bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing individual variability of the entorhinal subfields in health and disease
Authors: Oltmer Jan , Greve Douglas N. , Cerri Stefano , Slepneva Natalya , Llamas‐Rodríguez Josue , Iglesias Juan Eugenio , Van Leemput Koen , Champion Samantha N. , Frosch Matthew P. , Augustinack Jean C. 
Published: September 2023

AbstractInvestigating interindividual variability is a major field of interest in neuroscience. The entorhinal cortex (EC) is essential for memory and affected early in the progression of Alzheimer's disease (AD). We combined histology ground‐truth data with ultrahigh‐resolution 7T ex vivo MRI to analyze EC interindividual variability in 3D. Further, we characterized (1) entorhinal shape as a whole, (2) entorhinal subfield range and midpoints, and (3) subfield architectural location and tau burden derived from 3D probability maps. Our results indicated that EC shape varied but was not related to demographic or disease factors at this preclinical stage. The medial intermediate subfield showed the highest degree of location variability in the probability maps. However, individual subfields did not display the same level of variability across dimensions and outcome measure, each providing a different perspective. For example, the olfactory subfield showed low variability in midpoint location in the superior–inferior dimension but high variability in anterior–posterior, and the subfield entorhinal intermediate showed a large variability in volumetric measures but a low variability in location derived from the 3D probability maps. These findings suggest that interindividual variability within the entorhinal subfields requires a 3D approach incorporating multiple outcome measures. This study provides 3D probability maps of the individual entorhinal subfields and respective tau pathology in the preclinical stage (Braak I and II) of AD. These probability maps illustrate the subfield average and may serve as a checkpoint for future modeling.
A comprehensive modeling approach for the task mapping problem in heterogeneous systems with dataflow processing units
Authors: Wilhelm Martin , Geppert Hanna , Drewes Anna , Pionteck Thilo 
Published: September 2023

SummaryWe introduce a new model for the task mapping problem to aid in the systematic design of algorithms for heterogeneous systems including, but not limited to, CPUs, GPUs, and FPGAs. A special focus is set on the communication between the devices, its influence on parallel execution, as well as on device‐specific differences regarding parallelizability and streamability. We give a comprehensive description on how a given task mapping can be abstractly evaluated including mappings to dataflow‐based hardware accelerators. We show how this model can be utilized in different system design phases and present two novel mixed‐integer linear programs to demonstrate the usage of the model, showing significant improvements compared to pure CPU mapping for randomly generated task graphs. To the best of our knowledge, we present the first ILP for task mapping that considers pipelining effects when streaming tasks on an FPGA.
A Primer for Research Scientists on Assessing Mouse Gross and Histopathology Images in the Biomedical Literature
Authors: Gifford Andrew J. 
Published: September 2023

AbstractAdvances in genomic technologies have enabled the development of abundant mouse models of human disease, requiring accurate phenotyping to elucidate the consequences of genetic manipulation. Anatomic pathology, an important component of the mouse phenotyping pipeline, is ideally performed by human or veterinary pathologists; however, due to insufficient numbers of pathologists qualified to assess these mouse models morphologically, research scientists may perform “do‐it‐yourself” pathology, resulting in diagnostic error. In the biomedical literature, pathology data is commonly presented as images of tissue sections, stained with either hematoxylin and eosin or antibodies via immunohistochemistry, accompanied by a figure legend. Data presented in such images and figure legends may contain inaccuracies. Furthermore, there is limited guidance for non‐pathologist research scientists concerning the elements required in an ideal pathology image and figure legend in a research publication. In this overview, the components of an ideal pathology image and figure legend are outlined and comprise image quality, image composition, and image interpretation. Background knowledge is important for producing accurate pathology images and critically assessing these images in the literature. This foundational knowledge includes understanding relevant human and mouse anatomy and histology and, for cancer researchers, an understanding of human and mouse tumor classification and morphology, mouse stain background lesions, and tissue processing artifacts. Accurate interpretation of immunohistochemistry is also vitally important and is detailed with emphasis on the requirement for tissue controls and the distribution, intensity, and intracellular location of staining. Common pitfalls in immunohistochemistry interpretation are outlined, and a checklist of questions is provided by which any pathology image may be critically examined. Collaboration with pathologist colleagues is encouraged. This overview aims to equip researchers to critically assess the quality and accuracy of pathology images in the literature to improve the reliability and reproducibility of published pathology data. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.
Autoimmune uveitis in Behçet's disease and Vogt‐Koyanagi‐Harada disease differ in tissue immune infiltration and T cell clonality
Authors: Kang Hao , Sun Hongjian , Yang Yang , Tuong Zewen K , Shu Minglei , Wei Yunbo , Zhang Yu , Yu Di , Tao Yong 
Published: September 2023

AbstractObjectivesNon‐infectious uveitis is often secondary to systemic autoimmune diseases, with Behçet's disease (BD) and Vogt‐Koyanagi‐Harada disease (VKHD) as the two most common causes. Uveitis in BD and VKHD can show similar clinical manifestations, but the underlying immunopathogenesis remains unclear.MethodsTo understand immune landscapes in inflammatory eye tissues, we performed single‐cell RNA paired with T cell receptor (TCR) sequencing of immune cell infiltrates in aqueous humour from six patients with BD (N = 3) and VKHD (N = 3) uveitis patients.ResultsAlthough T cells strongly infiltrated in both types of autoimmune uveitis, myeloid cells only significantly presented in BD uveitis but not in VKHD uveitis. Conversely, VKHD uveitis but not BD uveitis showed an overwhelming dominance by CD4+ T cells (> 80%) within the T cell population due to expansion of CD4+ T cell clusters with effector memory (Tem) phenotypes. Correspondingly, VKHD uveitis demonstrated a selective expansion of CD4+ T cell clones which were enriched in pro‐inflammatory Granzyme H+ CD4+ Tem cluster and showed TCR and Th1 pathway activation. In contrast, BD uveitis showed a preferential expansion of CD8+ T cell clones in pro‐inflammatory Granzyme H+ CD8+ Tem cluster, and pathway activation for cytoskeleton remodelling, cellular adhesion and cytotoxicity.ConclusionSingle‐cell analyses of ocular tissues reveal distinct landscapes of immune cell infiltration and T‐cell clonal expansions between VKHD and BD uveitis. Preferential involvements of pro‐inflammatory CD4+ Th1 cells in VKHD and cytotoxic CD8+ T cells in BD suggest a difference in disease immunopathogenesis and can guide precision disease management.
Challenges of clinical translation from single‐cell sequencing to measures in clinical biochemistry of haematology: Definition of immune cell identities
Authors: Liu Xuanqi , Wang Diane C. , Powell Charles A. , Wang Xiangdong 
Published: September 2023

AbstractPeripheral immune cells play important roles in the maintenance of systemic and microenvironmental hemostasis. Measurements of circulating blood cells by single‐cell RNA sequencing (scRNA‐seq) were proposed as one of the routine measures in clinical biochemistry of hematology. Out of translational challenges, defining precise identities of cell subsets and states is more difficult, due to the complexity of immune cell development, location, regulation, function, and metabolism. It is also a challenge to precisely interpret clinical significance and impact of each cell identity marker gene panel (ciMGPs). ciMGPs have potential to advance the understanding of systemic responses of the disease, identify disease‐specific biomarkers, and to define cell heterogeneity. Recently, a large number of peripheral cell subsets and expending/activating states have been identified and validated for use in the fast developments in clinical single cell biomedicine. Defining specificity, measurability, and repeatability of cell subsets/states is important for translation of peripheral scRNA‐seq in clinical hematology and biochemistry. The development of standard operating procedure and performance of clinical trials in large populations at various ages, diseases, and therapies will promote the clinical translation of ciMGPs to measures. Thus, defining cell subset/state identities will provide the multi‐dimensional and comprehensive readouts of systemic immune cells, the precision monitoring of immune dynamics, and deeper‐understanding of the disease and response to therapy.
The new 222‐nm far ultraviolet‐C lowers bacterial contamination to endoscopists during esophagogastroduodenoscopy
Authors: Fukutoku Yukari , Kikuchi Hidezumi , Hoshi Kentaro , Narita Kouji , Asari Taka , Miyazawa Kuniaki , Sawada Yohei , Hayamizu Shiro , Tatsuta Tetsuya , Oota Shinji , Hasui Keisuke , Hiraga Hiroto , Chinda Daisuke , Mikami Tatsuya , Subsomwong Phawinee , Asano Krisana , Yamane Kyosuke , Ogawa Yoshimasa , Sasaki Masahiro , Koi Toru , Ohashi Hiroyuki , Nakane Akio , Sakuraba Hirotake 
Published: September 2023

AbstractObjectivesThis study aimed to clarify the disinfectant efficacy of the 222‐nm far ultraviolet‐C (UV‐C) during esophagogastroduodenoscopy using bacterial cultures.MethodsThe endoscopists performed esophagogastroduodenoscopy wearing a gown with a tryptic soy agar medium plate on their epigastric region and were divided into two groups: 222‐nm far UV‐C irradiation (UV group) and non‐UV irradiation (non‐UV group). As a control group, tryptic soy agar medium plates were placed about 110 cm above the floor. The incidence of bacterial contamination was determined by positive bacterial culture. The cultured bacteria were identified by 16S rRNA sequencing. Additionally, the actual UV exposure dose was measured using the UV‐indicator card which changed colors upon exposure to 222 nm far UV‐C.ResultsThe bacterial culture positivity in the UV group (5.03%) was significantly lower than that in the non‐UV group (25.76%), p < 0.0001. Most of the bacteria identified in the UV and non‐UV groups were normal constituents of the oral flora, including Streptococcus salivarius and Staphylococci. Conversely, pathogenic microbes were found in the control group. The actual exposure doses of 222‐nm far UV‐C at the endoscopists’ face, neck, and epigastric region were 2.09 ± 0.29, 5.89 ± 0.49, and 7.36 ± 0.58 mJ/cm2, respectively.ConclusionsThe 222‐nm far UV‐C irradiation reduced bacterial contamination for endoscopists. It can be used with conventional physical coverings to provide more effective infection control.
Perforation of pancreatic pseudocyst diagnosed with endoscopy and treated with percutaneous drainage
Authors: Koseki Mako , Hashimoto Yusuke 
Published: September 2023

AbstractPerforation is a rare but fatal complication of pancreatic pseudocysts. It is generally diagnosed by computed tomography imaging with hemorrhagic ascites and pneumoperitoneum. Traditionally, surgery was the mainstream for treating this critical state. Recently, alternative therapies have also been deemed useful. Herein, we describe the case of a 54‐year‐old with perforation of pancreatic pseudocyst which was confirmed by endoscopy, and managed by endoscopic and percutaneous drainage. The patient was initially referred to our hospital for treatment of a pancreatic pseudocyst with hemorrhagic ascites and underwent endoscopic ultrasonographic‐guided stent placement. The next day, imaging demonstrated pneumoperitoneum and worsening ascites consistent with perforation, and the patient was treated conservatively. One week later, the patient developed severe abdominal pain. Endoscopy showed a large perforation site inside the pseudocyst connected to a large fluid collection and direct visualization inside the pseudocyst and fluid collection. The fluid collection was treated with percutaneous drainage, and the patient was discharged one week later with no complications.
Access to Electron‐Rich Dibenzofurans through NBu4OAc‐Mediated Palladium Catalysis
Authors: Power Mark , Mackey Katrina , Light Mark E. , Jones David J. , McGlacken Gerard P. 
Published: September 2023

AbstractDibenzofuran and its derivatives are ubiquitous and important medicinal and natural products. Many contain electron‐rich aryl rings. Forming the key intramolecular Ar−Ar bond using traditional cross‐coupling is difficult. The C−H functionalisation (C−H activation) approach is, in principle, far more useful. However, we previously found that the well‐established conditions, which promote C−H functionalisation through Concerted Metalation‐Deprotonation (CMD), proved unsatisfactory. Herein, we report a Pd‐catalysed C−H functionalisation protocol that works with electron‐rich arenes. We use tetrabutylammonium acetate (NBu4OAc), which we suspect can act as base, ligand and solvent, rendering this protocol a simple and efficient route to electron‐rich dibenzofurans.
Isotherm and kinetic studies for sorption of Cr(VI) onto Prosopis cineraria leaf powder: A comparison of linear and non‐linear regression analysis
Authors: Singh Mohini , Rayaz Mohd. , Arti R. 
Published: September 2023

AbstractThis research investigated the utilization of Prosopis cineraria leaf powder (PCLP) as biosorbent in the removal of Cr(VI) from aqueous solution. The maximum monolayer biosorption capacity of Cr(VI) onto PCLP after 2 h was 10.283 mg g−1 under optimum conditions: initial concentration 10 mg L−1, pH 5, dose 0.4 g L−1 and temperature at 293 K. For equilibrium modeling, two‐parameters (Langmuir, Freundlich, Temkin) and three parameters (Redlich‐Peterson, Sips and Toth) isotherm models were used to fit the equilibrium data. Kinetic modeling was performed using Lagergren pseudo‐first‐order, pseudo‐second‐order, Elovich, Weber‐Morris intraparticle diffusion, and Bangham's model. Both linear and nonlinear regression were compared coupled with several error functions to determine the best fit and model parameters were evaluated. The results revealed that nonlinear method best explain the experimental data revealing Temkin (R2 = 0.9938) and pseuso‐second‐order (R2 = 0.9935) models as the best‐fitted models with lower error functions. Therefore, the present investigation convinced that PCLP could be used as cost effective, efficient and eco‐friendly biosorbent to reduce Cr(VI) concentration in aqueous solution.
Abolition of seizures following Forel‐H‐tomy for drug‐resistant epilepsy: A case report
Authors: Horisawa Shiro , Miyao Satoru , Hori Tomokatsu , Kim Kilsoo , Kawamata Takakazu , Taira Takaomi 
Published: September 2023

AbstractA 62‐year‐old female experienced an extensive cerebral contusion in the left frontotemporal lobe due to an acute subdural hematoma at the age of 44 years. Six months after the injury, the patient developed epileptic seizures. The seizures were generalized with right cervical rotation and fencing posture. Despite prescriptions for four antiepileptic drugs, partial seizures occurred several times a month and focal to bilateral tonic‐clonic seizures once every 2 months. Video‐electroencephalography showed epileptic discharges in the left frontal lobe. The patient was subsequently referred to our department for palliative surgery. The patient underwent a left Forel‐H‐tomy. The prescription of antiepileptic drugs was not changed, and the patient was seizure free for 1 year. Forel‐H‐tomy, a surgical procedure for intractable epilepsy, was pioneered by Dennosuke Jinnai. Despite its previously reported remarkable efficacy, Forel‐H‐tomy has not been performed for several decades. Nevertheless, it remains a potential alternative treatment option for drug‐resistant epilepsy.
Accelerated solutions of convection‐dominated partial differential equations using implicit feature tracking and empirical quadrature
Authors: Mirhoseini Marzieh Alireza , Zahr Matthew J. 
Published: September 2023

SummaryThis work introduces an empirical quadrature‐based hyperreduction procedure and greedy training algorithm to effectively reduce the computational cost of solving convection‐dominated problems with limited training. The proposed approach circumvents the slowly decaying ‐width limitation of linear model reduction techniques applied to convection‐dominated problems by using a nonlinear approximation manifold systematically defined by composing a low‐dimensional affine space with bijections of the underlying domain. The reduced‐order model is defined as the solution of a residual minimization problem over the nonlinear manifold. An online‐efficient method is obtained by using empirical quadrature to approximate the optimality system such that it can be solved with mesh‐independent operations. The proposed reduced‐order model is trained using a greedy procedure to systematically sample the parameter domain. The effectiveness of the proposed approach is demonstrated on two shock‐dominated computational fluid dynamics benchmarks.
Cultural proximity and cross‐border banking flows
Authors: Thang Doan Ngoc 
Published: September 2023

AbstractThis paper disentangles the impacts of cultural proximity on cross‐border banking flows, using large country‐pair data from 1996 to 2019. On applying the gravity model with the Poisson Pseudo Maximum Likelihood estimator, our main findings show that cultural proximity is both a push and pull factor, which robustly anticipates increased outflows (cross‐border lending) and inflows (cross‐border borrowing). The impacts of cultural proximity are transmitted throughout the information asymmetry and cost reduction channels. These impacts become pronounced for geographically proximate country pairs and hold for a different measure of cultural goods taxonomy and for controlling the endogeneity problem.
Suitability of different reconstructed human skin models in the skin and liver Chip2 microphysiological model to investigate the kinetics and first‐pass skin metabolism of the hair dye, 4‐amino‐2‐hydroxytoluene
Authors: Brandmair Katrin , Tao Thi‐Phuong , Gerlach Silke , Przibilla Julia , Schepky Andreas , Marx Uwe , Hewitt Nicola J. , Kühnl Jochen , Maschmeyer Ilka 
Published: September 2023

AbstractThe HUMIMIC skin‐liver Chip2 microphysiological systems model using the epidermal model, EpiDerm™, was reported previously to mimic application route‐dependent metabolism of the hair dye, 4‐amino‐2‐hydroxytoluene (AHT). Therefore, we evaluated the use of alternative skin models—SkinEthic™, EpiDermFT™ and PhenionFT™—for the same purpose. In static incubations, AHT permeation was similar using SkinEthic™ and EpiDerm™ models. Older Day 21 (D21) SkinEthic™ models with a thicker stratum corneum did not exhibit a greater barrier to AHT (overall permeation was the same in D17 and D21 models). All epidermal models metabolised AHT, with the EpiDerm™ exhibiting higher N‐acetylation than SkinEthic™ models. AHT metabolism by D21 SkinEthic™ models was lower than that by D17 SkinEthic™ and EpiDerm™ models, thus a thicker stratum corneum was associated with fewer viable cells and a lower metabolic activity. AHT permeation was much slower using PhenionFT™ compared to epidermal models and better reflected permeation of AHT through native human skin. This model also extensively metabolised AHT to N‐acetyl‐AHT. After a single topical or systemic application of AHT to Chip2 model with PhenionFT™, medium was analysed for parent and metabolites over 5 days. The first‐pass metabolism of AHT was demonstrated, and the introduction of a wash step after 30 min decreased the exposure to AHT and its metabolites by 33% and 40%–43%, respectively. In conclusion, epidermal and FT skin models used in the Chip2 can mimic the first‐pass skin metabolism of AHT. This highlights the flexibility of the Chip2 to incorporate different skin models according to the purpose.
Development of hydrogel‐based composite scaffolds containing eggshell particles for bone regeneration applications
Authors: Calvert Nicholas D. , Proulx Scott , Rodriguez‐Navarro Alejandro , Ahmed Tamer , Lehoux Eric A. , Hincke Maxwell T. , Catelas Isabelle 
Published: September 2023

AbstractThis study describes the development and characterization of novel composite scaffolds, made of an alginate‐chitosan hydrogel matrix containing eggshell (ES) particles, for bone tissue engineering applications. Scaffolds with ES particles, either untreated or treated with phosphoric acid to create a nanotextured particle surface, were compared to scaffolds without particles. Results indicate that the nanotexturing process exposed occluded ES proteins orthologous to those in human bone extracellular matrix. Scaffolds with ES or nanotextured ES (NTES) particles had a higher porosity (81 ± 4% and 89 ± 5%, respectively) than scaffolds without particles (59 ± 5%) (p = .002 and p < .001, respectively). Scaffolds with NTES particles had a larger median pore size (113 μm [interquartile range [IQ]: 88–140 μm]) than scaffolds with ES particles (94 μm [IQ: 75–112 μm]) and scaffolds without particles (99 μm [IQ: 74–135 μm]) (p < .001 and p = .011, respectively). The compressive modulus of the scaffolds with ES or NTES particles remained low (3.69 ± 0.70 and 3.14 ± 0.62 kPa, respectively), but these scaffolds were more resistant to deformation following maximum compression than those without particles. Finally, scaffolds with ES or NTES particles allowed better retention of human mesenchymal stem cells during seeding (53 ± 12% and 57 ± 8%, respectively, vs. 17 ± 5% for scaffolds without particles; p < .001 in both cases), as well as higher cell viability up to 21 days of culture (67 ± 17% and 61 ± 11%, respectively, vs. 15 ± 7% for scaffolds without particles; p < .001 in both cases). In addition, alkaline phosphatase (ALP) activity increased up to 558 ± 164% on day 21 in the scaffolds with ES particles, and up to 567 ± 217% on day 14 in the scaffolds with NTES particles (p = .006 and p = .002, respectively, relative to day 0). Overall, this study shows that the physicochemical properties of the alginate‐chitosan hydrogel scaffolds with ES or NTES particles are similar to those of cancellous bone. In addition, scaffolds with particles supported early osteogenic differentiation and therefore represent a promising new bone substitute, especially for non‐load bearing applications.