bluuebunny/crossref_metadata_2025 huggingface dataset:
Faster algorithms for the alignment of sparse correlated Erdős–Rényi random graphs
Authors: Muratori Andrea , Semerjian Guilhem
Published: November 2024

The correlated Erdős–Rényi random graph ensemble is a probability law on pairs of graphs with n vertices, parametrized by their average degree λ and their correlation coefficient s. It can be used as a benchmark for the graph alignment problem, in which the labels of the vertices of one of the graphs are reshuffled by an unknown permutation; the goal is to infer this permutation and thus properly match the pairs of vertices in both graphs. A series of recent works has unveiled the role of Otter’s constant α (that controls the exponential rate of growth of the number of unlabeled rooted trees as a function of their sizes) in this problem: for

s
>

α

and large enough λ, it is possible to recover in a time polynomial in n a positive fraction of the hidden permutation. The exponent of this polynomial growth is, however, quite large and depends on the other parameters, which limits the range of applications of the algorithm. In this work, we present a family of faster algorithms for this task, show through numerical simulations that their accuracy is only slightly reduced with respect to the original one and conjecture that they undergo, in the large λ limit, phase transitions at modified Otter’s thresholds

α
^

>

α

, with

α
^

related to the enumeration of a restricted family of trees.
Securing the State
Authors: O’Neill Ciaran
Published: November 2024

This chapter deals with the idea of the ‘security state’ and the ‘surveillance state’ in Union Ireland. It focuses on the infrastructures through which power ebbed and flowed. In 1810, Ireland had no real education system, no national police or welfare system, no truly national postal system, no asylum system, no railways, and no coordinated prison system. By 1850, Ireland had 4,321 schools, 538 miles of railways, 130 workhouses, 11 district asylums, and corresponding government departments and clerks charged with inspecting, maintaining, and coordinating them all. Drawing on work by Giorgio Agamben, this chapter seeks to understand the state that was built in these four decades or so.
The Ethnographic State
Authors: O’Neill Ciaran
Published: November 2024

This chapter examines state techniques of population and territory mapping, inspired by work on the ‘ethnographic state’. It focuses on a period of archive creation in the 1830s and then a reawakening of that ‘archival’ impulse towards the end of the nineteenth century, both within the state itself and in the civil sphere that buttressed it. In between these two points, it looks briefly at the ‘failure’ of the sympathetic relationship between the state and civil society in the 1840s and 1850s by analysing the Statistical Society in Dublin. By the 1890s, the production of coercive information had diffused, and Irish people were engaging in both colonial projects of racial production—racing others—and in the auto-exoticization of themselves: racing themselves.
Architectures of Containment and Contagion
Authors: O’Neill Ciaran
Published: November 2024

Drawing from Hannah Arendt, Michel Foucault, and Laura Doan, this chapter scrutinizes state practices of incarceration and reform. The Irish prison system provides a near-perfect demonstration of the thesis that Union Ireland continued to be governed by colonial logic in the first decades, and that this was being forcefully contested from the 1830s as part of a more integrative and assimilationist approach favoured by reform-minded liberals. The Irish penal systems have mostly been written about in domestic terms, with little connection to the imperial world it operated in and was in fact supplying. This chapter builds on Foucauldian analyses of the Irish prison system as well as major contributions to the Irish historiography by Richard Butler and Catherine Cox.
Conclusion—Killing Ireland with Kindness
Authors: O’Neill Ciaran
Published: November 2024

Returning to the theme of palliation, the conclusion examines the policies of ‘killing home rule with kindness’ in 1890s Ireland. It argues that these policies were a logical consequence of the palliative state’s evolution over the century. The idea of softer government, more amelioration, greater representation, and more diverse employment practices was promoted first by the Tory government and is often debated as ‘constructive unionism’. This was simply the logical outcome of the palliative approach outlined throughout the book. This concluding chapter looks back across the arc of the union and argues that the reliquary of the palliative state exists all around is in contemporary Ireland.
Divination in Roman Legal Measures
Authors: Janssen K P S
Published: November 2024

Chapter 2 focuses on the legal treatment of divination in the Roman world. It argues that measures dealing with this practice were not specially aimed at any particular divinatory method, like astrology, but were instead used to target a wider range of diviners. The chapter also discusses the prevalent idea that the overwhelming majority of interactions between the Roman authorities and those involved in divination found their legal basis in a long-lasting, empire-wide edict regulating divinatory enquiries that was supposedly issued by Augustus in 11 ce. Rather than following this line of thinking, however, it argues that this theory rests on shaky historical ground, and suggests that we are instead dealing with a much less cohesive collection of different kinds of legal measures, including expulsions of diviners as a group and trials against particular individuals, which were overwhelmingly local in nature, and furthermore were enforced for limited periods of time. The chapter also suggests that, while it is unlikely that involvement in private divination was systematically targeted, suspicious divinatory behaviour was frequently invoked among other accusations in trials related to the charge of maiestas, which contributed to the association between the practice, and the private practitioners involved in it, and societal disruption. Not until the third century do we see the gradual emergence of a coherent legal narrative on the subject in the works of the Roman jurists, although here, too, a notable variety in approaches continued to exist.
Indigenous Languages, Bilingualism, and Literacy in Hispania Citerior, Third Century bce–First Century ce
Authors: Moncunill Noemí
Published: November 2024

Hispania Citerior allows us to reconstruct the linguistic panorama prior to Latinization particularly well. Apart from the onomastic data that can be used to identify linguistic areas, this region also provides a substantial number of inscriptions in the different vernacular languages. This chapter exploits this rich epigraphic record, relating it to the development of Latin epigraphy in the area and to other relevant archaeological material, such as writing equipment, to analyse the evolution of local written culture, as well as language contact and bilingualism during the first centuries after the conquest. This approach aims to contribute to a better understanding of how and why most of the vernacular languages of Citerior were eventually replaced by Latin.
The Rise of Latin in Hispania Ulterior, Third Century bce–Second Century ce
Authors: Tolosa María José Estarán , Rando Javier Herrera
Published: November 2024

The chapter focuses on the southern and south-western regions of the Iberian Peninsula—namely, Republican Hispania Ulterior, which was later divided into the provinces of Baetica and Lusitania. These areas exhibit notable diversity: while some are highly urbanized and ‘Romanized’, others retain a more rural character and maintain a stronger indigenous influence. The limited number of epigraphic records from the Republican era is examined, with a special focus on those related to the local population, including coinage. From the time of Augustus onwards, written documentation increases significantly. However, while in Baetica this record reflects Roman customs, in Lusitania linguistic retention and bilingualism are evident, particularly in religious epigraphy. The factors that drove the process of Latinization, resulting in the spread of Latin as the dominant language, are identified, though the nature of the available evidence does not allow us to describe its regional variations.
The Languages and Epigraphies of Iron Age and Roman Gaul
Authors: Mullen Alex
Published: November 2024

To grasp the complexity of the languages and epigraphies of Gaul, this chapter takes an interdisciplinary and wide chronological perspective. The earliest epigraphic texts (sixth to second centuries bce) are in Greek, Iberian, Etruscan, and, later, Latin, and are relatively restricted in terms of spread, numbers, and functions. They nevertheless draw in some local communities and create the context for the adoption of the epichoric epigraphies. A reconstruction of the adoption and development of Gallo-Greek and Gallo-Latin underscores the importance of Mediterranean contacts, particularly with Italy, combined with local factors. The reflections of regionality and bilingualism, which become increasingly visible after the epigraphic boom beginning in the first century ce, reveal the complexity of cultural contacts and the persistence of local practices. We remodel the evidence for the obsolescence of Gaulish epigraphy and language, playing down the weight of the literary sources and playing up the evidence from Gallo-Latin epigraphy itself.
Writing Equipment and Latin Literacy in the Netherlands
Authors: Bruin Jasper de
Published: November 2024

Although an inventory of Roman writing equipment found at excavations in the Batavian area was published in 2006, a more comprehensive inventory of the occurrence of this group of literacy-related objects on a larger scale has not yet been carried out. In this chapter, an attempt is made to compile some of the new evidence, sometimes newly excavated, but also that found in many existing archaeological archives in the Netherlands. Despite representing only the tip of the iceberg in terms of actual numbers of writing implements that were present in Roman times, the evidence indicates that even the most remote settlements in the Netherlands came in contact with Latin writing. The question remains whether this contact indeed stimulated the mastery of the Latin language and the associated writing capabilities.
Languages and Literacies in Roman Britain
Authors: Mullen Alex
Published: November 2024

This chapter describes the languages, literacies, and identities across the variegated landscapes and communities of Britannia, using evidence and perspectives from multiple disciplines—primarily archaeological, historical, (socio)linguistic, and epigraphic. It begins with the advent of Latin and literacy, indicating in which Iron Age contexts these emerged, highlighting trade, immigration, diplomacy, and status as driving factors. Section 10.3 tackles the nature of Latinization, demonstrating regionality, and arguing that urban/rural divides are too simplistic. The story of regionality is continued through an exploration of the myriad Latins across time, place, and social groupings. Bilingualism was a factor in the creation of regional varieties, and the traces of its existence are discussed. Given that British Celtic still appears to have been widely spoken in some contexts at the end of Roman rule, consideration is finally given to the strikingly few possible examples of its written expression in the imperial period.
Intermezzo
Authors: Woolf Greg
Published: November 2024

This collection describes, with an unprecedented level of chronological and regional precision, the processes through which Latin language and Roman writing practices were taken up and became dominant throughout the north-western provinces. By giving as much attention to mobile texts and writing equipment as to lapidary inscriptions, it invites us to contextualize these changes within the Roman Object Revolution, and to think of the collective agency of texts in motion. It is clearer than ever that the Latinization of the north-west came about through a variety of convergent routes and practices. It also sets the agenda for studies of parallel processes throughout the Empire.
Setting the Scene
Authors: Whitehouse Deja
Published: November 2024

This chapter presents the social and cultural historical setting for the argument that Frieda Harris’s contribution in Aleister Crowley’s Book of Thoth far exceeded her perceived role as artist executant. Harris’s initial meeting with Crowley serves as a means to introduce their partnership and compare their societal backgrounds. Overviews of fin de si#x00E8;cle England, the British Occult Revival, Occult Tarot, and the specific involvement of women in esotericism are provided, with consideration to current commentary. Primary sources such as letters, diaries, transcripts of Crowley’s notes, etcetera, held in various archive collections, are identified, together with commentaries by Crowley’s and Harris’s contemporaries. Secondary sources are also discussed, and a book outline is provided.
Forensic Neuropsychological Foundations in Competency to Stand Trial Evaluations
Authors: Tussey Chriscelyn , Lacritz Megan , Arredondo Beth C , Marcopulos Bernice
Published: November 2024

Neuropsychological assessment can play a vital role in competency to stand trial (CST) evaluations. This article provides an overview of the brain and behavior-based conditions that may impact an individual’s ability to participate in their legal proceedings, as well as the relevant legal parameters that guide these types of forensic mental health evaluations. Circumstances that may warrant the involvement of a neuropsychologist in these evaluations are reviewed. For example, neuropsychologists’ expertise with validity testing, as well as their specialized knowledge of cognition, is useful from the onset of the evaluation through the end, where involved parties often want to know about restoration interventions and feasibility. Select neuropsychological testing measures and cultural considerations are also addressed. The article concludes with illustrative case examples that demonstrate the real-world application of neuropsychological involvement in this specific forensic context. Given the expanding opportunities for neuropsychologists to assist triers of fact, this work contributes to the necessary and developing education base for neuropsychologists who wish to provide informed, effective, and culturally sensitive CST evaluations or related consultation to the legal system.
A Précis of the Art and Science of Expert Witness Testimony: a Tribute to the Work and Ideas of Karen Postal
Authors: Hebben Nancy , Leritz Elizabeth
Published: November 2024

In this article, we present a summary of Dr. Karen Postal’s life’s work on communication in neuropsychological testimony. Her central thesis was that providing effective testimony as a neuropsychological expert requires one to step outside of the traditional academic communication style to which we are accustomed. In her books, The Art and Science of Expert Witness Testimony (2022) and Testimony that Sticks (2019), Karen Postal described foundational principles she called “disruptive shifts,” which she saw as the basis from which experts can develop credible and masterful testimony. These shifts begin with the fundamental and somewhat counterintuitive idea that the juror has the hardest job in the courtroom and it is our job as experts to create a direct, dynamic, and unique relationship with each juror. The article then focuses on ways to ensure jurors understand our testimony, including using good metaphors and analogies, showing visuals, avoiding jargon, and speaking in a way that conveys common sense. As Dr. Postal argued, following these principles will serve to establish, and ultimately bolster our credibility as experts with the people who have the most critical job in the courtroom. Finally, we discuss how these shifts can help us handle cross examination in a way that maintains the credibility we establish. The article concludes with a discussion of how mentorship, an incredibly important part of Dr. Postal’s work, is of utmost value when embarking in the field of forensic neuropsychology.
Neuropsychological Validity Assessment Beliefs and Practices: A Survey of North American Neuropsychologists and Validity Assessment Experts
Authors: Martin Phillip K , Schroeder Ryan W , Odland Anthony P
Published: November 2024

Objective

The present study sought to identify changes in neuropsychological validity assessment beliefs and practices relative to surveys of North American neuropsychologists conducted in 2015 and 2016, obtain a more nuanced understanding of such beliefs and practices, and examine salient validity assessment topics not addressed by previous surveys.

Methods

Adult focused neuropsychologists (n = 445) and neuropsychological validity assessment experts (n = 16) were surveyed regarding their perceptions and practices related to the following topics: (i) importance of validity testing; (ii) multiple performance validity test (PVT) administration and interpretation; (iii) suspected causes of invalidity; (iv) reporting on malingering; (v) assessment of examinees of diverse language, culture, and nation of origin; (vi) terminology; and (vii) most frequently utilized validity measures.

Results

There was general agreement, if not consensus, across multiple survey topics. The vast majority of neuropsychologists and experts view validity testing as mandatory in clinical and forensic evaluations, administer multiple PVTs regardless of setting, believe validity assessment to be important in the evaluation of all individuals including older adults and culturally diverse individuals, and view evaluations with few to no validity tests interspersed throughout the evaluation as being of lesser quality. Divergent opinions were also seen among respondents and between neuropsychologists and experts on some topics, including likely causes of invalidity and assessment and formal communication of malingering.

Conclusions

Current results highlight the necessity of formal validity assessment within both clinical and forensic neuropsychological evaluations, and findings document current trends and reported practices within the field.
The mathematical exploration for the mechanism of lung adenocarcinoma formation and progression
Authors: Han Yourui , Chen Bolin , Bi Zhongwen , Bian Jun , Kang Ruiming , Shang Xuequn
Published: November 2024

Lung adenocarcinoma, a prevalent subtype of lung cancer, represents one of the most lethal human malignancies. Despite substantial efforts to elucidate its biological underpinnings, the underlying mechanisms governing lung adenocarcinoma remain enigmatic. Modeling and comprehending the dynamics of gene regulatory networks are crucial for unraveling the fundamental mechanisms of lung adenocarcinoma. Conventionally, the cancer is modeled as an equilibrium process based on a time-invariant gene regulatory network to investigate stable cell states. However, the cancer is a nonequilibrium process and the gene regulatory network should be regarded as time-varying in actual. Therefore, a feasible framework was developed to explore the formation and progression of lung adenocarcinoma. On the one hand, to delve into the underlying mechanisms of lung adenocarcinoma formation, the time-invariant gene regulatory network for lung adenocarcinoma was initially undertaken, and the composition of stable cell states was elucidated based on landscape theory. Furthermore, the plasticity of different states was quantified using energy landscape decomposition theory by incorporating cell proliferation. And transition probabilities between different states were defined to elucidate the transition between stable cell states. Additionally, the global sensitivity analysis was performed and a total of three genes and three regulations were identified to be more critical for the formation lung adenocarcinoma, offering a novel strategy for designing network-based therapies for its treatment. On the other hand, the time-invariant gene regulatory network is extended as time-varying to delve into the underlying mechanisms of lung adenocarcinoma progression. The lung adenocarcinoma progression was characterized as four different disease stages based on the mixed states of cell population and the evolutionary direction. And the progressionary mechanism of transition between stages was expounded by evaluating their dynamical transport, with the dynamical transport cost between different stages quantified using Wasserstein metrics.
A metagene based similarity network fusion approach for multi-omics data integration identified novel subtypes in renal cell carcinoma
Authors: Jia Congcong , Wang Tong , Cui Dingtong , Tian Yaxin , Liu Gaiqin , Xu Zhaoyang , Luo Yanhong , Fang Ruiling , Yu Hongmei , Zhang Yanbo , Cui Yuehua , Cao Hongyan
Published: November 2024

Renal cell carcinoma (RCC) ranks among the most prevalent cancers worldwide, with both incidence and mortality rates increasing annually. The heterogeneity among RCC patients presents considerable challenges for developing universally effective treatment strategies, emphasizing the necessity of in-depth research into RCC’s molecular mechanisms, understanding the variations among RCC patients and further identifying distinct molecular subtypes for precise treatment. We proposed a metagene-based similarity network fusion (Meta-SNF) method for RCC subtype identification with multi-omics data, using a non-negative matrix factorization technique to capture alternative structures inherent in the dataset as metagenes. These latent metagenes were then integrated to construct a fused network under the Similarity Network Fusion (SNF) framework for more precise subtyping. We conducted simulation studies and analyzed real-world data from two RCC datasets, namely kidney renal clear cell carcinoma (KIRC) and kidney renal papillary cell carcinoma (KIRP) to demonstrate the utility of Meta-SNF. The simulation studies indicated that Meta-SNF achieved higher accuracy in subtype identification compared with the original SNF and other state-of-the-art methods. In analyses of real data, Meta-SNF produced more distinct and well-separated clusters, classifying both KIRC and KIRP into four subtypes with significant differences in survival outcomes. Subsequently, we performed comprehensive bioinformatics analyses focused on subtypes with poor prognoses in KIRC and KIRP and identified several potential biomarkers. Meta-SNF offers a novel strategy for subtype identification using multi-omics data, and its application to RCC datasets has yielded diverse biological insights which are highly valuable for informing clinical decision-making processes in the treatment of RCC.
CSPG4 involvement in endometrial decidualization contributes to the pathogenesis of preeclampsia
Authors: Zhang Tianying , Li Hua , Jiang Enhui , Zhang Liang , Liu Lisheng , Zhang Cong
Published: November 2024

Preeclampsia (PE) is a condition of pregnancy in which symptoms of hypertension develop after 20 weeks of gestation. it can lead to placental dysfunction, maternal and perinatal mortality and morbidity. The incidence of PE is increasing, posing a serious threat to the lives of pregnant women and their unborn children. Currently, most of the research on the pathogenesis of PE has focused on placenta, However, maternal decidualization is the basis for placental formation and growth. Chondroitin sulfate proteoglycan 4 (CSPG4) is a transmembrane protein that plays a role in cell proliferation, invasion, and migration. However, its function during decidualization is not yet understood. In this study, we investigated the role of CSPG4 and found that its expression was significantly down-regulated in the decidual tissue of patients with severe PE compared to normal pregnant women. During artificially induced decidualization, CSPG4 expression was significantly increased. Knockdown of CSPG4 by small interfering RNA inhibited decidualization, which, in turn, inhibited the invasion of trophoblast cells. In both pseudopregnant and pregnant mice, endometrial stromal cells proliferated rapidly and Cspg4 expression increased during decidualization. Therefore, we believe that CSPG4 plays a crucial role in the process of decidualization. The defect in decidualization caused by abnormal CSPG4 expression could lead to insufficient trophoblast invasion, ultimately contributing to the occurrence of PE.
MRI-based whole-brain elastography and volumetric measurements to predict brain age
Authors: Claros-Olivares Claudio Cesar , Clements Rebecca G , McIlvain Grace , Johnson Curtis L , Brockmeier Austin J
Published: November 2024

Brain age, as a correlate of an individual’s chronological age obtained from structural and functional neuroimaging data, enables assessing developmental or neurodegenerative pathology relative to the overall population. Accurately inferring brain age from brain magnetic resonance imaging (MRI) data requires imaging methods sensitive to tissue health and sophisticated statistical models to identify the underlying age-related brain changes. Magnetic resonance elastography (MRE) is a specialized MRI technique which has emerged as a reliable, non-invasive method to measure the brain’s mechanical properties, such as the viscoelastic shear stiffness and damping ratio. These mechanical properties have been shown to change across the life span, reflect neurodegenerative diseases, and are associated with individual differences in cognitive function. Here, we aim to develop a machine learning framework to accurately predict a healthy individual’s chronological age from maps of brain mechanical properties. This framework can later be applied to understand neurostructural deviations from normal in individuals with neurodevelopmental or neurodegenerative conditions. Using 3D convolutional networks as deep learning models and more traditional statistical models, we relate chronological age as a function of multiple modalities of whole-brain measurements: stiffness, damping ratio, and volume. Evaluations on held-out subjects show that combining stiffness and volume in a multimodal approach achieves the most accurate predictions. Interpretation of the different models highlights important regions that are distinct between the modalities. The results demonstrate the complementary value of MRE measurements in brain age models, which, in future studies, could improve model sensitivity to brain integrity differences in individuals with neuropathology.
Non-ketotic hyperglycaemia-induced hemichorea-hemiballism may represent glioma-like pattern on multimodal magnetic resonance imaging: can 1H spectroscopy help in the differentiation?
Authors: Lin Yu , Zhang Xiaoxiao , Yue Xin , Wang Jinan
Published: November 2024

Non-ketotic hyperglycaemia (NKH)-induced hemichorea-hemiballismus (HC-HB) is an infrequent reversible condition observed in individuals with poorly controlled diabetes. In this report, we present a case of NKH-induced HC-HB exhibiting distinctive morphological and functional alterations on conventional magnetic resonance imaging (MRI), diffusion-weighted imaging (DWI), and 1H magnetic resonance spectroscopy (MRS), followed by subsequent monitoring. A 70-year-old male with a 20-year history of diabetes presented with severe unilateral involuntary movement. Computer tomography revealed heightened attenuation in the left putamen and caudate nucleus. The conventional MRI revealed the presence of focal T2-hyperintensity, noticeable mass effect, and ring-like enhancement, which are indicative of glioma. Additionally, the DWI showed unrestricted diffusion of water molecules within the lesion. MRS analysis further demonstrated significantly elevated lactate (Lac) and lipids (Lip), minimal increased choline (Cho), basically stable creatine (Cr), and modest decreased N-acetylaspartate (NAA) levels (which remained larger than both Cho and Cr peaks), leading to a diagnosis of NKH-induced HC-HB. This report emphasizes the significance of acknowledging that NKH-induced HC-HB can manifest with imaging features that bear resemblance to those of glioma. The presence of a slightly elevated Cho/NAA ratio alongside a notable increase in Lac/Lip peak on MRS may aid in ruling out neoplastic conditions.
Examining threat responses through a developmental lens
Authors: Casey B J , Lin Yen-Chu , Meyer Heidi C
Published: November 2024

Adolescence has been characterized by risk taking and fearlessness. Yet, the emergence of anxiety disorders that are associated with fear peaks during this developmental period. Moreover, adolescents show heightened sensitivity to stress relative to children and adults. To address inconsistencies between the common characterization of adolescents as fearless and the evidence of heightened anxiety and stress during this time, we build upon foundational discoveries of threat-related circuitry and behavior in adult rodents by Joseph LeDoux and colleagues. Specifically, the conservation of this circuitry across species has provided opportunities for identifying mechanisms underlying threat responses that we have extended to developing humans and rodents. We elucidate situations in which adolescents show heightened threat responses and others where they appear fearless and link them to developmental changes of threat circuitry during this period. We discuss the potential adaptiveness of these threat responses for survival of the individual and species but also the potential risks for anxiety and stress. We end by offering potential new ways in which behavioral treatments for youth with anxiety and stress-related disorders may be optimized to target the developing vs developed brain.
Oxyamination of alkenes enabled by direct photoexcitation of fluorenone oxime derivatives
Authors: Tagata Asa , Sawamura Masaya , Shimizu Yohei
Published: November 2024

Visible-light-induced oxyamination of alkenes was developed using fluorenone oxime carbonate as a photoactivatable agent. The nitrogen atom was selectively incorporated at the internal position, constructing a sterically congested α-tertiary amine moiety. The reaction proceeded without any photocatalyst and in the presence of various additives with different functional groups, highlighting the simplicity and robustness of the protocol. Moreover, the fluorenone oxime motif proved effective for visible-light-induced decarboxylative carboamination and diamination of alkenes.
Liver manifestations in autosomal dominant polycystic kidney disease (ADPKD) and their impact on quality of life
Authors: Arjune Sita , Todorova Polina , Bartram Malte P , Grundmann Franziska , Müller Roman-Ulrich
Published: November 2024

Background

ADPKD is the most prevalent monogenic kidney disease with an estimated incidence of 1:1000. The condition is characterized by the formation of kidney cysts, which can cause kidney function loss and bear a significant risk of advancing to kidney failure. This study examined the prevalence of hepatic cysts in individuals with ADPKD, and the possible influence of these cysts on liver function and quality of life. Furthermore, the relationship between hepatic cysts and genotype was analysed.

Methods

Clinical data from 880 patients with ADPKD were analysed, including longitudinal patient data, genetic information, and laboratory parameters.

Results

The prevalence of hepatic cysts in adult ADPKD patients was 81.71%, consistent with previous studies. Prevalence increased with age, particularly in male patients. No clear association was observed between ADPKD genotype and the presence of liver cysts. Among male patients with liver cysts, glutamate pyruvate transaminase (GPT) levels significantly decreased with age, while female patients showed a significant increase in gamma-glutamyl transferase (γ-GT) levels. Overall, hepatic cysts had minimal impact on liver enzymes. Quality of life assessments using the SF-12 questionnaire revealed no significant influence of hepatic cysts on physical or mental well-being. However, physical quality of life was significantly lower in patients showing polycystic liver disease as a manifestation of ADPKD compared to all other patients, both with and without liver cysts.

Conclusions

Hepatic cysts are highly prevalent in adult patients with ADPKD, increasing with age. ADPKD genotype does not appear to be associated with the presence of hepatic cysts. Liver function, as indicated by enzyme levels, is minimally affected by hepatic cysts in most ADPKD patients. The quality of life of ADPKD patients is generally unaffected by the presence of hepatic cysts, except in severe cases of polycystic liver disease (PLD). Further research is needed to develop effective treatments for severe PLD and gain a better understanding of the factors influencing hepatic cyst incidence and progression in patients with ADPKD.
Factors influencing early response of IgA nephropathy following targeted-release budesonide (TRB) treatment: preliminary results from a multicenter study
Authors: Keskinis Christodoulos , Moysidou Eleni , Kapsia Eleni , Vaios Vasilios , Bintas Christos , Trivyza Maria , Christodoulou Michalis , Lioulios Georgios , Stai Stamatia , Nikolaidou Christina , Pateinakis Panagiotis , Papasotiriou Marios , Liakopoulos Vassilios , Marinaki Smaragdi , Stangou Maria
Published: November 2024

Background

Formation of galactose-deficient IgA1 (Gd-IgA1) immunoglobulin is the initial step in the immunological cascade leading to IgA nephropathy (IgAN). Targeted-release budesonide (TRB), an evidence-based regimen without major side-effects, has recently been approved for IgAN treatment; herein we present our preliminary real-world data regarding prompt response to TRB.

Methods

Patients with primary IgAN who remained with Uprot >1 g/24 h despite conventional treatment for 6 months were started on TRB, and re-evaluated at 3 (T3) and 6 (T6) months. Reduction of proteinuria by ≥30%, at T3 and T6 was regarded as very early (VER) and early response (ER), respectively. Kidney biopsies were evaluated according to Oxford classification (MEST-C) score.

Results

Thirty-seven IgAN patients, male/female 26/11, mean ± standard deviation age 50.38 ± 14.32 years and mean time since diagnosis 45.65 ± 56.67 months, were included. Seventeen (45.94%) patients demonstrated VER, increasing to 29 (78.3%) as ER (P = .004). Patients who demonstrated VER had a shorter time interval since diagnosis compared with non-VER, 29.41 ± 6.96 vs 65.37 ± 17.64 months (P = .05), and preserved estimated glomerular filtration rate at diagnosis and T0, while time since diagnosis was the main factor associated with ER, 38.36 ± 19.6 vs 78.67 ± 18.64 months, in ER and non-ER respectively (P = .05). Patients with M0, E0, S0 and T0 had no significant changes during T0–T6, while patients with M1, E1, S1 and even T1 had significantly reduced proteinuria (P = .006, P = .0011, P < .0001 and P < .0001, respectively).

Conclusions

Almost half of the patients showed proteinuria reduction after TRB treatment at 3 months, and the proportion increased significantly at 6 months. Patients likely to have a prompt proteinuria reduction were relatively close to diagnosis, retained kidney function and had active lesions in kidney biopsy.
Multiparametric MRI: can we assess renal function differently?
Authors: Tournebize Corentin , Schleef Maxime , De Mul Aurélie , Pacaud Sophie , Derain-Dubourg Laurence , Juillard Laurent , Rouvière Olivier , Lemoine Sandrine
Published: November 2024

We are lacking tools to evaluate renal performance. In this review, we presented the current knowledge and potential future applications in nephrology of new magnetic resonance imaging (MRI) techniques, focusing on diffusion-weighted (DWI) MRI, blood oxygen level-dependent (BOLD) MRI, and magnetic resonance relaxometry (T1 and T2 mapping). These sequences are sensitive to early changes in biological processes such as perfusion, oxygenation, edema, or fibrosis without requiring contrast medium injection and avoids irradiation and nephrotoxicity. Combining these different sequences into the so-called “multiparametric MRI” enables noninvasive, repeated exploration of renal performance on each kidney separately. DWI MRI, which evaluates the movement of water molecules, is a promising tool for noninvasive assessment of interstitial fibrosis and the cortical restricted diffusion has a prognostic value for the deterioration of renal function in diabetic nephropathy. BOLD MRI is sensitive to changes in renal tissue oxygenation based on the paramagnetic properties of deoxyhemoglobin and is of particular interest in the setting of renal artery stenosis to assess tissue oxygenation in the post-stenotic kidney. This sequence can be used for predicting degradation of renal function in chronic kidney diseases (CKD) and might be useful in preclinical studies to assess nephroprotective and nephrotoxic effects of drugs in development. T1 and T2 relaxation times change with tissue water content and might help assessing renal fibrosis. A corticomedullary dedifferentiation in T1 has been observed in CKD and negatively correlates with glomerular filtration rate. Data on the significance of T2 values in renal imaging is more limited. Multiparametric MRI has the potential to provide a better understanding of renal physiology and pathophysiology, a better characterization of renal lesions, an earlier and more sensitive detection of renal disease, and an aid to personalized patient-centered therapeutic decision-making. Further data and clinical trials are needed to allow its routine application in clinical practice.
Partial Enteral Nutrition in the Management of Crohn’s Disease: A Systematic Review and Meta-Analysis
Authors: Jatkowska Aleksandra , White Bernadette , Gkikas Konstantinos , Seenan John Paul , MacDonald Jonathan , Gerasimidis Konstantinos
Published: November 2024

Background

Exclusive enteral nutrition is an established treatment for active Crohn’s disease but the role of partial enteral nutrition (PEN) in the broader management of the disease is less clear. This systematic review and meta-analysis reviewed the literature on the role of PEN in Crohn’s disease management.

Methods

This review was conducted following Cochrane recommendations. The protocol was registered on PROSPERO. Findings were reported following the PRISMA guidelines.

Results

Sixty-four articles were identified, of which 11 reported data from randomized control trials. Good quality evidence suggests that PEN may be used as a maintenance and induction therapy, particularly at high dosages and/or alongside exclusion diets. A higher dosage of PEN is associated with a lower risk of subsequent disease relapse, with benefits observed at intakes above 35% of energy requirements (35%-50% PEN: OR [95% confidence intervals (CI)]: 0.42 [0.27-0.65]; > 50% PEN: OR [95% CI]: 0.27 [0.08-0.88]). Low-quality evidence suggests that postoperative use of PEN may prevent disease recurrence or enhance treatment outcomes when used as adjunct therapy to biologics. PEN can improve nutritional parameters, showing efficacy comparable to EEN in pediatric patients (weight: OR [95% CI]: −0.04 [−0.32, 0.25]). The effect of PEN on improving patients’ quality of life is comparable to that of EEN and anti-tumor necrosis factor alpha therapies.

Conclusions

Partial enteral nutrition may help in various aspects of Crohn’s disease management but much of the current evidence is of low quality. Well-designed randomized control trials are required to confirm findings from current literature and before clinical recommendations can be made.
Prognostic impact of mild renal dysfunction in patients undergoing valve surgery
Authors: Kim Kitae , Kim Taeksu , Yoon Sungsil , Kim Hong Rae , Kim Ho Jin , Kang Pil Je , Yoo Jae Suk , Jung Sung-Ho , Chung Cheol Hyun , Kim Joon Bum
Published: November 2024

OBJECTIVES

To analyse the impact of mild renal dysfunction on the prognosis of patients undergoing valve surgery.

METHODS

A total of 6210 consecutive patients (3238 women; mean age 59.2 ± 12.7 years) who underwent left-sided heart valve surgery between 2000 and 2022 were included in the study cohort. The primary outcome was all-cause death, and the secondary outcome was a composite of death, reoperation, stroke and heart failure. The restricted cubic spline function was utilized to investigate the association between estimated glomerular filtration rate and clinical outcomes, which was validated using inverse probability of treatment weighting-adjusted analysis.

RESULTS

Severities of baseline renal dysfunction were none in 1520 (24.5%), mild in 3557 (57.3%), moderate in 977 (15.7%), severe in 59 (1.0%) and end-stage in 97 (1.6%). Clinical outcomes varied significantly according to the degree of baseline renal dysfunction. The restricted cubic spline function curve showed a non-linear association, indicating that the significantly adverse effects of low estimated glomerular filtration rate on clinical outcomes were diminished in cases of mild renal dysfunction. This finding was corroborated by inverse probability of treatment weighting-adjusted analysis, and subgroup analyses did not show significant differences in clinical outcomes according to the presence of mild renal dysfunction (all-cause mortality, hazard ratio: 1.08; 95% confidence interval 0.90–1.28; P = 0.413; composite outcome, hazard ratio: 1.06; 95% confidence interval 0.92–1.21; P = 0.421).

CONCLUSIONS

In patients undergoing valve surgery, long-term clinical outcomes were significantly associated with the degree of baseline renal function impairment but not with the presence of mild renal dysfunction, demonstrating a non-linear association between baseline renal function and postoperative outcomes.
Nonobese young females with polycystic ovary syndrome are at high risk for long-term cardiovascular disease
Authors: Zhao Xingping , Wang Jie , Sun Dan , Xu Dabao , Lu Yao
Published: November 2024

Aims

Whether polycystic ovary syndrome (PCOS) is an independent risk factor for long-term cardiovascular disease (CVD) is unclear, and the risk of CVD in easily overlooked young nonobese PCOS patients is unknown. This study aimed to investigate the associations of PCOS with CVD and identify the management priorities.

Methods and results

Three thousand and eight hundred sixty-four participants (645 with PCOS) from UK Biobank were recruited from 2006 to 2010. The cumulative incidences of the CVD were calculated and compared between patients with and without PCOS via the log-rank test. Cox proportional risk regression models were used to assess the relationships of PCOS with CVD and the impact of PCOS treatments on CVD risk. Polygenic risk scores and linkage disequilibrium score regression were used to assess the genetic-level associations. Then, proteomics subgroup cohort was conducted to explore the significant biomarker involved in the PCOS–CVD associations. Compared with participants without PCOS, participants with PCOS had greater risks of CVD [hazard ratio (HR) = 1.77, 95% confidence interval (CI) = 1.19–2.65], coronary artery disease (HR = 2.27, 95% CI = 1.35–3.81), and myocardial infarction (HR = 2.08, 95% CI = 1.11–3.90) independent of genetic risk, especially for young nonobese PCOS patients (Pfor interaction < 0.05). Current commonly used treatments did not affect CVD incidence. Proteomics cohort revealed that discoidin, CUB, and LCCL domain-containing protein 2 (DCBLD2) may be specific CVD biomarker for patients with PCOS.

Conclusion

Patients with PCOS had an increased risk of CVD, and young nonobese PCOS patients should be prioritized for CVD risk management. These findings support the necessity of clinical surveillance and suggest DCBLD2 as a possible CVD biomarker in females with PCOS.
Environmental factors and potential probiotic lineages shape the active prokaryotic communities associated with healthy Penaeus stylirostris larvae and their rearing water
Authors: Giraud Carolane , Wabete Nelly , Lemeu Célia , Selmaoui-Folcher Nazha , Pham Dominique , Boulo Viviane , Callac Nolwenn
Published: November 2024

Microbial dysbiosis is hypothesized to cause larval mass mortalities in New Caledonian shrimp hatcheries. In order to confirm this hypothesis and allow further microbial comparisons, we studied the active prokaryotic communities of healthy Penaeus stylirostris larvae and their surrounding environment during the first 10 days of larval rearing. Using daily nutrient concentration quantitative analyses and spectrophotometric organic matter analyses, we highlighted a global eutrophication of the rearing environment. We also evidenced drastic bacterial community modifications in the water and the larvae samples using Illumina HiSeq sequencing of the V4 region of the 16S rRNA gene. We confirmed that Alteromonadales, Rhodobacterales, Flavobacteriales, Oceanospirillales, and Vibrionales members formed the core bacteriota of shrimp larvae. We also identified, in the water and the larvae samples, several potential probiotic bacterial strains that could lead to rethink probiotic use in aquaculture (AEGEAN 169 marine group, OM27 clade, Ruegeria, Leisingera, Pseudoalteromonas, and Roseobacter). Finally, investigating the existing correlations between the environmental factors and the major bacterial taxa of the water and the larvae samples, we suggested that deterministic and stochastic processes were involved in the assembly of prokaryotic communities during the larval rearing of P. stylirostris. Overall, our results showed that drastic changes mostly occurred during the zoea stages suggesting that this larval phase is crucial during shrimp larval development.
GenoTools: an open-source Python package for efficient genotype data quality control and analysis
Authors: Vitale Dan , Koretsky Mathew J , Kuznetsov Nicole , Hong Samantha , Martin Jessica , James Mikayla , Makarious Mary B , Leonard Hampton , Iwaki Hirotaka , Faghri Faraz , Blauwendraat Cornelis , Singleton Andrew B , Song Yeajin , Levine Kristin , Kumar-Sreelatha Ashwin Ashok , Fang Zih-Hua , Nalls Mike
Published: November 2024

GenoTools, a Python package, streamlines population genetics research by integrating ancestry estimation, quality control, and genome-wide association studies capabilities into efficient pipelines. By tracking samples, variants, and quality-specific measures throughout fully customizable pipelines, users can easily manage genetics data for large and small studies. GenoTools' “Ancestry” module renders highly accurate predictions, allowing for high-quality ancestry-specific studies, and enables custom ancestry model training and serialization specified to the user's genotyping or sequencing platform. As the genotype processing engine that powers several large initiatives, including the NIH's Center for Alzheimer's and Related Dementias and the Global Parkinson's Genetics Program, GenoTools was used to process and analyze the UK Biobank and major Alzheimer's disease and Parkinson's disease datasets with over 400,000 genotypes from arrays and 5,000 whole genome sequencing samples and has led to novel discoveries in diverse populations. It has provided replicable ancestry predictions, implemented rigorous quality control, and conducted genetic ancestry-specific genome-wide association studies to identify systematic errors or biases through a single command. GenoTools is a customizable tool that enables users to efficiently analyze and scale genotyping and sequencing (whole genome sequencing and exome) data with reproducible and scalable ancestry, quality control, and genome-wide association studies pipelines.