bluuebunny/crossref_metadata_2025_split huggingface dataset:
A review of label-free photonics-based techniques for cancer detection in the digestive and urinary systems
Authors: Castro-Olvera G , Baria E , Stoliarov D , Morselli S , Orlandini B , Vanoni M , Sayinc H , Koviarov A , Galiakhmetova D , Dickie J , Cicchi R , Serni S , Gacci M , Ribal M J , Pavone F S , Loza-Alvarez P , Rafailov E , Gumenyuk R 
Published: October 2024

Abstract
For a long time, it has been known that optics can provide a broad range of tools for addressing clinical needs, particularly diagnostics. Optical techniques can help in identifying diseases and detecting pathological tissues with non/minimally invasive and label-free methods. Given the current limitations of standard clinical procedures, such an approach could provide a powerful tool in detecting gastrointestinal and bladder cancers. However, each technique has serious limitations regarding one or more of the following features: biomarker sensitivity, penetration depth, acquisition times, or adaptation to the clinical environment. Hence there is an increasing need for approaches and instruments based on the concept of multimodality; in this regard, we review the application of different imaging/spectroscopy tools and methods operating in the first two optical windows (SHG, SPEF, TPEF, THG, 3PEF, CARS, Raman and reflectance) for tumour detection in the digestive and urinary systems. This article also explores the possibility of exploiting the third bio-tissue transmission window (1600–1900 nm) by reviewing state of the art in ultrafast laser sources development. Finally, we summarize the most recent results in developing multiphoton endoscopes—a key element for clinical in vivo translation of photonics-based diagnostics.
Data-driven investigation of thickness variations in multilayer thin film coatings
Authors: Liu Qing , Baghdasaryan Tigran , Ottevaere Heidi 
Published: October 2024

Abstract
Design and fabrication of multilayer thin film coatings for photonics applications require careful consideration of various parameters such as layer thickness, refractive indices and number of stacks. A growing trend uses machine learning for efficient navigation in the complex parameter space of photonics applications to efficiently extract valuable insights from the extensive datasets and to predict the optical performance. We developed an approach that combines Monte-Carlo and Finite-Difference Time-Domain simulations to model multilayer thin films. After conducting 95 200 runs, the data were analyzed using Neural Network fitting to explore how thickness variations influence the optical performance. An experiment validation on magnetron sputtered coated samples demonstrates the high accuracy of our method in predicting the optical performance of the thin film stacks (R
2 > 0.99), contributing to the understanding and enhancement of photonics stack properties for diverse optical applications using machine learning approaches.
The production of climate security futures in the West African Sahel
Authors: Charbonneau Bruno 
Published: October 2024

Abstract
Much has been written and said about the consequences of climate change on security in the West African Sahel. Sceptics argue that claims about the links between global warming and conflict dynamics rest on limited evidence and questionable assumptions. Others work on the institutionalization and operationalization of climate security. This implementation seems inevitable, if slow, difficult, and at times vague, as there is simply no consensus on what climate security implies in practice and what it is meant to achieve. What is climate security, and whose climate security are we talking about? This article analyses climate security as a structure of knowledge and a set of epistemic relationships that inform practices and relationships. It draws on participant observations of a Dakar-based research group that travelled to Bamako, Ouagadougou, and Niamey. At the intersection of research, policy, and programme implementation, this case study provides a unique look into the emergence of climate security relations and practices. The findings point to the rising structural force of climate security and how it can overcome both research uncertainties and sensitive diplomatic relations. The article shows that there is more to climate security than the focus on the conflict-climate nexus lets on.
Pilomatrix-like breast carcinoma: A mammary analog of pilomatrix-like high-grade endometrioid carcinoma (PiMHEC)
Authors: Xu Jin , Accola Molly A , Rehrauer William M , Weisman Paul S 
Published: October 2024

Abstract

Objectives
To describe what is, to our knowledge, the first recognized case of a triple-negative breast carcinoma (TNBC) with a PiMHEC-like phenotype. Pilomatrix-like high-grade endometrioid carcinoma (PiMHEC) is a high-grade carcinoma with divergent differentiation resembling cutaneous pilomatrix carcinoma that was recently described in the endometrium and ovary. For reference, pertinent features of PiMHEC include (1) high-grade basaloid to squamoid morphology with the presence of ghost cells; (2) only focal p63 and/or p40 expression despite a squamoid appearance; (3) CTNNB1 mutation, accompanied by diffusely aberrant β-catenin expression and LEF1 and/or CDX2 expression; and (4) loss of site-specific markers (ie, PAX8, ER).

Methods
Here we report the histologic, immunophenotypic and molecular genetic features of a case of a triple-negative breast carcinoma (TNBC) with a PiMHEC-like phenotype.

Results
The tumor developed immediately adjacent to a HER2+, androgen receptor (AR)+, GATA3+ conventional grade 3 invasive ductal carcinoma (IDC) with only membranous β-catenin expression. The PiMHEC-like component had all of the above-noted morphologic and immunophenotypic features of endometrial PiMHEC but with loss of GATA3 and AR rather than PAX8 and ER. Molecular analysis performed on both tumor components demonstrated a shared TP53 point mutation and an exon 3 CTNNB1 mutation restricted to the PiMHEC-like component, implying a clonal relationship with secondary acquisition of CTNNB1. Following neoadjuvant chemotherapy, the HER2+ conventional component had completely resolved, but the PiMHEC-like component had very little response.

Conclusions
This case demonstrates that a PiMHEC-like phenotype may be seen as a form of TNBC that can develop from conventional IDC, with loss of site-specific biomarkers, acquisition of CTNNB1 mutation, and resistance to conventional chemotherapy.
PathMethy: an interpretable AI framework for cancer origin tracing based on DNA methylation
Authors: Xie Jiajing , Song Yuhang , Zheng Hailong , Luo Shijie , Chen Ying , Zhang Chen , Yu Rongshan , Tong Mengsha 
Published: October 2024

Abstract
Despite advanced diagnostics, 3%–5% of cases remain classified as cancer of unknown primary (CUP). DNA methylation, an important epigenetic feature, is essential for determining the origin of metastatic tumors. We presented PathMethy, a novel Transformer model integrated with functional categories and crosstalk of pathways, to accurately trace the origin of tumors in CUP samples based on DNA methylation. PathMethy outperformed seven competing methods in F1-score across nine cancer datasets and predicted accurately the molecular subtypes within nine primary tumor types. It not only excelled at tracing the origins of both primary and metastatic tumors but also demonstrated a high degree of agreement with previously diagnosed sites in cases of CUP. PathMethy provided biological insights by highlighting key pathways, functional categories, and their interactions. Using functional categories of pathways, we gained a global understanding of biological processes. For broader access, a user-friendly web server for researchers and clinicians is available at https://cup.pathmethy.com.
Small extracellular vesicles derived from the crosstalk between early embryos and the endometrium potentially mediate corpus luteum function
Authors: Bridi Alessandra , Sangalli Juliano Rodrigues , Nociti Ricardo Perecin , dos Santos Angélica Camargo , Alves Luana , Bastos Natália Marins , Ferronato Giuliana de Ávila , Rosa Paola Maria da Silva , Fiorenza Mariani Farias , Pugliesi Guilherme , Meirelles Flávio Vieira , Chiaratti Marcos Roberto , da Silveira Juliano Coelho , Perecin Felipe 
Published: October 2024

Abstract
The first interactions among the embryo, endometrium, and corpus luteum are essential for pregnancy success. Small extracellular vesicles (sEVs) are part of these interactions. We previously demonstrated that small extracellular vesicles from in vivo- or in vitro-produced bovine embryos contain different miRNA cargos. Herein we show: (1) the presence and origin (in vivo or in vitro) of the blastocyst differentially reprograms endometrial transcriptional profiles; (2) the endometrial explant (EE) cultured with in vivo or in vitro embryos release small extracellular vesicles with different miRNA contents, and (3) the luteal explant (CLE) exposed to these small extracellular vesicles have distinct mRNA and miRNA profiles. To elucidate this, the endometrial explant were cultured in the presence or absence of a single Day-7 in vivo (EE–artificial insemination; EE-AI) or in vitro (EE–in vitro fertilization; EE-IVF) embryo. After of culture we found, in the endometrial explant, 45 and 211 differentially expressed genes associated with embryo presence and origin, respectively. Small extracellular vesicles were recovered from the conditioned media (CM) in which endometrial explant and embryos were co-cultured. Four miRNAs were differentially expressed between small extracellular vesicles from CC-EE-AI and CC-EE-IVF. Luteal explants exposed in culture to these small extracellular vesicles showed 1360 transcripts and 15 miRNAs differentially expressed. The differentially expressed genes associated with embryo presence and origin, modulating cells’ proliferation, and survival. These results demonstrate that in vivo- or in vitro-produced bovine embryos induce molecular alterations in the endometrium; and that the embryo and endometrium release small extracellular vesicles capable of modifying the messenger RNA (mRNA) and miRNA profile in the corpus luteum. Therefore, the small extracellular vesicles-mediated embryo–endometrium–corpus luteum interactions possibly regulate the corpus luteum viability to ensure pregnancy success.
Live cell fluorescence microscopy—an end-to-end workflow for high-throughput image and data analysis
Authors: Zahumensky Jakub , Malinsky Jan 
Published: October 2024

Abstract
Fluorescence microscopy images of biological samples contain valuable information but require rigorous analysis for accurate and reliable determination of changes in protein localization, fluorescence intensity, and morphology of the studied objects. Traditionally, cells for microscopy are immobilized using chemicals, which can introduce stress. Analysis often focuses only on colocalization and involves manual segmentation and measurement, which are time-consuming and can introduce bias. Our new workflow addresses these issues by gently immobilizing cells using a small agarose block on a microscope coverslip. This approach is suitable for cell-walled cells (yeast, fungi, plants, bacteria), facilitates their live imaging under conditions close to their natural environment and enables the addition of chemicals during time-lapse experiments. The primary focus of the protocol is on the presented analysis workflow, which is applicable to virtually any cell type—we describe cell segmentation using the Cellpose software followed by automated analysis of a multitude of parameters using custom-written Fiji (ImageJ) macros. The results can be easily processed using the provided R markdown scripts or available graphing software. Our method facilitates unbiased batch analysis of large datasets, improving the efficiency and accuracy of fluorescence microscopy research. The reported sample preparation protocol and Fiji macros were used in our recent publications: Microbiol Spectr (2022), DOI: 10.1128/spectrum.01961-22; Microbiol Spectr (2022), DOI: 10.1128/spectrum.02489-22; J Cell Sci (2023), DOI: 10.1242/jcs.260554.
Direct interrogation of cortical interneuron circuits in amyotrophic lateral sclerosis
Authors: van den Bos Mehdi A J , Menon Parvathi , Pavey Nathan , Higashihara Mana , Kiernan Matthew C , Vucic Steve 
Published: October 2024

Abstract
Cortical hyperexcitability is a key pathogenic feature of amyotrophic lateral sclerosis (ALS), believed to be mediated through complex interplay of cortical interneurons. To date, there has been no technological approach to facilitate the direct capture of cortical interneuron function.
Through combination of transcranial magnetic stimulation (TMS) with advanced EEG, the present study examined GABAergic dysfunction in ALS by recording focused cortical output whilst applying TMS over the primary motor cortex contralateral to the site of symptom onset. Using both a single-pulse and a novel inhibitory paired-pulse paradigm, TMS-EEG studies were undertaken on 21 ALS patients and results compared with healthy controls. TMS responses captured by EEG form a discrete waveform known as the transcranial evoked potential (TEP), with positive (P) or upward deflections occurring at 30 (P30), 60 (P60) and 190 ms (P190) after TMS stimulus. Negative (N) or downward deflections occur at 44 (N44), 100 (N100) and 280 ms (N280) after TMS stimulus. The single-pulse TEPs recorded in ALS patients demonstrated novel differences suggestive of cortical GABAergic dysfunction. When compared with controls, the N100 component was significantly reduced (P &lt; 0.05), whereas the P190 component increased (P &lt; 0.05) in ALS patients. Additionally, the N44 component was correlated with muscle weakness (r = −0.501, P &lt; 0.05). These findings were supported by reduced paired-pulse inhibition of TEP components in ALS patients (P60, P &lt; 0.01; N100, P &lt; 0.005), consistent with dysfunction of cortical interneuronal GABAA-ergic circuits. Furthermore, the reduction in short-interval intracortical inhibition, as reflected by changes in paired-pulse inhibition of the N100 component, was associated with longer disease duration in ALS patients (r = −0.698, P &lt; 0.001).
In conclusion, intensive and focused interrogation of the motor cortex using novel TMS-EEG combined technologies has established localized dysfunction of GABAergic circuits, supporting the notion that cortical hyperexcitability is mediated by cortical disinhibition in ALS. Dysfunction of GABAergic circuits was correlated with greater clinical disability and disease duration, implying pathophysiological significance.
Brain state identification and neuromodulation to promote recovery of consciousness
Authors: van der Lande Glenn J M , Casas-Torremocha Diana , Manasanch Arnau , Dalla Porta Leonardo , Gosseries Olivia , Alnagger Naji , Barra Alice , Mejías Jorge F , Panda Rajanikant , Riefolo Fabio , Thibaut Aurore , Bonhomme Vincent , Thirion Bertrand , Clasca Francisco , Gorostiza Pau , Sanchez-Vives Maria V , Deco Gustavo , Laureys Steven , Zamora-López Gorka , Annen Jitka 
Published: October 2024

Abstract
Experimental and clinical studies of consciousness identify brain states (i.e. quasi-stable functional cerebral organization) in a non-systematic manner and largely independent of the research into brain state modulation. In this narrative review, we synthesize advances in the identification of brain states associated with consciousness in animal models and physiological (sleep), pharmacological (anaesthesia) and pathological (disorders of consciousness) states of altered consciousness in humans. We show that in reduced consciousness the frequencies in which the brain operates are slowed down and that the pattern of functional communication is sparser, less efficient, and less complex. The results also highlight damaged resting-state networks, in particular the default mode network, decreased connectivity in long-range connections and especially in the thalamocortical loops. Next, we show that therapeutic approaches to treat disorders of consciousness, through pharmacology (e.g. amantadine, zolpidem), and (non-) invasive brain stimulation (e.g. transcranial direct current stimulation, deep brain stimulation) have shown partial effectiveness in promoting consciousness recovery. Although some features of conscious brain states may improve in response to neuromodulation, targeting often remains non-specific and does not always lead to (behavioural) improvements. The fields of brain state identification and neuromodulation of brain states in relation to consciousness are showing fascinating developments that, when integrated, might propel the development of new and better-targeted techniques for disorders of consciousness. We here propose a therapeutic framework for the identification and modulation of brain states to facilitate the interaction between the two fields. We propose that brain states should be identified in a predictive setting, followed by theoretical and empirical testing (i.e. in animal models, under anaesthesia and in patients with a disorder of consciousness) of neuromodulation techniques to promote consciousness in line with such predictions. This framework further helps to identify where challenges and opportunities lay for the maturation of brain state research in the context of states of consciousness. It will become apparent that one angle of opportunity is provided through the addition of computational modelling. Finally, it aids in recognizing possibilities and obstacles for the clinical translation of these diagnostic techniques and neuromodulation treatment options across both the multimodal and multi-species approaches outlined throughout the review.
From gay liberation to backlash: producing pride and New York’s LGBTQ public culture on The Emerald City
Authors: Herold Lauren 
Published: October 2024

Abstract
This article explores how The Emerald City (1977–1979), an LGBTQ public access cable television show, represented the evolving sociopolitical and geographic contexts of New York City in the 1970s and mediated the concept “gay pride.” Tracing its emplacement in New York alongside the development of cable television, this article discusses how the series played a role in producing dominant queer cultural imaginations of the city. Combining analysis of the show’s episodes with archival research and interviews with The Emerald City co-producer Steven Bie, this article argues both for the potential of public access to produce liberatory affective experiences of pride, as well as its role in idealizing a gay imaginary of New York limited by racialized and classed hierarchies. This article demonstrates how public access in the US provided opportunities for marginalized producers to experiment with creating gay television, as well as the structural constraints that limited its political promise.
Pneumococcal serotype-specific antibodies in children with recurrent oto-sinopulmonary infections
Authors: Ale Hanadys , Calderon Jose G , Gruber Joshua , Taylor Thomas , Blouin William R , Hernández-Trujillo Vivian P 
Published: October 2024

Abstract
Low titers to pneumococcal vaccine are a frequent finding in pediatric patients with recurrent oto-sinopulmonary infections. To characterize the pre- and post-immunization antibody trend for each serotype included in the pneumococcal 13-valent conjugate vaccine, in a cohort of pediatric patients with recurrent oto-sinopulmonary infections, this retrospective review identified 182 patients with recurrent oto-sinopulmonary infections (131 required an immune workup and 99 had low pneumococcal titers leading to a pneumococcal 13-valent conjugate vaccine booster). Baseline pneumococcal serotype-specific antibody titers at the initial visit and 6 weeks after the vaccine booster were obtained. An adequate response to the pneumococcal conjugate vaccine was deemed to be a 4-fold increase over baseline and/or a post-immunization titer of 1.3 µg/ml or greater. Overall, The pneumococcal 13-valent conjugate vaccine booster provided a significant improvement in the number of protective titers, increasing from 3.6 serotypes at baseline to 11.1 serotypes at 6 weeks (P &lt; 0.001). This increase correlated with improved clinical outcomes (81% showed no signs of recurrent infection after the first booster and 94% after a second booster). Post-immunization antibody concentrations were significantly higher than at baseline for all serotypes (P &lt; 0.05), and only 8, 9N, and 12F did not exhibit a greater than 4-fold increase (P &gt; 0.05) 6 weeks following booster. There were no differences between patients at different ages in post-immunization titer levels for all serotypes. In pediatric patients with recurrent oto-sinopulmonary infections, an additional pneumococcal booster proved to be effective in the protection of these children against further infections, across all age groups.
The sulci of the lateral superior parietal lobule: anatomical overview and nomenclatural consideration
Authors: Bakhit Mudathir , Hiruta Ryo , Iwatate Kensho , Fujii Masazumi 
Published: October 2024

Abstract
Discrepancies in the terminology describing sulcal structures within the lateral superior parietal lobule prompted our comprehensive investigation to clarify their morphology and nomenclature. We reviewed literature from the 19th century to the present, focusing on the intraparietal sulcus, interparietal sulcus, superior parietal sulcus, transverse parietal sulcus, paroccipital sulcus, and transverse occipital sulcus. Additionally, we analyzed neuroimaging data from 40 healthy young adults and two cadavers. Our investigation revealed that the original term intraparietal sulcus, introduced by Sir Turner, described a complex structure comprising the inferior segment of the postcentral sulcus, a horizontally extending component into the occipital lobe, and the transverse occipital sulcus. We also found that the superior parietal sulcus is often synonymous with transverse parietal sulcus, the sulcus of Brissaud is an eponym that shall describe the paroccipital sulcus’s dorsal parietal ramus, and the transverse occipital sulcus is the combination of the occipital rami of the paroccipital sulcus. Additionally, we identified an unnamed transverse segment of the intraparietal sulcus, the intraparietal sulcus–transverse. Based on these observations, we consider that the sulci of the lateral superior parietal lobule primarily include the intraparietal sulcus, with longitudinal and transverse segments, the transverse parietal sulcus of Brissaud, and the paroccipital sulcus of Wilder.
Emotional future simulations: neural and cognitive perspectives
Authors: Schacter Daniel L , Kalinowski Sarah E , Wilson Jenna M 
Published: October 2024

Abstract
LeDoux’s work on the emotional brain has had broad impact in neuroscience and psychology. Here, we discuss an aspect of the emotional brain that we have examined in our laboratory during the past two decades: emotional future simulations or constructed mental representations of positive and negative future experiences. Specifically, we consider research concerning (i) neural correlates of emotional future simulations, (ii) how emotional future simulations impact subsequent cognition and memory, (iii) the role of emotional future simulations in worry and anxiety, and (iv) individual differences in emotional future simulation related to narcissistic grandiosity. The intersection of emotion and future simulation is closely linked to some of LeDoux’s primary scientific concerns.