bluuebunny/crossref_metadata_2025_split huggingface dataset:
7 T Musculoskeletal MRI
Authors: Pazahr Shila , Nanz Daniel , Sutter Reto 
Published: July 2022

Abstract
This review summarizes the current state-of-the-art of musculoskeletal 7 T magnetic resonance imaging (MRI), the associated technological challenges, and gives an overview of current and future clinical applications of 1H-based 7 T MRI. The higher signal-to-noise ratio at 7 T is predominantly used for increased spatial resolution and thus the visualization of anatomical details or subtle lesions rather than to accelerate the sequences. For musculoskeletal MRI, turbo spin echo pulse sequences are particularly useful, but with altered relaxation times, B1 inhomogeneity, and increased artifacts at 7 T; specific absorption rate limitation issues quickly arise for turbo spin echo pulse sequences. The development of dedicated pulse sequence techniques in the last 2 decades and the increasing availability of specialized coils now facilitate several clinical musculoskeletal applications. 7 T MRI is performed in vivo in a wide range of applications for the knee joint and other anatomical areas, such as ultra-high-resolution nerve imaging or bone trabecular microarchitecture imaging. So far, however, it has not been shown systematically whether the higher field strength compared with the established 3 T MRI systems translates into clinical advantages, such as an early-stage identification of tissue damage allowing for preventive therapy or an influence on treatment decisions and patient outcome. At the moment, results tend to suggest that 7 T MRI will be reserved for answering specific, targeted musculoskeletal questions rather than for a broad application, as is the case for 3 T MRI. Future data regarding the implementation of clinical use cases are expected to clarify if 7 T musculoskeletal MRI applications with higher diagnostic accuracy result in patient benefits compared with MRI at lower field strengths.
Low-Dose CT Imaging of the Pelvis in Follow-up Examinations—Significant Dose Reduction and Impact of Tin Filtration
Authors: Schüle Simone , Gärtner Klaus , Halt Daniel , Beer Meinrad , Hackenbroch Carsten 
Published: July 2022

Objectives
Low-dose (LD) computed tomography (CT) is still rarely used in musculoskeletal (MSK) radiology. This study evaluates the potentials of LD CT for follow-up pelvic imaging with special focus on tin filtration (Sn) technology for normal and obese patients with and without metal implants.

Materials and Methods
In a phantom study, 5 different LD and normal-dose (ND) CT protocols with and without tin filtration were tested using a normal and an obese phantom. Iterative reconstruction (IR) and filtered back projection (FBP) were used for CT image reconstruction. In a subsequent retrospective patient study, ND CT images of 45 patients were compared with follow-up tin-filtered LD CT images with a 90% dose reduction. Sixty-four percent of patients contained metal implants at the follow-up examination. Computed tomography images were objectively (image noise, contrast-to-noise ratio [CNR], dose-normalized contrast-to-noise ratio [CNRD]) and subjectively, using a 6-point Likert score, evaluated. In addition, the figure of merit was calculated. For group comparisons, paired t tests, Wilcoxon signed rank test, analysis of variance, or Kruskal-Wallis tests were used, where applicable.

Results
The LD Sn protocol with 67% dose reduction resulted in equal values in qualitative (Likert score) and quantitative image analysis (image noise) compared with the ND protocol in the phantom study. For follow-up examinations, dose could be reduced up to 90% by using Sn LD CT scans without impairment in the clinical study. However, metal implants resulted in a mild impairment of Sn LD as well as ND CT images. Cancellous bone (P < 0.001) was assessed worse and cortical bone (P = 0.063) equally in Sn LD CT images compared with ND CT images. Figure of merit values were significant (P ≤ 0.02) lower and hence better in Sn LD as in ND protocols. Obese patients benefited in particular from tin filtration in LD MSK imaging in terms of image noise and CNR (P ≤ 0.05).

Conclusions
Low-dose CT scans with tin filtration allow maximum dose reduction while maintaining high image quality for certain clinical purposes, for example, follow-up examinations, especially metal implant position, material loosening, and consolidation controls. Overweight patients benefit particularly from tin filter technology. Although metal implants decrease image quality in ND as well as in Sn LD CT images, this is not a relevant limitation for assessability.
Developing and leading a sustainable organization for early career acute care surgeons: Lessons from the inaugural American Association for the Surgery of Trauma Associate Member Council
Authors: Dumas Ryan P. , Bankhead Brittany K. , Coleman Julia R. , Dhillon Navpreet K. , Meizoso Jonathan P. , Bessoff Kovi , Butler William J. , Strickland Matt , Dultz Linda A. , Davis Kimberly , Bulger Eileen M. , Reilly Patrick M. , Croce Martin A. , Spain David A. , Livingston David H. , Brasel Karen J. , Coimbra Raul , Knowlton Lisa M. 
Published: July 2022

ABSTRACT
The associate membership of the American Association for the Surgery of Trauma (AAST) was established in 2019 to create a defined but incorporated entity within the larger AAST for the next generation of acute care surgeons. The Associate Member Council (AMC) was subsequently established in 2020 to provide the new AM with an elected group of leaders who would represent them within the AAST. In its inaugural year, this cohort of junior faculty and surgical trainees had developed for the AM a set of bylaws, a mission statement, a strategic vision, and a succession plan. The experience of the AAST AMC is exemplary of what can be accomplished with collaboration, mentorship, innovation, and tenacity. It has the potential to serve as a template for the creation and vitalization of future professional groups. In this piece, the AMC proposes a blueprint for the successful conception of a new organization.
Pain-Related Vertex Evoked Potentials. Comparison of Surface Electrical to Heat Stimulation
Authors: Guiloff Roberto J. , Campero Mario , Barraza Gonzalo R. , Treede Rolf-Detlef , Matamala Jose M. , Castillo Jose L. 
Published: July 2022

Introduction:
Demonstration of nociceptive fiber abnormality is important for diagnosing neuropathic pain and small fiber neuropathies. This is usually assessed by brief heat pulses using lasers, contact heat, or special electrodes. We hypothesized that pain-related evoked potentials to conventional surface electrical stimulation (PREPse) can index Aδ afferences despite tactile Aß fibers coactivation. PREPse may be more readily used clinically than contact heat evoked potentials (CHEPS).

Methods:
Twenty-eight healthy subjects. Vertex (Cz-A1/A2) recordings. Electrical stimulation of middle finger and second toe with conventional ring, and forearm/leg skin with cup, electrodes. Contact heat stimulation to forearm and leg. Compression ischemic nerve blockade.

Results:
PREPse peripheral velocities were within the midrange of Aδ fibers. N1-P1 amplitude increased with pain numerical rating scale graded (0–10) electrical stimulation (n = 25) and decreased with increasing stimulation frequency. Amplitudes were unchanged by different presentation orders of four stimulation intensities. PREPse N1 (∼130 milliseconds) and N2 (∼345 milliseconds) peaks were approximately 40 milliseconds earlier than that with CHEPS. PREPse and CHEPS N1-N2 interpeak latency (∼207 milliseconds) were similar. PREPse became unrecordable with nerve blockade of Aδ fibers.

Conclusions:
PREPse earlier N1 and N2 peaks, and similar interpeak N1-N2 latencies and central conduction velocities, or synaptic delays, to CHEPS are consistent with direct stimulation of Aδ fibers. The relation of vertex PREPse amplitude and pain, or the differential effects of frequency stimulation, is similar to pain-related evoked potential to laser, special electrodes, or contact heat stimulation. The relationship to Aδ was validated by conduction velocity and nerve block. Clinical utility of PREPse compared with CHEPS needs validation in somatosensory pathways lesions.
Palidis: fast discovery of novel insertion sequences
Authors: Carr Victoria R. , Pissis Solon P. , Mullany Peter , Shoaie Saeed , Gomez-Cabrero David , Moyes David L. 
Published: July 2022

AbstractThe diversity of microbial insertion sequences, crucial mobile genetic elements in generating diversity in microbial genomes, needs to be better represented in current microbial databases. Identification of these sequences in microbiome communities presents some significant problems that have led to their underrepresentation. Here, we present a bioinformatics pipeline called Palidis that recognises insertion sequences in metagenomic sequence data rapidly by identifying inverted terminal repeat regions from mixed microbial community genomes. Applying Palidis to 264 human metagenomes identifies 879 unique insertion sequences, with 519 being novel and not previously characterised. Querying this catalogue against a large database of isolate genomes reveals evidence of horizontal gene transfer events across bacterial classes. We will continue to apply this tool more widely, building the Insertion Sequence Catalogue, a valuable resource for researchers wishing to query their microbial genomes for insertion sequences.Data SummaryPalidis is available here: github.com/blue-moon22/palidisThe Insertion Sequence Catalogue is available to download here:https://github.com/blue-moon22/ISCThe raw reads from the Human Microbiome Project can be retrieved using the download links provided in Supplementary Data 1The analysis for this paper is available here: github.com/blue-moon22/palidis_paper_analysisThe output of Palidis that was run on these reads is available in Supplementary Data 2Impact StatementInsertion sequences are a class of transposable element that play an important role in the dissemination of antimicrobial resistance genes. However, it is challenging to completely characterise the transmission dynamics of insertion sequences and their precise contribution to the spread of antimicrobial resistance. The main reasons for this are that it is impossible to identify all insertion sequences based on limited reference databases and thatde novocomputational methods are ill-equipped to make fast or accurate predictions based on incomplete genomic assemblies. Palidis generates a larger, more comprehensive catalogue of insertion sequences based on a fast algorithm harnessing genomic diversity in mixed microbial communities. This catalogue will enable genomic epidemiologists and researchers to annotate genomes for insertion sequences more extensively and advance knowledge of how insertion sequences contribute to bacterial evolution in general and antimicrobial resistance spread across microbial lineages in particular. This will be useful for genomic surveillance, and for development of microbiome engineering strategies targeting inactivation or removal of important transposable elements carrying antimicrobial resistance genes.
Neural correlates of changing food choices while bypassing values
Authors: Zahedi Anoushiravan , Artigas Sergio Oroz , Swaboda Nora , Wiers Corinde E. , Görgen Kai , Park Soyoung Q. 
Published: July 2022

AbstractCurrent theories suggest that altering choices requires value modification. To investigate this, normal-weight participants’ food choices and values were tested before and after an approach-avoidance training (AAT), while neural activity was recorded during the choice task using functional magnetic resonance imaging (fMRI). During AAT, participants consistently approached low-while avoiding high-calorie food cues. AAT facilitated low-calorie food choices, leaving food values unchanged. Instead, we observed a shift in indifference points, indicating the decreased contribution of food values in food choices. Training-induced choice shifts were associated with increased activity in the posterior cingulate cortex (PCC). In contrast, the medial PFC activity was not changed. Additionally, PCC grey matter density predicted individual differences in training-induced functional changes, suggesting anatomic predispositions to training impact. Our findings demonstrate neural mechanisms underlying choice modulation independent of valuation-related processes, with substantial theoretical significance for decision-making frameworks and translational implications for health-related decisions resilient to value shifts.
Mice lacking dopamine production in neurotensin receptor 1 neurons voluntarily undergo time-restricted feeding of high fat diet and resist obesity
Authors: Farahmand Firozeh , Sidikpramana Michael , Yousef Bara , Sharif Sarah , Shao Kieana , Tang Qijun , Leinninger Gina M. , Güler Ali D. , Steele Andrew D. 
Published: July 2022

AbstractThe introduction of processed foods high in fat and sugars has caused a dramatic increase in obesity in humans. Diet-induced obesity (DIO) can be modeled in laboratory mice by increasing the fat content of their diet. Previously, it was determined that mice lacking dopamine receptor 1 (Drd1) are completely resistant to DIO and do not eat as much food during the day as control mice. Surprisingly, when Drd1 is restored to the suprachiasmatic nucleus (SCN), which is the central regulator of circadian rhythms, these mice increase day-eating and become obese. The source of dopamine in the SCN is the ventral tegmental area (VTA), but the genetic identity of the dopamine neurons is unknown. Here we create conditional deletion mutants for tyrosine hydroxylase (TH) using neurotensin receptor 1 (Ntsr1) Cre and other Cre drivers and measure feeding and body weight homeostasis on standard and high fat diets. Control mice were susceptible to DIO and overate during the day whereas Ntsr1-Cre conditional knockouts for TH mice did not increase day-eating, nor did they gain much weight on HFD. We used an adeno-associated virus to selectively restore TH to the VTA Ntsr1 neurons and observed an increase in body weight and increased day-eating of HFD. These results implicate VTA Ntsr1 dopamine neurons as promoting out-of-phase feeding behavior on a high fat diet that could be an important contributor to diet-induced obesity.
Correspondence of Newcomb-Benford Number Law with Ecological Processes
Authors: Davic Robert D. 
Published: July 2022

ABSTRACTThe Newcomb-Benford number law has been applied in the natural sciences for decades, with little ecological attention. Empirical data transformed into significant digits reveal statistical correspondence between the discrete Benford probability distribution and physical systems in dynamic equilibrium along a continuum of stability. Analytic methods are presented to detect this mathematical representation across multiple levels of ecological organization and spatial scale. Case studies demonstrate novel application to help identify bidirectional regime changes to alternative states of dynamic equilibrium. Widespread documentation of the surprising phenomenon is anticipated as ecologists revisit historic sets of random measurement data and design future sampling protocols. Controlled experiments with measurement variables that span multiple orders of magnitude would be well suited for future empirical and theoretical inquiry.
Variations in microbial diversity affect the stability and function of dark fermentation bioreactors
Authors: Navarro-Díaz Marcelo , Aparicio-Trejo Valeria , Valdez-Vazquez Idania , Carrillo-Reyes Julián , Avitia Morena , Escalante Ana E. 
Published: July 2022

AbstractThe relationship between the taxonomic diversity and the function of microbial communities is complex. Specifically, the ecological mechanisms that drive the dynamics of microbial populations and the consequences of these dynamics on functional traits have remained elusive. Among the simplest but natural microbial communities are dark fermentation consortia, a subset of the more diverse and complex microbial communities, anaerobic digestion communities. Dark fermentation consortia have been of interest as they produce biofuels such as hydrogen and different alcohols that can be used as fossil fuels alternatives. However, these hydrogen-producing communities have unresolved instability and low yield issues. We have previously proposed that instability and low yields in dark fermentation communities could be due to reduced diversity that results from aggressive pretreatments of original anaerobic digestion communities. In this work, we used dark fermentation communities to examine experimentally the effect of diversity reduction in functional traits, including stability and microbial interactions. We established two types of treatment, (i) maintaining strict culture conditions that are known to induce hydrogen production and ii) applying a heat-shock treatment known for selecting hydrogen-producing bacteria, which resulted in two types of communities, high and low diversity. Each treatment consisted of 12 replicates that were transferred to fresh medium daily (during 28 days for the non-treated bioreactors and 61 days for the heat-shock treated bioreactors). Microbial communities of the two treatments were characterized in their function as well as resistance to invasion. Microbial composition was characterized by culture-independent 16S rRNA gene amplicon sequencing. We analyzed microbial community composition and function through time, establishing statistical relationships between bacterial groups and metabolite production. Also, we inferred the potential ecological interactions that might have been established. Results show that the replicate bioreactors for each treatment predictably shifted to a similar composition and increased and stable biogas production. The non-treated bioreactors showed less susceptibility to the invasion (with the invasive bacteria establishing only in one replicate in the non-treated bioreactors vs 6 invaded replicates of the heat-shock treated bioreactors). However, the effect observed in the non-treated bioreactor replicate where the invader bacteria established was more drastic since the invasive bacteria managed to become dominant.
Analysis of Alzheimer’s disease Polygenic Risk Scores using RNA-sequencing provides further novel biological pathways
Authors: Crawford K. , Leonenko G. , Baker E. , Grozeva D. , Lan-Leung B. , Holmans P. , Williams J. , O’Donovan M. C. , Escott-Price V. , Ivanov DK. 
Published: July 2022

AbstractPolygenic risk scores (PRS) have been widely adopted as a tool for measuring common variant liability and it has been shown to predict lifetime risk of Alzheimer’s disease (AD) development. However, the relationship between PRS and AD pathogenesis is largely unknown. We aimed to address some of the knowledge gaps with respect to the downstream molecular consequences associated with PRS. We also make a direct comparison of the disrupted biological mechanisms in a case/control classification and in response to PRS in the same individuals.We performed an integrative computational analysis of the transcriptome of the largest human brain-derived cohort sample (288 individuals; cerebellum and temporal cortex; MayoRNAseq; AMP-AD) with matched AD genetic and gene-expression data (WGS; bulk-brain RNA-seq). There was little overlap in terms of differentially expressed genes in case/control and PRS analyses, but a consensus of commonly disrupted biological mechanisms. Genes implicated by previous AD GWAS were found to be significantly enriched with respect to PRS in temporal cortex only. We identified mechanisms that were previously implicated in AD, including immune/stress response, lipid/cholesterol/fatty acid metabolism, endosome, death/apoptosis, neuronal processes, ageing and the involvement of glial cells. We also provide novel evidence for the significant involvement in AD of cellular structures, including the Golgi apparatus and endoplasmic reticulum as well as mitochondrial function.The largely common biological mechanisms between a case/control classification and in association with PRS suggests that PRS stratification can be used for studies where suitable case/control samples are not available or the selection of individuals with high and low PRS in clinical trials.
Automatic Bolus Tracking in Abdominal CT scans with Convolutional Neural Networks
Authors: Li Angela , Noël Peter B. , Shapira Nadav 
Published: July 2022

AbstractBackgroundBolus tracking can optimize the time delay between contrast injection and diagnostic scan initiation in contrast-enhanced computed tomography (CT), yet the procedure is time-consuming and subject to inter- and intra-operator variances which affect the enhancement levels in diagnostic scans. The objective of the current study is to use artificial intelligence algorithms to fully automate the bolus tracking procedure in contrast-enhanced abdominal CT exams for improved standardization and diagnostic accuracy while providing a simplified imaging workflow.MethodsThis retrospective study used abdominal CT exams collected under a dedicated IRB. Input data consisted of CT topograms and images with high heterogeneity in terms of anatomy, sex, cancer pathologies, and imaging artifacts acquired with four different CT scanner models. Our method consisted of two sequential steps: (i) automatic locator scan positioning on topograms, and (ii) automatic ROI positioning within the aorta on locator scans. The task of locator scan positioning is formulated as a regression problem, where the limited amount of annotated data is circumvented using transfer learning. The task of ROI positioning is formulated as a segmentation problem.ResultsOur locator scan positioning network offered improved positional consistency compared to a high degree of variance in manual slice positionings, verifying inter-operator variance as a significant source of error. When trained using expert-user ground truth labels, the locator scan positioning network achieved a sub-centimeter error (9.76 ± 6.78 mm) on a test dataset. The ROI segmentation network achieved a sub-millimeter absolute error (0.99 ± 0.66 mm) on a test dataset.ConclusionsLocator scan positioning networks offer improved positional consistency compared to manual slice positionings and verified inter-operator variance as an important source of error. By significantly reducing operator-related decisions, this method opens opportunities to standardize and simplify the workflow of bolus tracking procedures for contrast-enhanced CT.
Disruption of lactate metabolism in the peripheral nervous system leads to motor-selective deficits
Authors: Bloom A. Joseph , Hackett Amber R. , Strickland Amy , Yamada Yurie , Ippolito Joseph , Schmidt Robert E. , Sasaki Yo , DiAntonio Aaron , Milbrandt Jeffrey 
Published: July 2022

AbstractSchwann cells (SCs) myelinate and provide trophic support to axons in the peripheral nervous system (PNS) and disruption of SC cellular metabolism leads to demyelination and axon degeneration, both symptoms of peripheral neuropathies. The lactate shuttle hypothesis proposes that glycolytic support cells supply lactate to adjacent axons to sustain their high metabolic demands, a process that requires the interconversion of lactate and pyruvate via lactate dehydrogenase (LDH) in both SCs and neurons. To test this hypothesis in the PNS, we selectively knocked out the genes for both LDH enzymes, LDHA and LDHB, in motor neurons (MNs), sensory neurons (SNs), or SCs. Interestingly, motor axons and their synapses progressively degenerate when LDH is deleted from either MNs or SCs; however, defects in sensory axons or their terminals were not observed when LDH was excised from either SNs or SCs. Deletion of LDH in SCs also leads to a decrease in total ATP levels in peripheral nerves despite a marked accumulation of pyruvate and glycolytic intermediates, consistent with the failure of pyruvate to lactate conversion in SCs leading to energetic deficits in axons. These results support a model in which motor axons are more dependent on SC-derived lactate than are sensory axons, a specific dependency that suggests LDH and lactate shuttling influence the course of motor-dominated neuropathies such as ALS.