has captured student learning experiences, the perspectives of social workers supervising student placements have received less attention. This article examines the training and development needs of practice educators (PEs), also known as field educators, from across Aotearoa New Zealand, reporting on findings from a national survey. Drawing attention to desired areas for development, gaps in provision, low levels of satisfaction, and challenges to accessing training including cost, time, and visibility of opportunities, the findings suggest the current level of professional development specific to this role is variable, and PEs are interested in accessing further training. These findings reiterate the importance of resourcing and highlight considerations for establishing partnerships across education institutions, the professional association, and potentially the regulation authority to support consistency, development, and delivery.
Serum Ammonia Screening and Donor Mollicute Detection for Hyperammonemia Syndrome Post-Lung Transplant: A Prospective Observational Study
Authors: Walti Laura N , Ng Chun Fai , Kaur Simran , Almansour Sarah , Mazzulli Tony , Bitterman Roni , Sidhu Aman , Keshavjee Shaf , Chaparro Cecilia , Martinu Tereza , Tikkanen Jussi , del Sorbo Lorenzo , Husain Shahid 
Published: February 2025

Abstract

Background
Hyperammonemia syndrome (HS) is a rare but potentially fatal complication of Lung Transplantation (LT). Optimal screening methods are unknown: Here we investigated serum ammonia screening (SAS) for HS and compared it with PCR for Mollicutes (ureaplasma-producing bacteria).

Methods
All LT recipients from 07/2019-02/2020 and 10/2021-11/2022 with available donor bronchial wash samples from the LT biobank were included. Mollicute-PCR was performed using two commercially available kits. Daily ammonia serum levels were measured for the first 14 days. Recipients were prospectively followed for HS for 30 days post-LT. HS was defined by new neurological symptoms and the presence of elevated serum ammonium (&gt;1x &gt;70 µmol/l).

Results
Of 241 LT recipients, 5 (2%) developed HS within the first month post-LT. Median time to HS was 8 days (IQR 5-10). All HS were diagnosed within the first 14 days post-LT, while daily SAS was in place.
Ammonia was confirmed elevated (&gt;1x &gt;70µmol/l) in 4% (9/241) during follow-up however, outside of HS, 4 were found to be liver disease-related. Donor Mollicute-PCR was positive in 8% (19/241), recipient M-PCR in 1% (1/72) at transplant. Donor Mollicute-PCR, in contrast to recipient Mollicute-PCR, was associated with HS but only in 2 of the 5 HS cases. No HS patient died within 90 days post-LT.

Conclusion
HS was a rare complication in our LT cohort. Daily post-LT SAS might add to early HS diagnosis and treatment and is potentially associated with improved outcome. Donor screening with Mollicute-PCR has limited predictive value for HS post-LT.
Primary FSGS is not associated with worse kidney outcome compared to other FSGS subtypes
Authors: Deleersnijder Dries , Cleenders Evert , Coemans Maarten , Dendooven Amélie , Koshy Priyanka , Claes Kathleen , De Vusser Katrien , Meijers Björn K , Sprangers Ben , Van Laecke Steven , Van Craenenbroeck Amaryllis H 
Published: February 2025

Abstract

Background
Studies that compare kidney outcomes across patients with different forms of focal segmental glomerulosclerosis (FSGS) are lacking.

Methods
This retrospective study compared annual estimated glomerular filtration rate (eGFR) slope and kidney failure (KF) rate (eGFR &lt; 15 mL/min/1.73 m2 or initiation of kidney replacement therapy) across patients with biopsy-proven primary, maladaptive, genetic and undetermined FSGS. Patients were included from two Belgian tertiary referral hospitals, from 2010 until 2022. Associations between covariates and KF were estimated using Cox and Fine and Gray models. eGFR slopes were estimated using linear mixed-effects models.

Results
Eighty-two patients were subdivided into primary (28.1%), maladaptive (40.2%), genetic (14.6%) and undetermined FSGS (17.1%) groups. KF occurred in 22 patients (26.8%). Primary FSGS patients exhibited higher baseline eGFR and less chronic changes on biopsy. The annual eGFR slope was -2.5 mL/min in primary, -2.5 mL/min in maladaptive, -4.6 mL/min in genetic and -4.4 mL/min in undetermined FSGS. Female sex was associated with a lower KF rate and higher eGFR slope. Higher proteinuria at biopsy was associated with a higher KF rate, lower eGFR slope and a higher mortality rate. Global sclerosis on kidney biopsy was associated with lower baseline eGFR, while a higher percentage of segmental sclerosis rather associated with more rapid eGFR decline (-1.5 mL/min/year per 10% increase, 95% CI [-2.2, -0.7]).

Conclusions
Patients with primary FSGS were biopsied earlier in their disease course and exhibited surprisingly good kidney outcome. Overall, sex, baseline eGFR, proteinuria and the degree of focal and global glomerulosclerosis play a more important role in estimating the prognosis of patients with FSGS, than merely the FSGS etiology.
Serial Dependence Robust Bootstrap Test for Cross-Sectional Correlation
Authors: Hounyo Ulrich , Kao Chihwa , Kim Min Seong 
Published: February 2025

Abstract
We propose a novel bootstrap-based test for cross-sectional dependence (CD) in panel models, maintaining robustness against serial dependence. While serial dependence is common in panel data, existing tests often assume serial independence. Our cluster wild bootstrap CD test procedure mirrors Pesaran’s original CD test and is very simple to implement. This procedure preserves serial dependence while testing for cross-sectional independence. Theoretical validity is established for our bootstrap-based test, with simulations highlighting its performance in finite samples. Using R&D investment panel data, we illustrate the utility of our bootstrap methods.
Effect of chlorine atoms on inhibition effect between amide herbicides and urease enzyme: molecular mechanism and structure-activity relationship
Authors: Wang Xiaoning , Wang Wenyue , Lin Jingyan , Wu Yongkun , Zhao Yuhan , Ding Jiayin , Hong Shan , Wan Ziheng , Sun Kaipeng , Chen Dong , Tang Yizhen , Xiao Yihua , Zhao Weihua , Sun Haofen , Wang Weiliang , Yang Chuanxi 
Published: February 2025

Abstract
Amide herbicides (AHs) were disturbed urease (UA) activity and soil microbial community, caused soil nutrient changes. Activity of UA was inhibited by AHs via groups of chlorine, benzene ring, peptide bond (-N-/-CO-). Difference of surface charge distribution were mainly derived from position to connected -Cl, distance of -O- from ether group and -N from peptide bond, difference of structure/length for hydrocarbon chain, and different regions of negative charge enrichment. Developmental toxicity (DT) for alachlor was strongest related to smaller structure and weaker steric hindrance effect, mutagenicity for propanil was weakest could be related to missing ether group. Molecular mechanism and structural activity relationship for inhibition of AHs and UA based on functional groups, amino acids with high frequency, hydrogen bonds, hydrophobic interactions, binding area (BA) of butachlor (396.3 Å2), absolute value of binding energy (|BE|) of propanil (2.93 kJ/mol) (which as highest), quantitative structural relationship between BA and |BE|, which was negative correlation. BA for AHs and UA had negatively correlation for density with correlation coefficient (r) as -0.937 (p ≤ 0.01). |BE| for AHs and UA had positively correlation for density with r as 0.847 (p ≤ 0.05), and negatively correlation for molecular weight (MW) with r as -0.973 (p ≤ 0.001). Results provided technological support and theoretical foundation for toxic effects of SEs activity, health effects, risk regulation and control of AHs.
Anther modes influence diversification rates in the animal-pollinated species-rich Didymocarpoideae
Authors: Ling Shao-Jun , Yao Xiao-Lan , Xiang Wen-Qian , Ren Ming-Xun 
Published: February 2025

Abstract
Stamen traits significantly influence pollen presentation patterns and play a critical role in mating systems, floral evolution, and the diversification of angiosperms. Anthers within a flower can either develop freely or be united, resulting in three primary modes: separated anthers, synandry, and paired-united anthers. The impact of these anther modes on species diversification remains inadequately understood. In this study, we employed 14 plastid and nuclear ribosomal markers from 789 species to reconstruct the phylogenetic relationships of the Old World Didymocarpoideae, which are predominantly bee pollinated. We then investigated the evolutionary patterns of anther modes and assessed their potential role in species diversification. Our findings indicate that the evolution of anther modes and associated floral traits exhibited significant trait conservatism. Paired-united anthers likely represent the ancestral form of Didymocarpoideae, characterized by four fertile stamens with exserted locations for the anthers. Notably, derived synandry was associated with relatively high rates of species diversification, particularly in the species-rich Cyrtandra, Primulina, and Streptocarpus, which could be due to enhanced pollination precision facilitated by aggregations of anthers and pollen grains. This study elucidates the evolutionary transitions of different anther modes while highlighting their influence on diversification rates within Didymocarpoideae.
Phosphatases control the duration and range of cAMP/PKA microdomains
Authors: Conca Filippo , Bayburtlu Doruk Kaan , Vismara Mauro , Surdo Nicoletta C , Tavoni Alessandra , Nogara Leonardo , Sarra Adamo , Ciciliot Stefano , Benedetto Giulietta Di , Iannucci Liliana F , Lefkimmiatis Konstantinos 
Published: February 2025

Abstract
The spatiotemporal interplay between the second messenger cyclic AMP (cAMP) and its main effector, Protein kinase A (PKA) is crucial for the pleiotropic nature of this cascade. To maintain a high degree of specificity, the cAMP/PKA axis is organised into functional units called microdomains, precisely distributed within the cell. While the subcellular allocation of PKA is guaranteed by a family of tethers called A-Kinase-anchoring Proteins (AKAPs), the mechanisms underlying the efficient confinement of a microdomain's functional effects are not fully understood. Here we used FRET-based sensors to detect cAMP levels and PKA-dependent phosphorylation within specific subcellular compartments. We find that cellular cAMP levels may depend on different mechanisms and are responsible for the activation of local PKA enzymes. On the other hand, the dephosphorylating actions of phosphatases dictate the duration of the microdomain's effects. To test the range of action of PKA microdomains we used rigid aminoacidic nanorulers to distance our FRET sensors from their original location for 10 or 30 nm. Interestingly, we established that cAMP levels do not affect the spatial range of the microdomain while on the contrary, phosphatase activity provides a functional boundary for phosphorylated PKA targets. Finally, using the same strategy to distance phosphatases from the mitochondria we found that enzymes close to the outer mitochondrial membrane produced a fragmented phenotype that was not observed when phosphatases were moved to 30 nm from the organelle's surface. Our findings contribute to the design of a picture where two microdomain-forming events have distinct roles. Cyclic AMP elevations trigger the initial activation of subcellular PKA moieties, while the temporal and spatial extent of the PKA's actions are regulated by phosphatases.