bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surgical exploration for stable patients with penetrating cardiac box injuries: When and how? A cohort of 155 patients from Marseille area
Authors: Vasse Matthieu , Belaroussi Yaniss , Avaro Jean-Philippe , Biri Nazim , Lerner Antoine , Thomas Pascal-Alexandre , de Lesquen Henri 
Published: February 2022

BACKGROUND
The management of penetrating thoracic injuries in moribund or unstable patients is clearly described in contrast to that of stable patients, particularly for those with a cardiac box injury. This anatomic location suggests a potentially lethal cardiac injury and requires urgent therapeutic decision making. The present study aims at determining when surgical exploration is beneficial for stable patients presenting with penetrating cardiac box injuries (PCBIs).

METHODS
This was a retrospective study of stable civilian patients with PCBI referred to level I trauma centers in the Marseille area between January 2009 and December 2019. Using post hoc analysis of the management outcomes, patients whose surgery was considered therapeutic (group A) were compared with those whose surgery was considered nontherapeutic and with nonoperated patients (group B).

RESULTS
A total of 155 patients with PCBI were included, with 88% (n = 137) of stab wound injuries. Overall, surgical exploration was performed in 54% (n = 83), considered therapeutic in 71% (n = 59), and performed by video-assisted thoracoscopy surgery in 42% (n = 35) with a conversion rates of 14% (n = 5). Initial extended fast assessment with sonography for trauma revealed the presence of hemopericardium in 29% (n = 29) in group A versus 9.5% (n = 7) in group B, p = 0.010, and was associated with a negative predictive value of 93% regarding the presence of a cardiac injury. Chest tube flow was significantly higher in patients who required surgery, with a median (interquartile range) of 600.00 (350.00–1200.00) mL versus 300.0 (150.00–400.00) mL (p = 0.001).

CONCLUSION
Extended fast assessment with sonography for trauma and chest tube flow are the cornerstones of the management of stable PCBI. Video-assisted thoracoscopy represents an interesting approach to check intrathoracic wounds while minimizing surgical morbidity.

LEVEL OF EVIDENCE
Therapeutic/Care Management; Level IV.
The public health burden of geriatric trauma: Analysis of 2,688,008 hospitalizations from Centers for Medicare and Medicaid Services inpatient claims
Authors: Fakhry Samir M. , Shen Yan , Biswas Saptarshi , Duane Therese M. , McBride Katherine M. , Elkbuli Adel , Wyse Ransom J. , Wilson Nina Y. , Garland Jeneva M. , Kurek Stanley J. , Plurad David S. , Banton Kaysie L. , Fisher Chris , Gage Alexis , Hunt Diane L.S. , Lieser Mark J. , Shillinglaw William R.C. , Watts Dorraine D. 
Published: February 2022

BACKGROUND
Geriatric trauma care (GTC) represents an increasing proportion of injury care, but associated public health research on outcomes and expenditures is limited. The purpose of this study was to describe GTC characteristics, location, diagnoses, and expenditures.

METHODS
Patients at short-term nonfederal hospitals, 65 years or older, with ≥1 injury International Classification of Diseases, Tenth Revision, were selected from 2016 to 2019 Centers for Medicare and Medicaid Services Inpatient Standard Analytical Files. Trauma center levels were linked to Inpatient Standard Analytical Files data via American Hospital Association Hospital ID and fuzzy string matching. Demographics, care location, diagnoses, and expenditures were compared across groups.

RESULTS
A total of 2,688,008 hospitalizations (62% female; 90% White; 71% falls; mean Injury Severity Score, 6.5) from 3,286 hospitals were included, comprising 8.5% of all Medicare inpatient hospitalizations. Level I centers encompassed 7.2% of the institutions (n = 236) but 21.2% of hospitalizations, while nontrauma centers represented 58.5% of institutions (n = 1,923) and 37.7% of hospitalizations. Compared with nontrauma centers, patients at Level I centers had higher Elixhauser scores (9.0 vs. 8.8) and Injury Severity Score (7.4 vs. 6.0; p < 0.0001). The most frequent primary diagnosis at all centers was hip/femur fracture (28.3%), followed by traumatic brain injury (10.1%). Expenditures totaled $32.9 billion for trauma-related hospitalizations, or 9.1% of total Medicare hospitalization expenditures and approximately 1.1% of the annual Medicare budget. The overall mortality rate was 3.5%.

CONCLUSION
Geriatric trauma care accounts for 8.5% of all inpatient GTC and a similar percentage of expenditures, the most common injury being hip/femur fractures. The largest proportion of GTC occurs at nontrauma centers, emphasizing their vital role in trauma care. Public health prevention programs and GTC guidelines should be implemented by all hospitals, not just trauma centers. Further research is required to determine the optimal role of trauma systems in GTC, establish data-driven triage guidelines, and define the impact of trauma centers and nontrauma centers on GTC mortality.

LEVEL OF EVIDENCE
Therapeutic/care management, Level III.
Predictors of Willingness to Enroll in Hypothetical Alzheimer Disease Biomarker Studies that Disclose Personal Results
Authors: Erickson Claire M. , Chin Nathaniel A. , Ketchum Frederick B. , Jonaitis Erin M. , Zuelsdorff Megan L. , Gleason Carey E. , Clark Lindsay R. 
Published: February 2022

Introduction:
We examined factors related to willingness to enroll in hypothetical Alzheimer disease (AD) biomarker studies.

Methods:
Using linear regression, we assessed the relationship among enrollment willingness and demographics, family dementia history, research attitudes, concern about AD, experiences of discrimination, and belief in AD risk modifiability. Inductive coding was used to assess qualitative data.

Results:
In middle-aged and older adult AD research participants (n=334), willingness to enroll in biomarker studies was driven by biomarker collection method, research attitudes, and disclosure of personal results. Predictors of willingness were similar for Black and White participants. Themes associated with increased willingness included a desire to learn biomarker results and support research.

Discussion:
Research attitudes were an important predictor of biomarker study willingness regardless of race. As seen elsewhere, Black participants were more hesitant to participate in biomarker research. Disclosure of biomarker results/risk can bolster willingness to enroll in biomarker studies, particularly for Black participants.
Before trilobite legs:Pygmaclypeatus daziensisreconsidered and the ancestral appendicular organization of Cambrian artiopods
Authors: Schmidt Michel , Hou Xianguang , Zhai Dayou , Mai Huijuan , Belojević Jelena , Chen Xiaohan , Melzer Roland R. , Ortega-Hernández Javier , Liu Yu 
Published: February 2022

The Cambrian Stage 3 Chengjiang biota in South China is one of the most influential Konservat-Lagerstätten worldwide thanks to the fossilization of diverse non-biomineralizing organisms through pyritization. Despite their contributions to understanding the evolution of early animals, several Chengjiang species remain poorly known owing to their scarcity and/or incomplete preservation. Here, we use micro-computed tomography to reveal in detail the ventral appendage organization of the enigmatic non-trilobite artiopodPygmaclypeatus daziensis—one of the rarest euarthropods in Chengjiang—and explore its functional ecology and broader evolutionary significance.Pygmaclypeatus daziensispossesses a set of uniramous antennae and 14 pairs of post-antennal biramous appendages, the latter of which show an unexpectedly high degree of heteronomy based on the localized differentiation of the protopodite, endopodite and exopodite along with the antero-posterior body axis. The small body size (less than 2 cm), the presence of delicate spinose endites and well-developed exopodites with multiple paddle-shaped lamellae on the appendages ofP. daziensisindicate a nekto-benthic mode of life and a scavenging/detritus feeding strategy.Pygmaclypeatus daziensisshows that appendage heteronomy is phylogenetically widespread within Artiopoda—the megadiverse clade that includes trilobites and their relatives with non-biomineralizing exoskeletons—and suggests that a single exopodite lobe with paddle-like lamellae is ancestral for this clade.This article is part of the theme issue ‘The impact of Chinese palaeontology on evolutionary research’.
ModInterv COVID-19: An online platform to monitor the evolution of epidemic curves
Authors: Brum Arthur A. , Vasconcelos Giovani L. , Duarte-Filho Gerson C. , Ospina Raydonal , Almeida Francisco A. G. , Macêdo Antônio M. S. 
Published: February 2022

AbstractWe present the software ModInterv as an informatics tool to monitor, in an automated and user-friendly manner, the evolution and trend of COVID-19 epidemic curves, both for cases and deaths. The ModInterv software uses parametric generalized growth models, together with LOWESS regression analysis, to fit epidemic curves with multiple waves of infections for countries around the world as well as for states and cities in Brazil and the USA. The software automatically accesses publicly available COVID-19 databases maintained by the Johns Hopkins University (for countries as well as states and cities in the USA) and the Federal University of Viçosa (for states and cities in Brazil). The richness of the implemented models lies in the possibility of quantitatively and reliably detecting the distinct acceleration regimes of the disease. We describe the backend structure of software as well as its practical use. The software helps the user not only to understand the current stage of the epidemic in a chosen location but also to make short term predictions as to how the curves may evolve. The app is freely available on the internet (http://fisica.ufpr.br/modinterv), thus making a sophisticated mathematical analysis of epidemic data readily accessible to any interested user.
Can the Kuznetsov Model Replicate and Predict Cancer Growth in Humans?
Authors: Wajeh Mohammad El , Jung Falco , Bongartz Dominik , Kappatou Chrysoula Dimitra , Laleh Narmin Ghaffari , Mitsos Alexander , Kather Jakob Nikolas 
Published: February 2022

AbstractSeveral mathematical models to predict tumor growth over time have been developed in the last decades. A central aspect of such models is the interaction of tumor cells with immune effector cells. The Kuznetsov model (Kuznetsov et al. (1994), Bulletin of Mathematical Biology, vol. 56, no. 2, pp. 295–321) is the most prominent of these models and has been used as a basis for many other related models and theoretical studies. However, none of these models have been validated with large-scale real-world data of human patients treated with cancer immunotherapy. In addition, parameter estimation of these models remains a major bottleneck on the way to model-based and data-driven medical treatment. In this study, we quantitatively fit Kuznetsov’s model to a large dataset of 1472 patients, of which 210 patients have more than six data points, by estimating the model parameters of each patient individually. We also conduct a global practical identifiability analysis for the estimated parameters. We thus demonstrate that several combinations of parameter values could lead to accurate data fitting. This opens the potential for global parameter estimation of the model, in which the values of all parameters are fixed for all patients. Furthermore, by omitting the last two or three data points, we show that the model can be extrapolated and predict future tumor dynamics. This paves the way for a more clinically relevant application of mathematical tumor modeling, in which the treatment strategy could be adjusted in advance according to the model’s future predictions.
Optical Genome Mapping And Single Nucleotide Polymorphism Microarray: An Integrated Approach For Investigating Challenging Cases Of Products Of Conception
Authors: Sahajpal Nikhil S , Mondal Ashis K , Ananth Sudha , Pundkar Chetan , Jones Kimya , Williams Colin , Fee Timothy , Weissman Amanda , Tripodi Giuseppe , Oza Eesha , Gavrilova-Jordan Larisa , Omar Nivin , Hastie Alex , DuPont Barbara R , Layman Lawrence , Chaubey Alka , Kolhe Ravindra 
Published: February 2022

AbstractConventional cytogenetic analysis of products of conception (POC) is of limited utility because of failed cultures, microbial and maternal cell contamination (MCC). Optical genome mapping (OGM) is an emerging technology that has the potential to replace conventional cytogenetic methods. The use of OGM precludes the requirement for culturing (and related microbial contamination). However, a high percentage of MCC impedes a definitive diagnosis, which can be addressed by an additional pre-analytical quality control step that includes histological assessment of H&E stained slides from FFPE tissue with macro-dissection for Chorionic villi to enrich fetal tissue component for Single nucleotide polymorphism (SNP) microarray analysis. An internal audit of POC cases subjected to karyotype-only analysis showed a low yield on clinically actionable information that contributed to patient care. To improve the diagnostic yield, an integrated workflow was devised that included MCC characterization of POC tissue, followed by OGM for MCC negative cases or SNPM with histological assessment for MCC positive cases. A result was obtained in 93% (29/31) cases with a diagnostic yield of 45.1% (14/31) with proposed workflow compared to 9.6% (3/31) and 6.4% (2/31) with routine workflow, respectively. The integrated workflow with these technologies demonstrates the clinical utility and higher diagnostic yield in evaluating POC specimens.
Recurrent circuits amplify corticofugal signals and drive feedforward inhibition in the inferior colliculus
Authors: Oberle Hannah M. , Ford Alexander N. , Czarny Jordyn E. , Rogalla Meike M. , Apostolides Pierre F. 
Published: February 2022

AbstractThe inferior colliculus (IC) is a midbrain hub critical for perceiving complex sounds such as speech. In addition to processing ascending inputs from most auditory brainstem nuclei, the IC receives descending inputs from auditory cortex that control IC neuron feature selectivity, plasticity, and certain forms of perceptual learning. Although corticofugal synapses primarily release the excitatory transmitter glutamate, many physiology studies show that auditory cortical activity has a net inhibitory effect on IC neuron spiking. Perplexingly, anatomy studies imply that corticofugal axons primarily target glutamatergic IC neurons while only sparsely innervating IC GABA neurons.Corticofugal inhibition of the IC may thus occur largely independently of feedforward activation of local GABA neurons. We shed light on this paradox usingin vitroelectrophysiology in acute IC slices from fluorescent reporter mice of either sex. Using optogenetic stimulation of corticofugal axons, we find that excitation evoked with single light flashes is indeed stronger in presumptive glutamatergic neurons compared to GABAergic neurons. However, many IC GABA neurons fire tonically at rest, such that sparse and weak excitation suffices to significantly increase their spike rates.Furthermore, a subset of glutamatergic IC neurons fire spikes during repetitive corticofugal activity, leading to polysynaptic excitation in IC GABA neurons owing to a dense intra-collicular connectivity. Consequently, recurrent excitation amplifies corticofugal activity, drives spikes in IC GABA neurons, and generates substantial local inhibition in the IC. Thus, descending signals engage intra-collicular inhibitory circuits despite apparent constraints of monosynaptic connectivity between auditory cortex and IC GABA neurons.Significance StatementDescending “corticofugal” projections are ubiquitous across mammalian sensory systems, and enable the neocortex to control subcortical activity in a predictive or feedback manner. Although corticofugal neurons are glutamatergic, neocortical activity often inhibits subcortical neuron spiking. How does an excitatory pathway generate inhibition? Here we study the corticofugal pathway from auditory cortex to inferior colliculus (IC), a midbrain hub important for complex sound perception. Surprisingly, cortico-collicular transmission was stronger onto IC glutamatergic compared to GABAergic neurons. However, corticofugal activity triggered spikes in IC glutamate neurons with local axons, thereby generating strong polysynaptic excitation and feed-forward spiking of GABAergic neurons. Our results thus reveal a novel mechanism that recruits local inhibition despite limited monosynaptic convergence onto inhibitory networks.
Large-scale biophysically detailed model of somatosensory thalamocortical circuits in NetPyNE
Authors: Borges Fernando S. , Moreira Joao V.S. , Takarabe Lavinia M. , Lytton William W. , Dura-Bernal Salvador 
Published: February 2022

AbstractThe primary somatosensory cortex (S1) of mammals is critically important in the perception of touch and related sensorimotor behaviors. In 2015, the Blue Brain Project developed a groundbreaking rat S1 microcircuit simulation with over 31,000 neurons with 207 morpho-electrical neuron types, and 37 million synapses, incorporating anatomical and physiological information from a wide range of experimental studies. We have implemented this highly-detailed and complex S1 model in NetPyNE, using the data available in the Neocortical Microcircuit Collaboration Portal. NetPyNE provides a Python high-level interface to NEURON and allows defining complicated multiscale models using an intuitive declarative standardized language. It also facilitates running parallel simulations, automates the optimization and exploration of parameters using supercomputers, and provides a wide range of built-in analysis functions. This will make the S1 model more accessible and simpler to scale, modify and extend in order to explore research questions or interconnect to other existing models. Despite some implementation differences, the NetPyNE model preserved the original cell morphologies, electrophysiological responses and spatial distribution for all 207 cell types; and the connectivity properties of all 1941 pathways, including synaptic dynamics and short-term plasticity (STP). The NetPyNE S1 simulations produced reasonable physiological firing rates and activity patterns across all populations. The network generated a 1 Hz oscillation comparable to the original model in vitro-like state. By then reducing the extracellular calcium concentration, the model reproduced the original S1 in vivo-like states with asynchronous activity. These results validate the original study using a new modeling tool. Simulated local field potentials (LFPs) exhibited realistic oscillatory patterns and features, including distance- and frequency-dependent attenuation. The model was extended by adding thalamic circuits, including 6 distinct thalamic populations with intrathalamic, thalamocortical and corticothalamic connectivity derived from experimental data. The thalamic model reproduced single known cell and circuit-level dynamics, including burst and tonic firing modes and oscillatory patterns, providing a more realistic input to cortex and enabling study of thalamocortical interactions. Overall, our work provides a widely accessible, data-driven and biophysically-detailed model of the somatosensory thalamocortical circuits that can be employed as a community tool for researchers to study neural dynamics, function and disease.
Data-driven multiscale model of macaque auditory thalamocortical circuits reproduces in vivo dynamics
Authors: Dura-Bernal Salvador , Griffith Erica Y , Barczak Annamaria , O’Connell Monica N , McGinnis Tammy , Schroeder Charles E , Lytton William W , Lakatos Peter , Neymotin Samuel A 
Published: February 2022

AbstractWe developed a biophysically-detailed model of the macaque auditory thalamocortical circuits, including primary auditory cortex (A1), medial geniculate body (MGB) and thalamic reticular nuclei (TRN), using the NEURON simulator and NetPyNE multiscale modeling tool. We simulated A1 as a cortical column with a depth of 2000 μm and 200 μm diameter, containing over 12k neurons and 30M synapses. Neuron densities, laminar locations, classes, morphology and biophysics, and connectivity at the long-range, local and dendritic scale were derived from published experimental data. The A1 model included 6 cortical layers and multiple populations of neurons consisting of 4 excitatory and 4 inhibitory types, and was reciprocally connected to the thalamus (MGB and TRN), mimicking anatomical connectivity. MGB included core and matrix thalamocortical neurons with layer-specific projection patterns to A1, and thalamic interneurons projecting locally. Auditory stimulus-related inputs to the MGB were simulated using phenomenological models of the cochlear/auditory nerve and the inferior colliculus. The model generated cell type and layer-specific firing rates consistent with experimentally observed ranges, and accurately simulated the corresponding local field potentials (LFPs), current source density (CSD), and electroencephalogram (EEG) signals. Laminar CSD patterns during spontaneous activity, and in response to speech input, were similar to those recorded experimentally. Physiological oscillations emerged spontaneously across frequency bands without external rhythmic inputs and were comparable to those recorded in vivo. We used the model to unravel the contributions from distinct cell type and layer-specific neuronal populations to oscillation events detected in CSD, and explored how these relate to the population firing patterns. Overall, the computational model provides a quantitative theoretical framework to integrate and interpret a wide range of experimental data in auditory circuits. It also constitutes a powerful tool to evaluate hypotheses and make predictions about the cellular and network mechanisms underlying common experimental measurements, including MUA, LFP and EEG signals.
Multiscale model of primary motor cortex circuits predicts in vivo cell type-specific, behavioral state-dependent dynamics
Authors: Dura-Bernal Salvador , Neymotin Samuel A , Suter Benjamin A , Dacre Joshua , Schiemann Julia , Duguid Ian , Shepherd Gordon MG , Lytton William W 
Published: February 2022

AbstractUnderstanding cortical function requires studying multiple scales: molecular, cellular, circuit and behavior. We developed a biophysically detailed multiscale model of mouse primary motor cortex (M1) with over 10,000 neurons and 30 million synapses. Neuron types, densities, spatial distributions, morphologies, biophysics, connectivity and dendritic synapse locations were tightly constrained by experimental data. The model includes long-range inputs from 7 thalamic and cortical regions, as well as noradrenergic inputs from locus coeruleus. Connectivity depended on cell class and cortical depth at sublaminar resolution. The model accurately predicted in vivo layer- and cell type-specific responses (firing rates and LFP) associated with behavioral states (quiet wakefulness and movement) and experimental manipulations (noradrenaline receptor blocking and thalamus inactivation). It also enabled evaluation of multiple mechanistic hypotheses underlying the observed activity. This quantitative theoretical framework can be used to integrate and interpret M1 experimental data and sheds light on the cell type-specific multiscale dynamics associated with a range of experimental conditions and behaviors.