bluuebunny/crossref_metadata_2025_split huggingface dataset:
A rare clinical case of systemic AA amyloidosis with cardiac involvement complicating ankylosing spondylitis: a case report
Authors: Barakat Leïla , Echchilali Khadija , Moudatir Mina , El Kabli Hassan , Ettagmouti Yassine , Haboub Mériem , Arous Salim , Benouna Mohamed Ghali , Drighil Abdenasser , Habbal Rachida , Azim Meryame , Mazti Asmae , Regragui Meriem , Bennani Guebessi Nissrine , Karkouri Mehdi 
Published: March 2024

Abstract
Background
Ankylosing spondylitis (AS) is a type of chronic inflammation that is most prevalent in young adults and is characterized by an inflammatory enthesiopathy that gradually develops toward ossification and ankylosis. If inflammation is left unchecked, it can potentially lead to complications such as secondary amyloidosis, also known as AA amyloidosis, involving the deposition of amyloid serum A protein. Our case presents with a thyroid localization of AA amyloidosis which is secondary to this AS. Such a case has been described in only four cases in the literature. Cardiac localization of AA amyloidosis has been exceptionally described in the literature.

Case presentation
We report the case of a young patient with severe AS complicated by secondary amyloidosis with thyroid, cardiac, and probably renal localization. He was treated with anti-TNF therapy, and his condition improved significantly.

Conclusions
Our case presents several localizations of AA amyloidosis secondary to this AS. Although cardiac involvement is rare in secondary AA amyloidosis, it should always be screened for, even in a cardiacly asymptomatic patient.
Human Epidermal Growth Factor Receptor 2–Low Breast Cancer Brain Metastases: An Opportunity for Targeted Systemic Therapies in a High-Need Patient Population
Authors: Chehade Rania , Nofech-Mozes Sharon , Plotkin Anna , Fan Kevin Yijun , Das Sunit , Sahgal Arjun , Moravan Veronika , Jerzak Katarzyna Joanna 
Published: March 2024

PURPOSE Trastuzumab deruxtecan is a new treatment option for patients with advanced human epidermal growth factor receptor 2 (HER2)–low breast cancer (BC). Although HER2-low status has been characterized in early and advanced BC, it has yet to be fully characterized in brain metastases (BrM). METHODS Patients who underwent surgery for BC BrM at Sunnybrook Health Sciences Centre and for whom HER2 status was available on resected BrM were studied. Estrogen receptor, progesterone receptor, and HER2 status were assessed on the basis of ASCO/College of American Pathologists (CAP) guidelines. HER2-zero was defined as immunohistochemistry (IHC) 0; HER2-low was defined as IHC 1+ or IHC 2+ with fluorescence in situ hybridization (FISH)–negative status. HER2-positive (HER2+) was defined as IHC 3+ or IHC 2+ with positive FISH. Clinicopathologic features were recorded. We also assessed the prognostic association between extent of HER2 expression and (1) brain-specific progression-free survival (bsPFS), as well as (2) overall survival (OS). RESULTS In this retrospective cohort of 102 patients with resected BC BrM, 53% (n = 54) were HER2+, 29.4% (n = 30) were HER2-low, and 17.6% (n = 18) had HER2-zero status. Among BrM that were triple-negative on the basis of ASCO/CAP guidelines, 63.6% (n = 14/22) were reclassified as being HER2-low. Sixty percent (n = 15/25) of BrM that were hormone receptor–positive/HER2-negative (HR+/HER2–) were reclassified as being HER2-low. In total, 51 patients had matched primary breast and BrM tissue available; results of HER2 status when categorized as HER2-zero, HER2-low, and HER2+ were concordant in 82.3% (n = 42/51) of cases (Cohen's kappa, 0.58; P = .07). There was no significant association between HER2-zero, HER2-low, and HER2+ status in BrM and either bsPFS or OS. CONCLUSION Among patients with surgically resected BrM, a high proportion of those with metastatic triple-negative BC and HR+/HER2– disease have HER2-low BrM with potential to benefit from HER2-targeted therapy.
Comprehensive Immunogenomic Profiling of IDH1-/2-Altered Cholangiocarcinoma
Authors: Makawita Shalini , Lee Sunyoung , Kong Elisabeth , Kwong Lawrence N. , Abouelfetouh Zeyad , Danner De Armas Anaemy , Xiao Lianchun , Murugesan Karthikeyan , Danziger Natalie , Pavlick Dean , Korkut Anil , Ross Jeffrey S. , Javle Milind 
Published: March 2024

PURPOSE Isocitrate dehydrogenase ( IDH) 1/ 2 genomic alterations (GA) occur in 20% of intrahepatic cholangiocarcinoma (iCCA); however, the immunogenomic landscape of IDH1-/2-mutated iCCA is largely unknown. METHODS Comprehensive genomic profiling (CGP) was performed on 3,067 cases of advanced iCCA. Tumor mutational burden (TMB), PD-L1 expression (Dako 22C3), microsatellite instability (MSI), and genomic loss of heterozygosity (gLOH) as a surrogate marker for homologous recombination deficiency were examined. RNA sequencing of 73 patient samples was analyzed for differences in stromal/immune cell infiltration, immune marker expression, and T-cell inflammation. Tissue microarray arrays were subjected to multiplex immunohistochemistry and colocalization analysis in 100 surgical samples. Retrospective clinical data were collected for 501 patients with cholangiocarcinoma to examine median overall survival (mOS) in IDH1/2+ versus IDHwt. RESULTS Of 3,067 iCCA cases subjected to CGP, 426 (14%) were IDH1+ and 125 (4%) were IDH2+. IDH1 GA included R132C (69%) and R132L/G/S/H/F (16%/7%/4%/3%/<1%). IDH2 GA occurred at R172 (94.4%) and R140 (6.6%). No significant difference was seen in median gLOH between IDH1+ versus IDHwt iCCA ( P = .37), although patterns of comutations differed. MSI-High ( P = .009), TMB ≥10 mut/Mb ( P < .0001), and PD-L1 positivity were lower in IDH1/2+ versus IDHwt iCCA. Resting natural killer cell population, CD70, and programmed cell death 1 expression were significantly higher in non– IDH1-mutated cases, whereas V-set domain containing T-cell activation inhibitor 1 (B7-H4) expression was significantly higher in IDH1+. No significant difference in mOS was observed between IDH1/2+ versus IDHwt patients. CONCLUSION Significant differences in GA and immune biomarkers are noted between IDH1/ 2+ and IDHwt iCCA. IDH1-/2-mutated tumors appear immunologically cold without gLOH. These immunogenomic data provide insight for precision targeting of iCCA with IDH alterations.
Efficient genome editing using modified Cas9 proteins in zebrafish
Authors: Dorner Laura , Stratmann Benedikt , Bader Laura , Podobnik Marco , Irion Uwe 
Published: March 2024

ABSTRACT
The zebrafish (Danio rerio) is an important model organism for basic as well as applied bio-medical research. One main advantage is its genetic tractability, which was greatly enhanced by the introduction of the CRISPR/Cas method a decade ago. The generation of loss-of-function alleles via the production of small insertions or deletions in the coding sequences of genes with CRISPR/Cas systems is now routinely achieved with high efficiency. The method is based on the error prone repair of precisely targeted DNA double strand breaks by non-homologous end joining (NHEJ) in the cell nucleus. However, editing the genome with base pair precision, by homology-directed repair (HDR), is by far less efficient and therefore often requires large-scale screening of potential carriers by labour intensive genotyping. Here we confirm that the Cas9 protein variant SpRY, with relaxed PAM requirement, can be used to target some sites in the zebrafish genome. In addition, we demonstrate that the incorporation of an artificial nuclear localisation signal (aNLS) into the Cas9 protein variants not only enhances the efficiency of gene knockout but also the frequency of HDR, thereby facilitating the efficient modification of single base pairs in the genome. Our protocols provide a guide for a cost-effective generation of versatile and potent Cas9 protein variants and efficient gene editing in zebrafish.
Loss of UBE2S causes meiosis I arrest with normal spindle assembly checkpoint dynamics in mouse oocytes
Authors: Sun Si-Min , Zhao Bing-Wang , Li Yuan-Yuan , Liu Hong-Yang , Xu Yuan-Hong , Yang Xue-Mei , Guo Jia-Ni , Ouyang Ying-Chun , Weng Chang-Jiang , Guan Yi-Chun , Sun Qing-Yuan , Wang Zhen-Bo 
Published: March 2024

ABSTRACT
The timely degradation of proteins that regulate the cell cycle is essential for oocyte maturation. Oocytes are equipped to degrade proteins via the ubiquitin-proteasome system. In meiosis, anaphase promoting complex/cyclosome (APC/C), an E3 ubiquitin-ligase, is responsible for the degradation of proteins. Ubiquitin-conjugating enzyme E2 S (UBE2S), an E2 ubiquitin-conjugating enzyme, delivers ubiquitin to APC/C. APC/C has been extensively studied, but the functions of UBE2S in oocyte maturation and mouse fertility are not clear. In this study, we used Ube2s knockout mice to explore the role of UBE2S in mouse oocytes. Ube2s-deleted oocytes were characterized by meiosis I arrest with normal spindle assembly and spindle assembly checkpoint dynamics. However, the absence of UBE2S affected the activity of APC/C. Cyclin B1 and securin are two substrates of APC/C, and their levels were consistently high, resulting in the failure of homologous chromosome separation. Unexpectedly, the oocytes arrested in meiosis I could be fertilized and the embryos could become implanted normally, but died before embryonic day 10.5. In conclusion, our findings reveal an indispensable regulatory role of UBE2S in mouse oocyte meiosis and female fertility.
Elevation-dependent growth trends of Picea orientalis (L.) Peterm forests in the Fırtına Creek Basin (Rize/Turkey)
Authors: Işık Fatih , Bahadır Muhammet , Zeybek Halil İbrahim , Hatipoğlu İlter Kutlu 
Published: March 2024

Changes in climatic conditions have ecological and economic consequences or impact for trees and forest stands. In this respect, it is crucial to understand the radial growth trends of trees, their ecological response across elevation gradients, and the possible impacts of climate change on the species. In this study, Picea orientalis (L.) Peterm, located in the Fırtına Creek Basin in the northern part of the Eastern Black Sea Mountains in northeastern Turkey, was investigated along different elevation gradients in the context of climate-growth response. In the study, six site chronologies along an elevation gradient from 900 m to 2050 m were developed. Dendroclimatological methods were applied to assess the elevation-dependent radial growth characteristics of trees. In total, 200 increment cores were collected from 98 living trees. The relationships between climate and tree ring growth along the elevation gradient showed a positive relationship between growth and temperature at upper elevations (1700–1900 m) and a positive relationship between growth and precipitation at middle elevations (1400–1600 m). In particular, January–April mean temperatures and May rainfall were positively correlated with tree-ring growth. At lower elevations (900–1100 m), the correlation coefficients between climate and growth are insignificant because, at these altitudes, the species have optimum ecological conditions. It was also found that mean temperatures between 0 °C and 2 °C in January–April and total precipitation between 60 and 100 mm in January–February positively affect tree growth. However, if these thresholds are exceeded, it is possible that growth may be adversely affected. This research underscores the complex interplay between climate variables and tree growth along elevation gradients, highlighting the need for adaptive management strategies in the face of changing climatic conditions.
Path-Based Formulations for the Design of On-demand Multimodal Transit Systems with Adoption Awareness
Authors: Guan Hongzhao , Basciftci Beste , Van Hentenryck Pascal 
Published: March 2024

This paper reconsiders the On-Demand Multimodal Transit Systems (ODMTS) Design with Adoptions problem (ODMTS-DA) to capture the latent demand in on-demand multimodal transit systems. The ODMTS-DA is a bilevel optimization problem, for which Basciftci and Van Hentenryck proposed an exact combinatorial Benders decomposition. Unfortunately, their proposed algorithm only finds high-quality solutions for medium-sized cities and is not practical for large metropolitan areas. The main contribution of this paper is to propose a new path-based optimization model, called P-Path, to address these computational difficulties. The key idea underlying P-Path is to enumerate two specific sets of paths which capture the essence of the choice model associated with the adoption behavior of riders. With the help of these path sets, the ODMTS-DA can be formulated as a single-level mixed-integer programming model. In addition, the paper presents preprocessing techniques that can reduce the size of the model significantly. P-Path is evaluated on two comprehensive case studies: the midsize transit system of the Ann Arbor – Ypsilanti region in Michigan (which was studied by Basciftci and Van Hentenryck) and the large-scale transit system for the city of Atlanta. The experimental results show that P-Path solves the Michigan ODMTS-DA instances in a few minutes, bringing more than two orders of magnitude improvements compared with the existing approach. For Atlanta, the results show that P-Path can solve large-scale ODMTS-DA instances (about 17 millions variables and 37 millions constraints) optimally in a few hours or in a few days. These results show the tremendous computational benefits of P-Path which provides a scalable approach to the design of on-demand multimodal transit systems with latent demand. History: Accepted by Andrea Lodi, Area Editor for Design & Analysis of Algorithms—Discrete. Funding: This work was partially supported by National Science Foundation Leap-HI [Grant 1854684] and the Tier 1 University Transportation Center (UTC): Transit - Serving Communities Optimally, Responsively, and Efficiently (T-SCORE) from the U.S. Department of Transportation [69A3552047141]. Supplemental Material: The software that supports the findings of this study is available within the paper and its Supplemental Information ( https://pubsonline.informs.org/doi/suppl/10.1287/ijoc.2023.0014 ) as well as from the IJOC GitHub software repository ( https://github.com/INFORMSJoC/2023.0014 ). The complete IJOC Software and Data Repository is available at https://informsjoc.github.io/ .
Effect of Biodeterioration on Modeling Parameters of Code-Compliant Cross-Laminated Timber Lateral Connections
Authors: Morrell Ian , Udele Kenneth E. , Morrell Jeffrey J. , Sinha Arijit 
Published: March 2024

Abstract
The effect of biodeterioration on the structural connection performance of timber for conventional framing and mass timber has been investigated recently, but there is a need for additional data as well as for the development of analytical models to utilize these data. An empirical material model (seismic analysis of wood frame shear walls) was fitted to cyclic connection test data of four species of cross-laminated timber at different levels of biodeterioration by two brown-rot fungi. These model inputs were then analyzed to account for trends between wood species and fungal species. Weak trends were most prominent for initial stiffness, intercept load, and displacement at peak force. Correlations were poor with postyield and postpeak stiffness modifiers. These relationships were consistent both as a function of time and as a function of mass loss, but additional data are needed to more accurately predict the effects. The limited relationships likely reflect the variations in fungal decay across the test members.
Inclusion in an Interdisciplinary Leadership Training Program: Perspectives From Self-Advocates
Authors: Wayne Allison P. , Roach Andrew T. , LaMotte Krysta , Crenshaw Mark , Graybill Emily 
Published: March 2024

Abstract
Leadership Education in Neurodevelopmental and Related Disabilities (LEND) programs are interdisciplinary, graduate-level training programs that seek to promote improved outcomes for individuals with disabilities and their families. Many of these programs include individuals with disabilities as members of the self-advocacy discipline. In this study, 10 self-advocate trainees were interviewed to provide insight into the value of including self-advocates in training and the kinds of accommodations and supports that facilitated their success and inclusion. Interviewees endorsed the importance of including self-advocates in LEND programs. Although several accommodations were discussed as helpful, interpersonal supports from faculty and peers were equally important in ensuring their success and inclusion in LEND. The findings from this study provide support for the expansion of self-advocacy as a formal discipline in LEND programs.
Compact polarization transceiver module for fiber optic gyroscopes
Authors: Yu Xueke , Zhang Zuchen , Yu Wenqi , Zhang Shaobo 
Published: March 2024

This paper reports a transceiver module with a high polarization extinction ratio (PER) for the polarization-maintaining interferometric fiber optic gyroscope (PM-IFOG). This transceiver utilizes a graded-index lens featuring a slanted face coated with a multilayer film, enabling simultaneous collimation and beam splitting. Configurations of the graded-index splitter lens and the corresponding transceiver module are simulated and designed using the ray matrix method and physical optical propagation. The optical loss of the transceiver module is about 3.77 dB, and the PER exceeds 25 dB. The IFOG prototype is implemented by integrating the transceiver module with a PM sensing coil. The bias instability of the IFOG prototype is evaluated to be 0.51°/h by Allan variance. This research contributes to the reduction in size, weight, power consumption, and cost of PM-IFOG systems.
Selbstbestimmte Identitäten im E-Commerce:
Authors: Braun Simone , Sauer Max , Sürmeli Jan , Thessen Jonas 
Published: March 2024

ZusammenfassungDer Online-Handel verzeichnet seit Jahren ein stetiges Wachstum. Durch die
COVID-19-Pandemie kaufen nun auch Nutzende, die zuvor physische Kanäle bevorzugten,
vermehrt online ein. Der Anbietererfolg hängt dabei wesentlich von der Kenntnis über die
Kund*innen ab. Allerdings dominieren einige große Anbieter den Markt, während kleinere
Online-Shops Schwierigkeiten haben, ihre Angebote zu personalisieren. Eine Lösung bietet
der Ansatz selbstbestimmter Identitäten. Dieser ermöglicht Kund*innen, ihre eigenen
Shoppingdaten zu kontrollieren und sie selektiv mit Online-Shops zu teilen. Dadurch
können individuelle Wünsche und Anforderungen der Kund*innen in Online-Shops
berücksichtigt und ein personalisiertes Angebot sowie eine gute Nutzungserfahrung
geboten werden. Trotz des großen Potenzials selbstbestimmter Identitäten ist der Ansatz
in Deutschland kaum verbreitet. Dieser Beitrag beleuchtet den Einsatz selbstbestimmter
Identitäten im Online-Handel. Mithilfe eines menschenzentrierten Gestaltungsprozesses
wurden Personas und Ist-Szenarien erstellt, sowie daraus resultierend Anforderungen
erhoben und Potenziale identifiziert. Auf Basis dessen konnte ein Daten- und
Architekturmodell zur Integration von selbstbestimmten Identitäten im Online-Handel
entwickelt werden.
Efficacy and safety of biologic agents for IgA nephropathy: A protocol for systematic review and meta-analysis
Authors: Ma Jia , Xing Jianyue , Zhang Yupeng , Liu Guangzhen 
Published: March 2024

Background
IgA nephropathy (IgAN) is the most prevalent primary glomerulonephritis worldwide and a leading cause of chronic kidney failure. There are currently no definitive therapeutic regimens to treat or prevent the progression of IgAN. However, biologic agents offer novel therapeutic approaches that target immunological mechanisms to slow or halt disease progression. The objective of this study is to evaluate the efficacy and safety of biologic agents in patients with IgA nephropathy.

Methods
We will systematically search PubMed, EMbase, Web of Science, Cochrane Library, and www.clinicaltrials.gov for randomized controlled trials of biologic agents for the treatment of IgA nephropathy. The search period will span from the establishment of each database until October 2023. The quality assessment of included studies will be performed individually using the revised Cochrane risk-of-bias tool for randomized trials (RoB 2), and meta-analysis will be conducted using Revman 5.4.1 software.

Conclusions
The results of this study will provide evidence-based medical evidence for the clinical application of biologic agents in patients with IgA nephropathy.

Prospero registration number
CRD42023400450.
Enhanced amygdala–anterior cingulate white matter structural connectivity in Sahaja Yoga Meditators
Authors: Perez-Diaz Oscar , Góngora Daylín , González-Mora José L. , Rubia Katya , Barrós-Loscertales Alfonso , Hernández Sergio Elías 
Published: March 2024

Objective
To study the white matter connections between anterior cingulate cortex, anterior insula and amygdala as key regions of the frontal-limbic network that have been related to meditation.

Design
Twenty experienced practitioners of Sahaja Yoga Meditation and twenty nonmeditators matched on age, gender and education level, were scanned using Diffusion Weighted Imaging, using a 3T scanner, and their white matter connectivity was compared using diffusion tensor imaging analyses.

Results
There were five white matter fiber paths in which meditators showed a larger number of tracts, two of them connecting the same area in both hemispheres: the left and right amygdalae and the left and right anterior insula; and the other three connecting left anterior cingulate with the right anterior insula, the right amygdala and the left amygdala. On the other hand, non-meditators showed larger number of tracts in two paths connecting the left anterior insula with the left amygdala, and the left anterior insula with the left anterior cingulate.

Conclusions
The study shows that long-term practice of Sahaja Yoga Meditation is associated with larger white matter tracts strengthening interhemispheric connections between limbic regions and connections between cingulo-amygdalar and cingulo-insular brain regions related to top-down attentional and emotional processes as well as between top-down control functions that could potentially be related to the witness state perceived through the state of mental silence promoted with this meditation. On the other hand, reduced connectivity strength in left anterior insula in the meditation group could be associated to reduced emotional processing affecting top-down processes.
Somatic Mutational Analysis in Endoscopic Ultrasound–Guided Biopsy of Pancreatic Adenocarcinoma: Assessing Yield and Impact
Authors: Dong Sue , Agarunov Emil , Fasullo Matthew , Kim Ki-Yoon , Khanna Lauren , Haber Gregory , Janec Eileen , Simeone Diane , Oberstein Paul , Gonda Tamas 
Published: March 2024

INTRODUCTION:
We sought to determine the yield of somatic mutational analysis from endoscopic ultrasound (EUS)-guided biopsies of pancreatic adenocarcinoma compared with that of surgical resection and to assess the impact of these results on oncologic treatment.

METHODS:
We determined the yield of EUS sampling and surgical resection. We evaluated the potential impact of mutational analysis by identifying actionable mutations and its direct impact by reviewing actual treatment decisions.

RESULTS:
Yield of EUS sampling was 89.5%, comparable with the 95.8% yield of surgical resection. More than a quarter in the EUS cohort carried actionable mutations, and of these, more than 1 in 6 had treatment impacted by mutational analysis.

DISCUSSION:
EUS sampling is nearly always adequate for somatic testing and may have substantial potential and real impact on treatment decisions.