bluuebunny/crossref_metadata_2025_split huggingface dataset:
Classification of Individual Pain Response Trajectories Following Medically Indicated Heel Lances in Preterm Infants During Their NICU Admission
Authors: Hundert Amos , Woolcott Christy , Dorling Jon , Benoit Britney , Campbell-Yeo Marsha 
Published: December 2021

Objectives:
Infants born preterm are exposed to repeated painful procedures during neonatal intensive care unit admission. Particularly in preterm infants, trajectories of pain response are not well understood. The aim of this study was to classify pain response trajectories over 2 minute following medically indicated heel lances in preterm infants.

Materials and Methods:
This study used existing clinical trial data (NCT01561547) that evaluated the efficacy of kangaroo care and sucrose for infant pain control. Pain was measured using the Premature Infant Pain Profile at 30, 60, 90, and 120 seconds following a heel lance. Group-based trajectory modeling was used to classify pain response in this 2 minute period.

Results:
A total of 236 infants with median gestational age of 33 weeks contributed 610 procedures. A model with 5 trajectory classes best fit the data. Three trajectories were stable over time at different levels of intensity from low-mild to low-moderate pain. One trajectory reflected a linear reduction from high-moderate to low-moderate pain. The final trajectory showed variable moderate-high pain. At all times points, 3 classes were at least 1-point different from the overall sample mean pain score. Only 21 (9%) infants maintained the same class for all 3 procedures.

Discussion:
In this sample of preterm infants receiving pain relief, most pain trajectories reflected mild to low-moderate pain that was stable over 2 minute after heel lance initiation. Trajectories were not consistent over multiple procedures within infants, and an overall mean pain score for the sample may misrepresent subgroups of pain response.
Hybrid Therapy Versus Total En Bloc Spondyectomy in the Treatment of Solitary Radioresistant Spinal Metastases
Authors: Zheng Jianping , Wu Longyun , Shi Jiandang , Niu Ningkui , Yang Zongqiang , Ding Huiqiang 
Published: December 2021

Study Design:
This was a retrospective study.

Objective:
To compare the treatment efficacy of hybrid therapy (HT) with that of total en bloc spondylectomy (TES) in patients with solitary radioresistant high-grade epidural spinal cord compression (ESCC) spinal metastases.

Summary of Background Data:
Both HT and TES can yield good results for solitary radioresistant metastatic spinal tumors with high-grade ESCC. However, there is still a lack of comparative studies on the treatment efficacy of these 2 methods.

Materials and Methods:
We retrospectively reviewed patients with the above-mentioned tumors between January 2012 and May 2019. A total of 157 patients underwent surgery, 64 of whom received HT and 93 were treated with TES. Propensity score matching (1:1 ratio) allowed the generation of best-matched pairs for the 2 categories. Local control rates and survival rates were estimated using the Kaplan-Meier method.

Results:
All patients had a minimum 2-year follow-up. The longest follow-up period was 88 months. The survival rates and local progression-free survival rates after HT were comparable with those after TES at 1 year (84.6% vs. 83.1% and 90.2% vs. 90%, respectively), 2 years (60.8% vs. 64.3% and 64.1% vs. 62.1%, respectively), and 5 years (18.8% vs. 24.1% and 24.4% vs. 28.4%, respectively). There were no significant differences in pain control, improvement in neurological status, spine stabilization restoration, incidence of perioperative complications, and improvement in quality of life between the groups. However, HT showed more advantages than TES in that it had a shorter operative time and lower intraoperative blood loss.

Conclusions:
HT can obtain satisfactory results comparable to TES for solitary radioresistant metastatic spinal tumors with high-grade ESCC. In addition, HT has a shorter operative time and fewer perioperative complications than TES. HT may be a promising treatment for solitary radioresistant metastatic spinal tumors with high-grade ESCC.
Fingerstall-type Tissue Oximetry Reduced Anxiety of Nurses in Postoperative Nursing Monitoring of Free Flaps
Authors: Tsuge Itaru , Yamanaka Hiroki , Katsube Motoki , Sakamoto Michiharu , Saito Susumu , Morimoto Naoki 
Published: December 2021

Background:
Postoperative free flap monitoring is essential for immediately detecting obstruction of anastomosed vessels with successive recovery surgery for salvaging flaps. We performed postoperative nursing monitoring using handheld Doppler sonography, but nurses reported feeling anxious with this approach and demanded a clear-cut evaluation method. Therefore, we implemented monitoring with the fingerstall-type tissue oximeter Toccare, a noninvasive device that enables easy flap checking by simply touching the flap with a probe.

Method:
Handheld Doppler was used for nursing monitoring from April to October 2020, with anxiety associated with its use reported. We collected information via an anonymous questionnaire to determine the reason for the anxiety. Toccare was subsequently applied for postoperative free flap monitoring by nurses. The protocol involved measuring tissue oxygen saturation by touching the flap with a Toccare probe every 4 hours from 24 to 100 hours postoperatively. Seven months later, a second anonymous questionnaire was conducted, and results were compared.

Result:
Free deep inferior epigastric artery perforator flaps and anterolateral thigh flaps (n = 5 each) were included. The average tissue oxygen saturation values in the deep inferior epigastric artery perforator and anterolateral thigh flaps were 52.0% and 52.4%, respectively. According to the second questionnaire about Toccare, 7% felt anxious, 62% felt slightly anxious, and 31% did not feel anxious. Toccare was preferred by 89% of nurses who had used both methods.

Conclusions:
Flap monitoring using Toccare reduced nurses’ anxiety. A numerical evaluation method with easy handling and clear doctor call criteria is essential for low-anxiety nursing monitoring.
Development and Validation of a Model for Prediction of End-Stage Liver Disease in People With HIV
Authors: Kim H. Nina , Nance Robin M. , Lo Re Vincent , Silverberg Michael J. , Franco Ricardo , Sterling Timothy R. , Cachay Edward R. , Horberg Michael A. , Althoff Keri N. , Justice Amy C. , Moore Richard D. , Klein Marina , Crane Heidi M. , Delaney Joseph A. , Kitahata Mari M. 
Published: December 2021

Background:
End-stage liver disease (ESLD) is a leading cause of non–AIDS-related death among people with HIV (PWH). Factors that increase the progression of liver disease include comorbidities and HIV-specific factors, but we currently lack a tool to apply this evidence into clinical practice.

Methods:
We developed and validated a risk prediction model for ESLD among PWH who received care in 12 cohorts of the North American AIDS Cohort Collaboration on Research and Design between 2000 and 2016 and had fibrosis-4 index > 1.45. The first occurrence of ascites, variceal bleed, spontaneous bacterial peritonitis, or hepatic encephalopathy was verified by standardized medical record review. The Bayesian model averaging was used to select predictors among biomarkers and diagnoses and the Harrell C statistic to assess model discrimination.

Results:
Among 13,787 PWH in the training set, 82% were men and 54% were Black with a mean age of 48 years. Three hundred ninety ESLD events occurred over a mean 5.4 years. Among the ESLD cases, 52% had hepatitis C virus, 15% hepatitis B virus, and 31% alcohol use disorder. Twelve factors together predicted ESLD risk moderately well (C statistic 0.79, 95% confidence interval: 0.76 to 0.81): age, sex, race/ethnicity, chronic hepatitis B or C, and routinely collected laboratory values reflecting hepatic impairment (serum albumin, aspartate aminotransferase, total bilirubin, and platelets) and lipid metabolism (triglycerides, high-density lipoprotein, and total cholesterol). Our model performed well in the test set (C statistic 0.81, 95% confidence interval: 0.76 to 0.86).

Conclusion:
This model of readily accessible clinical parameters predicted ESLD in a large diverse population of PWH.
Quantum pattern recognition algorithms for charged particle tracking
Authors: Gray H. M. 
Published: December 2021

High-energy physics is facing a daunting computing challenge with the large datasets expected from the upcoming High-Luminosity Large Hadron Collider in the next decade and even more so at future colliders. A key challenge in the reconstruction of events of simulated data and collision data is the pattern recognition algorithms used to determine the trajectories of charged particles. The field of quantum computing shows promise for transformative capabilities and is going through a cycle of rapid development and hence might provide a solution to this challenge. This article reviews current studies of quantum computers for charged particle pattern recognition in high-energy physics.
This article is part of the theme issue ‘Quantum technologies in particle physics’.
Dynamics of the habitat use of three predatory freshwater fish in a lentic ecosystem
Authors: Říha Milan , Rabaneda-Bueno Ruben , Jarić Ivan , Souza Allan T. , Vejřík Lukáš , Draštík Vladislav , Blabolil Petr , Holubová Michaela , Jůza Tomas , Gjelland Karl Ø. , Rychtecký Pavel , Sajdlová Zuzana , Kočvara Luboš , Tušer Michal , Prchalová Marie , Seďa Jaromír , Peterka Jiří 
Published: December 2021

AbstractTo understand the conditions of coexistence in multiple-species predator community, we studied longitudinal and vertical movement of pike (Esox lucius), pikeperch (Sander lucioperca) and catfish (Silurus glanis) in the Římov Reservoir, using an autonomous telemetry system for 11 months. We found significant differences among these three species in movement and depth that varied considerably in time, with the greatest differences between warm (late spring and early autumn) and cold season (late autumn to early spring). Preference for different sections of the reservoir was stable for pike, while pikeperch and catfish frequently visited tributary during the warm season, and moved closer to the dam during the cold season. Pike longitudinal activity was highest in the cold season, pikeperch in the warm season, and catfish activity peaked in both the warm and cold seasons. Overlap in the depth used among species was higher in the warm season, when all species used the upper layer of the water column, and lower in cold season, when pikeperch and catfish used deeper areas. These results demonstrated ability of predators to actively inspect a large portion of the reservoir in both longitudinal and vertical dimensions, although differing in the timing of their habitat use and activity.
Orbitofrontal cortex contributes to the comparison of values underlying economic choices
Authors: Ballesta Sébastien , Shi Weikang , Padoa-Schioppa Camillo 
Published: December 2021

Economic choices between goods entail the computation and comparison of subjective values. Previous studies examined neuronal activity in the orbitofrontal cortex (OFC) of monkeys choosing between different types of juices. Three groups of neurons were identified: offer value cells encoding the value of individual offers, chosen juice cells encoding the identity of the chosen juice, and chosen value cells encoding the value of the chosen offer. The encoded variables capture both the input (offer value) and the output (chosen juice, chosen value) of the decision process, suggesting that values are compared within OFC. Recent work demonstrates that choices are causally linked to the activity of offer value cells. Conversely, the hypothesis that OFC contributes to value comparison has not been confirmed. Here we show that weak electrical stimulation of OFC specifically disrupts value comparison without altering offer values. This result implies that neuronal populations in OFC participate in the decision process.SignificanceEconomic choices encompass two mental stages: values are assigned to the available offers, and a decision is made by comparing values. Previous work showed that choices are causally related to offer values encoded in the orbitofrontal cortex (OFC). Conversely, the neural underpinnings of value comparison remain poorly understood. Here we show that weak electrical stimulation of OFC selectively disrupts the decision process without affecting offer values. Hence, neurons in OFC contribute to value comparison.
Skin resident memory cells generated by the L. major centrin gene deleted parasites mediate protective immune response analogous to leishmanization
Authors: Ismail Nevien , Karmakar Subir , Bhattacharya Parna , Sepahpour Telly , Takeda Kazuyo , Hamano Shinjiro , Matlashewski Greg , Satoskar Abhay R. , Gannavaram Sreenivas , Dey Ranadhir , Nakhasi Hira L. 
Published: December 2021

ABSTRACTLeishmaniasis is a vector-borne parasitic disease transmitted through the bite of a sand fly with no available vaccine for humans. Recently, we have developed a live attenuated Leishmania major centrin gene deleted parasite strain (LmCen-/-) that induced protection against a homologous and heterologous challenges. The protection is mediated by IFNγ secreting CD4+ T effector cells and multifunctional T cells, which is analogous to leishmanization. Previously, skin tissue resident memory T cells (TRM cells) were shown to be crucial for host protection in a leishmanization model. In this study, we evaluated generation and function of skin TRM cells following immunization with LmCen-/- parasites and compared those with leishmanization. In the absence of recoverable LmCen-/- parasites, the skin of immunized mice showed functional TRM cells comparable to leishmanized mice. The generation of the skin TRM cells was supported by the induction of cytokines and chemokines essential for their production and survival. Following challenge infection with wild type L. major, TRM cells specific to L. major were rapidly recruited and proliferated at the site of infection in the immunized mice which was similar to leishmanization. Further, upon challenge, CD4+ TRM cells induced higher levels of IFNγ and Granzyme B in the immunized and leishmanized mice than non-immunized mice. Taken together, our studies demonstrate that a genetically modified live attenuated Leishmania vaccine generates functional CD4+ TRM cells that mediate protection and can be a safer alternative to leishmanization.
Emergent Diversity and Persistent Turnover in Evolving Microbial Cross-Feeding Networks
Authors: Lücken Leonhard , Lennartz Sinikka T. , Froehlich Jule , Blasius Bernd 
Published: December 2021

AbstractA distinguishing feature of many ecological networks in the microbial realm is the diversity of substrates that could potentially serve as energy sources for microbial consumers. The microorganisms are themselves the agents of compound diversification via metabolite excretion or overflow metabolism. It has been suggested that the emerging richness of different substrates is an important condition for the immense biological diversity in microbial ecosystems. In this work, we study how complex cross-feeding networks (CFN) of microbial species may develop from a simple initial community given some elemental evolutionary mechanisms of resource-dependent speciation and extinctions using a network flow model. We report results of several numerical experiments and report an in-depth analysis of the evolutionary dynamics. We find that even in stable environments, the system is subject to persisting turnover, indicating an ongoing co-evolution. Further, we compare the impact of different parameters, such as the ratio of mineralization, as well as the metabolic versatility and variability on the evolving community structure. The results imply that high microbial and molecular diversity is an emergent property of evolution in cross-feeding networks, which affects transformation and accumulation of substrates in natural systems, such as soils and oceans, with potential relevance to biotechnological applications.
Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic
Authors: Mogro Ezequiel G. , Bottero Daniela , Lozano Mauricio J. 
Published: December 2021

AbstractSARS-CoV-2, the seventh coronavirus known to infect humans, can cause severe life-threatening respiratory pathologies. To better understand SARS-CoV-2 evolution, genome-wide analyses have been made, including the general characterization of its codons usage profile. Here we present a bioinformatic analysis of the evo-lution of SARS-CoV-2 codon usage over time using complete genomes collected since December 2019. Our results show that SARS-CoV-2 codon usage pattern is antagonistic to, and it is getting farther away from that of the human host. Further, a selection of deoptimized codons over time, which was accompanied by a decrease in both the codon adaptation index and the effective number of codons, was observed. All together, these findings suggest that SARS-CoV-2 could be evolving, at least from the perspective of the synonymous codon usage, to become less pathogenic.Graphical Abstract
Caste- and sex-specific DNA methylation in a bumblebee is associated with codon degeneracy
Authors: Marshall H. , Nicholas M.T. , van Zweden J.S. , Wäckers F. , Ross L. , Wenseleers T. , Mallon E.B. 
Published: December 2021

AbstractSocial insects display extreme phenotypic differences between sexes and castes even though the underlying genome can be almost identical. Epigenetic processes have been proposed as a possible mechanism for mediating these phenotypic differences. Using whole genome bisulfite sequencing of queens, males and reproductive female workers we have characterised the sex- and caste-specific methylome of the bumblebee Bombus terrestris. We have identified a potential role for DNA methylation in histone modification processes which may influence sex and caste phenotypic differences. We also find differentially methylated genes generally show low levels of DNA methylation which may suggest a separate function for lowly methylated genes in mediating transcriptional plasticity. Unlike highly methylated genes which are usually involved in housekeeping functions. We also examined the relationship between the underlying genome and the methylome using whole genome re-sequencing of the same queens and males. We find DNA methylation is enriched at zero-fold degenerate sites. We suggest DNA methylation may be acting as a mutagen at these sites thereby providing substrate for selection via changes in gene transcription mediated by the underlying genotype. However, we did not see any relationship between DNA methylation and rates of positive selection in our samples. In order to fully assess a possible role for DNA methylation in adaptive processes a specifically designed study using natural population data is needed.
Disrupted Peyer’s patch microanatomy in COVID-19 including germinal centre atrophy independent of local virus
Authors: Trevelin Silvia C. , Pickering Suzanne , Todd Katrina , Bishop Cynthia , Pitcher Michael , Mesa Jose Garrido , Montorsi Lucia , Spada Filomena , Petrov Nedyalko , Green Anna , Shankar-Hari Manu , Neil Stuart J.D. , Spencer Jo 
Published: December 2021

AbstractConfirmed SARS-coronavirus-2 infection with gastrointestinal symptoms and changes in microbiota associated with coronavirus disease 2019 (COVID-19) severity have been previously reported, but the disease impact on the architecture and cellularity of ileal Peyer’s patches (PP) remains unknown. Here we analysed post-mortem tissues from throughout the gastrointestinal (GI) tract of patients who died with COVID-19. When virus was detected by PCR in the GI tract, immunohistochemistry identified virus in epithelium and lamina propria macrophages, but not in lymphoid tissues. Immunohistochemistry and imaging mass cytometry (IMC) analysis of ileal PP revealed depletion of germinal centres (GC), disruption of B cell/T cell zonation and decreased potential B and T cell interaction and lower nuclear density in COVID-19 patients. This occurred independent of the local viral levels. The changes in PP demonstrate that the ability to mount an intestinal immune response is compromised in severe COVID-19, which could contribute to observed dysbiosis.
ILC homeostasis phenotyping in various tissues, aging, and sex differences
Authors: Mobley Alexis S , Garrido Jesus Bautista , Honarpisheh Pedram , d’Aigle John , McCullough Louise D , Aronowski Jaroslaw 
Published: December 2021

AbstractInnate lymphoid cells are the innate counterpart to CD4+ T cells that are mediated by the same transcription factors and produce similar cytokines. ILCs are being investigated in many different disease states, but the field current lacks foundational information on ILC representation whether it be in tissues, between males and females, or in aging as these are all vital components in disease etiology and severity. Our descriptive study used flow cytometry to characterize ILCs compared to the entire CD45+ (e.g., lymphocyte) and lineage negative (e.g., ILC) compartments to understand their homeostatic balance and plasticity. Moreover, we defined ILC2 expression and subsets based on their cytokine production and created several mathematical models to elucidate the correlation of extra- and intra-cellular ILC2 markers from least to most complex. ILC studies would benefit from more unbiased, holistic experiments including RNA-seq and mass spectroscopy to further define ILCs in steady state before adding more complex pathways like different disease states to enhance translational value and therapeutic targeting of these cells.
DeepMed: A unified, modular pipeline for end-to-end deep learning in computational pathology
Authors: van Treeck Marko , Cifci Didem , Laleh Narmin Ghaffari , Saldanha Oliver Lester , Loeffler Chiara M. L. , Hewitt Katherine J. , Muti Hannah Sophie , Echle Amelie , Seibel Tobias , Seraphin Tobias Paul , Trautwein Christian , Foersch Sebastian , Luedde Tom , Truhn Daniel , Kather Jakob Nikolas 
Published: December 2021

AbstractThe interpretation of digitized histopathology images has been transformed thanks to artificial intelligence (AI). End-to-end AI algorithms can infer high-level features directly from raw image data, extending the capabilities of human experts. In particular, AI can predict tumor subtypes, genetic mutations and gene expression directly from hematoxylin and eosin (H&E) stained pathology slides. However, existing end-to-end AI workflows are poorly standardized and not easily adaptable to new tasks. Here, we introduce DeepMed, a Python library for predicting any high-level attribute directly from histopathological whole slide images alone, or from images coupled with additional meta-data (https://github.com/KatherLab/deepmed). Unlike earlier computational pipelines, DeepMed is highly developer-friendly: its structure is modular and separates preprocessing, training, deployment, statistics, and visualization in such a way that any one of these processes can be altered without affecting the others. Also, DeepMed scales easily from local use on laptop computers to multi-GPU clusters in cloud computing services and therefore can be used for teaching, prototyping and for large-scale applications. Finally, DeepMed is user-friendly and allows researchers to easily test multiple hypotheses in a single dataset (via cross-validation) or in multiple datasets (via external validation). Here, we demonstrate and document DeepMed’s abilities to predict molecular alterations, histopathological subtypes and molecular features from routine histopathology images, using a large benchmark dataset which we release publicly. In summary, DeepMed is a fully integrated and broadly applicable end-to-end AI pipeline for the biomedical research community.