bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping brain function in adults and young children during naturalistic viewing with high‐density diffuse optical tomography
Authors: Tripathy Kalyan , Fogarty Morgan , Svoboda Alexandra M. , Schroeder Mariel L. , Rafferty Sean M. , Richter Edward J. , Tracy Christopher , Mansfield Patricia K. , Booth Madison , Fishell Andrew K. , Sherafati Arefeh , Markow Zachary E. , Wheelock Muriah D. , Arbeláez Ana María , Schlaggar Bradley L. , Smyser Christopher D. , Eggebrecht Adam T. , Culver Joseph P. 
Published: May 2024

AbstractHuman studies of early brain development have been limited by extant neuroimaging methods. MRI scanners present logistical challenges for imaging young children, while alternative modalities like functional near‐infrared spectroscopy have traditionally been limited by image quality due to sparse sampling. In addition, conventional tasks for brain mapping elicit low task engagement, high head motion, and considerable participant attrition in pediatric populations. As a result, typical and atypical developmental trajectories of processes such as language acquisition remain understudied during sensitive periods over the first years of life. We evaluate high‐density diffuse optical tomography (HD‐DOT) imaging combined with movie stimuli for high resolution optical neuroimaging in awake children ranging from 1 to 7 years of age. We built an HD‐DOT system with design features geared towards enhancing both image quality and child comfort. Furthermore, we characterized a library of animated movie clips as a stimulus set for brain mapping and we optimized associated data analysis pipelines. Together, these tools could map cortical responses to movies and contained features such as speech in both adults and awake young children. This study lays the groundwork for future research to investigate response variability in larger pediatric samples and atypical trajectories of early brain development in clinical populations.
Have you been there before? Decoding recognition of spatial scenes from fMRI signals in precuneus
Authors: Bogler Carsten , Zangrossi Andrea , Miller Chantal , Sartori Giuseppe , Haynes John‐Dylan 
Published: May 2024

AbstractOne potential application of forensic “brain reading” is to test whether a suspect has previously experienced a crime scene. Here, we investigated whether it is possible to decode real life autobiographic exposure to spatial locations using fMRI. In the first session, participants visited four out of eight possible rooms on a university campus. During a subsequent scanning session, subjects passively viewed pictures and videos from these eight possible rooms (four old, four novel) without giving any responses. A multivariate searchlight analysis was employed that trained a classifier to distinguish between “seen” versus “unseen” stimuli from a subset of six rooms. We found that bilateral precuneus encoded information that can be used to distinguish between previously seen and unseen rooms and that also generalized to the two stimuli left out from training. We conclude that activity in bilateral precuneus is associated with the memory of previously visited rooms, irrespective of the identity of the room, thus supporting a parietal contribution to episodic memory for spatial locations. Importantly, we could decode whether a room was visited in real life without the need of explicit judgments about the rooms. This suggests that recognition is an automatic response that can be decoded from fMRI data, thus potentially supporting forensic applications of concealed information tests for crime scene recognition.
Verbal memory network mapping in individual patients predicts postoperative functional impairments
Authors: Wang Feng , Ren Jianxun , Cui Weigang , Zhou Ying , Yao Peisen , Lai Xuemiao , Pang Yue , Chen Zhili , Lin Yuanxiang , Liu Hesheng 
Published: May 2024

AbstractVerbal memory decline is a significant concern following temporal lobe surgeries in patients with epilepsy, emphasizing the need for precision presurgical verbal memory mapping to optimize functional outcomes. However, the inter‐individual variability in functional networks and brain function‐structural dissociations pose challenges when relying solely on group‐level atlases or anatomical landmarks for surgical guidance. Here, we aimed to develop and validate a personalized functional mapping technique for verbal memory using precision resting‐state functional MRI (rs‐fMRI) and neurosurgery. A total of 38 patients with refractory epilepsy scheduled for surgical interventions were enrolled and 28 patients were analyzed in the study. Baseline 30‐min rs‐fMRI scanning, verbal memory and language assessments were collected for each patient before surgery. Personalized verbal memory networks (PVMN) were delineated based on preoperative rs‐fMRI data for each patient. The accuracy of PVMN was assessed by comparing post‐operative functional impairments and the overlapping extent between PVMN and surgical lesions. A total of 14 out of 28 patients experienced clinically meaningful declines in verbal memory after surgery. The personalized network and the group‐level atlas exhibited 100% and 75.0% accuracy in predicting postoperative verbal memory declines, respectively. Moreover, six patients with extra‐temporal lesions that overlapped with PVMN showed selective impairments in verbal memory. Furthermore, the lesioned ratio of the personalized network rather than the group‐level atlas was significantly correlated with postoperative declines in verbal memory (personalized networks: r = −0.39, p = .038; group‐level atlas: r = −0.19, p = .332). In conclusion, our personalized functional mapping technique, using precision rs‐fMRI, offers valuable insights into individual variability in the verbal memory network and holds promise in precision verbal memory network mapping in individuals.
The development of brain metastases in patients with different therapeutic strategies for metastatic renal cell cancer
Authors: Derks Sophie H. A. E. , van der Meer Edgar L. , Joosse Arjen , de Jonge Maja J. A. , Slagter Cleo , Schouten Joost W. , Hoop Esther Oomen‐de , Smits Marion , van den Bent Martin J. , Jongen Joost L. M. , van der Veldt Astrid A. M. 
Published: May 2024

AbstractA diagnosis of brain metastasis (BM) significantly affects quality of life in patients with metastatic renal cell cancer (mRCC). Although systemic treatments have shown efficacy in mRCC, active surveillance (AS) is still commonly used in clinical practice. In this single‐center cohort study, we assessed the impact of different initial treatment strategies for metastatic RCC (mRCC) on the development of BM. All consecutive patients diagnosed with mRCC between 2011 and 2022 were included at the Erasmus MC Cancer Institute, the Netherlands, and a subgroup of patients with BM was selected. In total, 381 patients with mRCC (ECM, BM, or both) were identified. Forty‐six patients had BM of whom 39 had metachronous BM (diagnosed ≥1 month after ECM). Twenty‐five (64.1%) of these 39 patients with metachronous BM had received prior systemic treatment for ECM and 14 (35.9%) patients were treatment naive at BM diagnosis. The median BM‐free survival since ECM diagnosis was significantly longer (p = .02) in previously treated patients (29.0 [IQR 12.6–57.0] months) compared to treatment naive patients (6.8 [IQR 1.0–7.0] months). In conclusion, patients with mRCC who received systemic treatment for ECM prior to BM diagnosis had a longer BM‐free survival as compared to treatment naïve patients. These results emphasize the need for careful evaluation of treatment strategies, and especially AS, for patients with mRCC.
Early evaluation of a novel alert within cardiac procedural areas to facilitate genotype‐guided antiplatelet therapy
Authors: Van Heukelom Joel , Weaver Max , Max Carson , Baye Jordan F. , Peterson Ashley , Maryniak Andrii , Stys Tomsaz P. , Massmann Amanda 
Published: May 2024

AbstractIntroductionClopidogrel remains widely utilized in patients undergoing percutaneous coronary intervention despite compelling evidence that genetic variation impacts patient response to clopidogrel. Clinical decision support (CDS) is frequently used to aid in precision medicine; however, limitations within the electronic medical record can hinder reliable CDS. Procedural areas where standard order entry is not utilized create a barrier to CDS implementation.ObjectivesWe aimed to evaluate the implementation of a novel alerting mechanism on genotype‐guided antiplatelet prescribing within the cardiac catheterization laboratory procedural setting.MethodsA retrospective cohort study was conducted to assess the rate of antiplatelet ordering in patients with one or two loss‐of‐function cytochrome P450 2C19 (CYP2C19) alleles before and after alert implementation. Pharmacogenomic congruence was measured before and after the alert via chart abstraction that included the CYP2C19 genotype and antiplatelet medications ordered within that encounter.ResultsA total of 236 patients were included in analyses, 127 encounters within the cohort before alert implementation and 136 encounters in the cohort after alert implementation. Prior to alert implementation, 40.9% (n = 127) were prescribed clopidogrel compared with 25.7% (n = 136) post implementation. After implementing a genotype‐guided alert within the cardiac catheterization laboratory procedural setting, providers were 2.22 times more likely to prescribe an alternative antiplatelet (p = 0.024). Clopidogrel‐naïve patients were 9.75 times more likely to receive a genotype‐guided antiplatelet order following alert implementation (p < 0.05).ConclusionProviders were responsive to a novel alert within the cardiac catheterization laboratory procedural setting. Genotype‐guided antiplatelet prescribing significantly increased following the alert implementation.
Interpretation of molecular electron transport in ab initio many‐electron framework incorporating zero‐point nuclear motion effects
Authors: Jelenfi Dávid P. , Tajti Attila , Szalay Péter G. 
Published: May 2024

AbstractA computational methodology, founded on chemical concepts, is presented for interpreting the role of nuclear motion in the electron transport through single‐molecule junctions (SMJ) using many‐electron ab initio quantum chemical calculations. Within this approach the many‐electron states of the system, computed at the SOS‐ADC(2) level, are followed along the individual normal modes of the encapsulated molecules. The inspection of the changes in the partial charge distribution of the many‐electron states allows the quantification of the electron transport and the estimation of transmission probabilities. This analysis improves the understanding of the relationship between internal motions and electron transport. Two SMJ model systems are studied for validation purposes, constructed from a conductor (BDA, benzene‐1,4‐diamine) and an insulator molecule (DABCO, 1,4‐diazabicyclo[2.2.2]octane). The trends of the resulting transmission probabilities are in agreement with the experimental observations, demonstrating the capability of the approach to distinguish between conductor and insulator type systems, thereby offering a straightforward and cost‐effective tool for such classifications via quantum chemical calculations.
Efficient Reductive N‐11C‐Methylation Using Arylamines or Alkylamines and In Situ–Generated [11C]Formaldehyde From [11C]Methyl Iodide
Authors: Kikuchi Tatsuya , Okamura Toshimitsu , Zhang Ming‐Rong 
Published: May 2024

ABSTRACTReductive N‐11C‐methylation using [11C]formaldehyde and amines has been used to prepare N‐11C‐methylated compounds. However, the yields of the N‐11C‐methylated compounds are often insufficient. In this study, we developed an efficient method for base‐free reductive N‐11C‐methylation that is applicable to a wide variety of substrates, including arylamines bearing electron‐withdrawing and electron‐donating substituents. A 2‐picoline borane complex, which is a stable and mild reductant, was used. Dimethyl sulfoxide was used as the primary reaction solvent, and glacial acetic acid or aqueous acetic acid was used as a cosolvent. While reductive N‐11C‐methylation efficiently proceeded under anhydrous conditions in most cases, the addition of water to the reductive N‐11C‐methylation generally increased the yield of the N‐11C‐methylated compounds. Substrates with hydroxy, carboxyl, nitrile, nitro, ester, amide, and phenone moieties and amine salts were applicable to the reaction. This proposed method for reductive N‐11C‐methylation should be applicable to a wide variety of substrates, including thermo‐labile and base‐sensitive compounds because the reaction was performed under relatively mild conditions (70°C) without the need for a base.
Reproducibility of Quantitative Double‐Echo Steady‐State T2 Mapping of Knee Cartilage
Authors: Williams Ashley A. , Asay Jessica L. , Asare Daniella , Desai Arjun D. , Gold Garry E. , Hargreaves Brian A. , Chaudhari Akshay S. , Chu Constance R. 
Published: May 2024

BackgroundCartilage T2 can detect joints at risk of developing osteoarthritis. The quantitative double‐echo steady state (qDESS) sequence is attractive for knee cartilage T2 mapping because of its acquisition time of under 5 minutes. Understanding the reproducibility errors associated with qDESS T2 is essential to profiling the technical performance of this biomarker.PurposeTo examine the combined acquisition and segmentation reproducibility of knee cartilage qDESS T2 using two different regional analysis schemes: 1) manual segmentation of subregions loaded during common activities and 2) automatic subregional segmentation.Study TypeProspective.Subjects11 uninjured participants (age: 28 ± 3 years; 8 (73%) female).Field Strength/Sequence3‐T, qDESS.AssessmentTest–retest T2 maps were acquired twice on the same day and with a 1‐week interval between scans. For each acquisition, average cartilage T2 was calculated in four manually segmented regions encompassing tibiofemoral contact areas during common activities and 12 automatically segmented regions from the deep‐learning open‐source framework for musculoskeletal MRI analysis (DOSMA) encompassing medial and lateral anterior, central, and posterior tibiofemoral regions. Test–retest T2 values from matching regions were used to evaluate reproducibility.Statistical TestsCoefficients of variation (%CV), root‐mean‐square‐average‐CV (%RMSA‐CV), and intraclass correlation coefficients (ICCs) assessed test–retest T2 reproducibility. The median of test–retest standard deviations was used for T2 precision. Bland–Altman (BA) analyses examined test–retest biases. The smallest detectable difference (SDD) was defined as the BA limit of agreement of largest magnitude. Significance was accepted for P < 0.05.ResultsAll cartilage regions across both segmentation schemes demonstrated intraday and interday qDESS T2 CVs and RMSA‐CVs of ≤5%. T2 ICC values >0.75 were observed in the majority of regions but were more variable in interday tibial comparisons. Test–retest T2 precision was <1.3 msec. The T2 SDD was 3.8 msec.Data ConclusionExcellent CV and RMSA‐CV reproducibility may suggest that qDESS T2 increases or decreases >5% (3.8 msec) could represent changes to cartilage composition.Level of Evidence2.Technical EfficacyStage 2.
Regulation of soil organic carbon dynamics by microbial communities during reforestation of Chinese fir plantations after clear‐cutting
Authors: Wang Ying , Chen Liang , Xiang Wenhua , Zhang Xiulan , Ren Yan , Guo Zhiming , Gunina Anna 
Published: May 2024

AbstractReforestation after forest clear‐cutting is an effective measure to increase soil organic carbon (SOC) sequestration; still, the soil C balance under reforestation and the role of microbial communities in that process remain to be determined. Samples of organic (0–2 cm) and mineral (2–10 cm) horizons were collected from the 7‐, 15‐, 20‐, 29‐, and 36‐year‐old forest stands of Chinese fir (Cunninghamia lanceolata) after plantation clear‐cutting in subtropical zone under the condition of phosphorus limitation. Particulate organic carbon (POC), mineral‐associated organic carbon (MAOC), microbial phospholipid fatty acids (PLFAs), and enzymatic activities for C, nitrogen (N), and phosphorus (P) acquisition were analyzed. The lowest contents of POC (10%) and MAOC (13%) in the organic horizon were found in 7‐year‐old stands due to the slow tree regrowth and extensive decomposition of SOC in the first years of forest regrowth. POC (2.0×) and MAOC (0.8×) increases in the organic horizon with forest age were attributed to the stand development and accumulation of above‐ and belowground litter. The organic horizon had a higher POC:MAOC ratio than the mineral (0.7–1.1 vs. 0.2–0.5), indicating lower SOC stability in the first one. The ratio of POC:MAOC increased with the Gram‐positive to Gram‐negative bacteria (G+:G‐) ratio, pointing out that microbial communities developed a specific community structure and substrate utilization strategies of organic matter under plantation restoration. The increase of total PLFAs and the G+:G‐ ratio was closely linked with the microbial C and P limitations, indicating that microorganisms shifted community structure to slow‐growing species and increased their content to cope with the C and P restrictions. In the soils of young plantations, microorganisms were limited by C and P; however, the C limitation was alleviated in the 36‐year‐old plots in the organic horizon due to increased litter input, whereas the P limitation was not. This discrepancy between C and P limitation suppressed the decomposition of litter entering the soil, which was seen in decreased specific activity of C degrading enzymes and led to the accumulation of POC in the organic horizon. Thus, soil C sequestration under reforestation of Chinese fir can be controlled by the amount of litter entering the soil and by metabolic C, N, and P limitations that force microorganisms to shift community structure and change their activity.
Predicting river phytoplankton blooms and community succession using ecological niche modeling
Authors: Bowes Michael J. , Hutchins Michael G. , Nicholls David J. E. , Armstrong Linda K. , Scarlett Peter M. , Jürgens Monika D. , Bachiller‐Jareno Nuria , Fournier Isabelle , Read Daniel S. 
Published: May 2024

AbstractExcessive phytoplankton concentrations in rivers can result in the loss of plant and invertebrate communities, and threaten drinking water supplies. Whilst the physicochemical controls on algal blooms have been identified previously, how these factors combine to control the initiation, size, and cessation of blooms in rivers is not well understood. We applied flow cytometry to quantify diatom, chlorophyte, and cyanobacterial group abundances in the River Thames (UK) at weekly intervals from 2011 to 2022, alongside physicochemical data. A niche modeling approach was used to identify thresholds in water temperature, flow, solar radiation, and soluble reactive phosphorus (SRP) concentrations required to produce periods of phytoplankton growth, with blooms only occurring when all thresholds were met. The thresholds derived from the 2011 to 2018 dataset were applied to a test data set (2019–2022), which predicted the timing and duration of blooms at accuracies of > 80%. Diatoms and nano‐chlorophyte blooms were initiated by flow and water temperature, and usually terminated due to temperature and flow going out of the threshold range, or SRP and Si becoming limiting. Cyanobacterial bloom dynamics were primarily controlled by water temperature and solar radiation. This simple methodology provides a key understanding of phytoplankton community succession and inter‐annual variation and can be applied to any river with similar water quality and phytoplankton data. It provides early warnings of algal and cyanobacterial bloom timings, which support future catchment management decisions to safeguard water resources, and provides a basis for modeling changing phytoplankton bloom risk due to future climate change.
Improved quantification in CEST‐MRI by joint spatial total generalized variation
Authors: Huemer Markus , Stilianu Clemens , Maier Oliver , Fabian Moritz Simon , Schmidt Manuel , Doerfler Arnd , Bredies Kristian , Zaiss Moritz , Stollberger Rudolf 
Published: May 2024

AbstractPurposeIn this work, the use of joint Total Generalized Variation (TGV) regularization to improve Multipool‐Lorentzian fitting of chemical exchange saturation transfer (CEST) Spectra in terms of stability and parameter signal‐to‐noise ratio (SNR) was investigated.Theory and MethodsThe joint TGV term was integrated into the nonlinear parameter fitting problem. To increase convergence and weight the gradients, preconditioning using a voxel‐wise singular value decomposition was applied to the problem, which was then solved using the iteratively regularized Gauss–Newton method combined with a Primal‐Dual splitting algorithm. The TGV method was evaluated on simulated numerical phantoms, 3T phantom data and 7T in vivo data with respect to systematic errors and robustness. Three reference methods were also implemented: The standard nonlinear fitting, a method using a nonlocal‐means filter for denoising and the pyramid scheme, which uses downsampled images to acquire accurate start values.ResultsThe proposed regularized fitting method showed significantly improved robustness (compared to the reference methods). In testing, over a range of SNR values the TGV fit outperformed the other methods and showed accurate results even for large amounts of added noise. Parameter values found were closer or comparable to the ground truth. For in vivo datasets, the added regularization increased the parameter map SNR and prevented instabilities.ConclusionThe proposed fitting method using TGV regularization leads to improved results over a range of different data‐sets and noise levels. Furthermore, it can be applied to all Z‐spectrum data, with different amounts of pools, where the improved SNR and stability can increase diagnostic confidence.
Multiparametric exchange protons using Z‐spectrum analysis proton (ZAP) and CEST on phantoms and human abdomen
Authors: Malis Vadim , Miyazaki Mitsue 
Published: May 2024

AbstractPurposeThis study aims to investigate a multiparametric exchange proton approach using CEST and Z‐spectrum analysis protons (ZAP) in human abdominal organs, focusing on tissue differentiation for a potential early biomarker of abnormality. Prior to human studies, CEST and ZAP effects were studied in phantoms containing exchange protons.MethodsPhantoms composed of iopamidol and iohexol solutions with varying pH levels, along with 12 human subjects, were scanned on a clinical 3T MR scanner. Subsequent ZAP analyses employed a two‐Lorentzian pool model to provide free and restricted apparent , and their fractions for data acquired across a wide range of offset frequencies (±100 kHz or ± 800 ppm), while a narrower range (±7 ppm or ± 900 Hz) was used for CEST analysis to estimate magnetization transfer ratio asymmetry (MTRAsym) for exchange protons like hydroxyl (—OH), amine (—NH2), and amide (—NH), resonating ˜1, 2, and 3.5 ppm, respectively. Differences in ZAP metrics across various organs were statistically analyzed using one‐way analysis of variance (ANOVA).ResultsThe phantom study differentiated contrast agents based on resonance peaks detected from CEST analysis, while ZAP metrics showed sensitivity to pH variations. In human, ZAP metrics revealed significant differences in abdominal organs, with a subgroup study indicating changes in ZAP metrics due to the presence of gallstones.ConclusionCEST and ZAP techniques demonstrated promise in specific CEST protons and wide range ZAP protons and identifying tissue‐specific characteristics. The preliminary findings underscore the necessity for more extensive study involving a broader subject pool to potentially establish biomarkers for diseased states.