bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding the impact of preprocessing pipelines on neuroimaging cortical surface analyses
Authors: Bhagwat Nikhil , Barry Amadou , Dickie Erin W , Brown Shawn T , Devenyi Gabriel A , Hatano Koji , DuPre Elizabeth , Dagher Alain , Chakravarty Mallar , Greenwood Celia M T , Misic Bratislav , Kennedy David N , Poline Jean-Baptiste 
Published: January 2021

Abstract

Background
The choice of preprocessing pipeline introduces variability in neuroimaging analyses that affects the reproducibility of scientific findings. Features derived from structural and functional MRI data are sensitive to the algorithmic or parametric differences of preprocessing tasks, such as image normalization, registration, and segmentation to name a few. Therefore it is critical to understand and potentially mitigate the cumulative biases of pipelines in order to distinguish biological effects from methodological variance.

Methods
Here we use an open structural MRI dataset (ABIDE), supplemented with the Human Connectome Project, to highlight the impact of pipeline selection on cortical thickness measures. Specifically, we investigate the effect of (i) software tool (e.g., ANTS, CIVET, FreeSurfer), (ii) cortical parcellation (Desikan-Killiany-Tourville, Destrieux, Glasser), and (iii) quality control procedure (manual, automatic). We divide our statistical analyses by (i) method type, i.e., task-free (unsupervised) versus task-driven (supervised); and (ii) inference objective, i.e., neurobiological group differences versus individual prediction.

Results
Results show that software, parcellation, and quality control significantly affect task-driven neurobiological inference. Additionally, software selection strongly affects neurobiological (i.e. group) and individual task-free analyses, and quality control alters the performance for the individual-centric prediction tasks.

Conclusions
This comparative performance evaluation partially explains the source of inconsistencies in neuroimaging findings. Furthermore, it underscores the need for more rigorous scientific workflows and accessible informatics resources to replicate and compare preprocessing pipelines to address the compounding problem of reproducibility in the age of large-scale, data-driven computational neuroscience.
Towards structural imaging using seismic ambient field correlation artefacts
Authors: Retailleau Lise , Beroza Gregory C 
Published: January 2021

SUMMARY
Correlations of the ambient seismic field recorded by seismic stations carry information about the wave propagation between the stations. They also contain information about the ambient field—both the source of the ambient field, and sources of scattering that contribute to it. The waves that comprise the ambient field are subject to scattering due to the heterogeneous Earth, which can generate supplementary arrivals on the correlation functions. We use these effects to locate sources of signals linked to scattering. For this analysis, we use correlation functions computed from continuous signals recorded between 2013 and 2015 by a line of seismic stations in Central California. We identify spurious arrivals on the Vertical to Vertical and Transverse to Transverse correlation functions and use array analysis to map the source of scattering, which is linked to strong structural variations in the Coast ranges and at the border of the Great Valley.
Monocytes and Macrophages, Targets of Severe Acute Respiratory Syndrome Coronavirus 2: The Clue for Coronavirus Disease 2019 Immunoparalysis
Authors: Boumaza Asma , Gay Laetitia , Mezouar Soraya , Bestion Eloïne , Diallo Aïssatou Bailo , Michel Moise , Desnues Benoit , Raoult Didier , La Scola Bernard , Halfon Philippe , Vitte Joana , Olive Daniel , Mege Jean-Louis 
Published: January 2021

Abstract

Background
Coronavirus disease 2019 (COVID-19) clinical expression is pleiomorphic, severity is related to age and comorbidities such as diabetes and hypertension, and pathophysiology involves aberrant immune activation and lymphopenia. We wondered if the myeloid compartment was affected during COVID-19 and if monocytes and macrophages could be infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Methods
Monocytes and monocyte-derived macrophages (MDMs) from COVID-19 patients and controls were infected with SARS-CoV-2 and extensively investigated with immunofluorescence, viral RNA extraction and quantification, and total RNA extraction followed by reverse-transcription quantitative polymerase chain reaction using specific primers, supernatant cytokines (interleukins 6, 10, and 1β; interferon-β; transforming growth factor–β1, and tumor necrosis factor–α), and flow cytometry. The effect of M1- vs M2-type or no polarization prior to infection was assessed.

Results
SARS-CoV-2 efficiently infected monocytes and MDMs, but their infection is abortive. Infection was associated with immunoregulatory cytokines secretion and the induction of a macrophagic specific transcriptional program characterized by the upregulation of M2-type molecules. In vitro polarization did not account for permissivity to SARS-CoV-2, since M1- and M2-type MDMs were similarly infected. In COVID-19 patients, monocytes exhibited lower counts affecting all subsets, decreased expression of HLA-DR, and increased expression of CD163, irrespective of severity.

Conclusions
SARS-CoV-2 drives monocytes and macrophages to induce host immunoparalysis for the benefit of COVID-19 progression.
SARS-CoV-2 infection of macrophages induces a specific M2 transcriptional program. In Covid-19 patients, monocyte subsets were decreased associated with up-expression of the immunoregulatory molecule CD163 suggesting that SARS-CoV-2 drives immune system for the benefit of Covid-19 disease progression.
Impact of Adding Protein Supplementation to Exercise Training on Lean Body Mass and Muscle Strength in Burn Patients
Authors: Badawy Manar M , Allam Nesma M 
Published: January 2021

Abstract
Protein catabolism is a common complication after burn injury, leading to a loss of muscle mass and a decrease in muscle strength. The present study was aimed to evaluate the efficacy of combining exercise training with protein supplementation on lean body mass and muscle strength in patients with severe burn. Sixty participants with severe burn &gt;30% of TBSA were randomly distributed into four equal groups of 15 participants per group. Group A (Exercise and Protein) received oral protein supplementation (Inkospor X-TREME; 1.5–2.0 g/kg/d), exercise program, and traditional burn care; group B (Protein) received oral protein supplementation and traditional burn care; group C (Exercise) received exercise program and traditional burn care; and group D (Control) received traditional burn care. Lean body mass was measured using dual-energy x-ray absorptiometry, whereas muscle strength was measured using Biodex 3 Dynamometer System before treatment and 12 weeks after treatment. A significant increase in lean body mass was found in group A compared with that of group B, group C, and group D post-treatment (P &lt; .001). Also, a significant increase was recorded in peak torque of group A compared with that of group B, group C, and group D post-treatment (P &lt; .001). Exercise training can significantly increase lean body mass and peak torque. Protein supplementation can significantly increase lean body mass but cannot significantly increase muscle strength, whereas protein + exercise group has a great impact on lean body mass and muscle power than exercise group and protein group in burn patients.
Burn Unit Design—The Missing Link for Quality and Safety
Authors: Gus Eduardo , Almeland Stian Kreken , Barnes David , Elmasry Moustafa , Singer Yvonne , Sjöberg Folke , Steinvall Ingrid , van Zuijlen Paul , Cleland Heather 
Published: January 2021

Abstract
The relationship between infrastructure, technology, model of care, and human resources influences patient outcomes and safety, staff productivity and satisfaction, retention of personnel, and treatment and social costs. This concept underpins the need for evidence-based design and has been widely adopted to inform hospital infrastructure planning. The aim of this review is to establish evidence-based, universally applicable key features of a burn unit that support function in a comprehensive patient-centered model of care. A literature search in medical, architectural, and engineering databases was conducted. Burn associations’ guidelines and relevant articles published in English, between 1990 and 2020, were included, and the available evidence is summarized in the review. Few studies have been published on burn unit design in the past 30 years. Most of them focus on the role of design in infection control and prevention and consist primarily of descriptive or observational reports, opportunistic historical cohort studies, and reviews. The evidence available in the literature is not sufficient to create a definitive infrastructure guideline to inform burn unit design, and there are considerable difficulties in creating evidence that will be widely applicable. In the absence of a strong evidence base, consensus guidelines on burn unit infrastructure should be developed, to help healthcare providers, architects, and engineers make informed decisions, when designing new or renovated facilities.
A New Resuscitation Formula Based on Burn Index Provides More Reliable Prediction for Fluid Requirement in Adult Major Burn Patients
Authors: Tan Jianglin , Zhou Junyi , Li Ning , Yuan Lili , Luo Gaoxing 
Published: January 2021

Abstract
The Third Military Medical University (TMMU) formula is widely used in fluid resuscitation in China. However, the actual volume needs usually exceed the prediction provided by the TMMU formula in major burn patients with a high proportion of full-thickness burn wounds. This retrospective study included 149 adult major burn patients (≥40% TBSA) who were admitted to the Burn Department, Southwest Hospital from 2014 to 2020 and received appropriate fluid resuscitation by the TMMU protocol. The actual volume infused in the first 48 hours postburn was compared to the estimation by the TMMU formula. A new fluid volume prediction formula was developed by multivariate linear regression analysis. The mean fluid requirements were 2.35 ml/kg/% TBSA and 1.75 ml/kg/% TBSA in the first and second 24 hours postburn, respectively. The TMMU formula underestimated the fluid requirement, and its prediction accuracy was 54.1% and 25.8% for the first and second 24 hours, respectively. The proportion of full-thickness burn wound was found to be associated with the fluid requirements postburn. A revised multifactorial formula consisting of the burn index, body weight, and inhalation injury was developed. Using the revised formula, the prediction reliability of resuscitation fluid volume improved to 65.3% and 61.1% in the first and second 24 hours, respectively. The TMMU formula showed low accuracy in predicting fluid requirements among major burn patients. A revised formula based on burn index was developed to provide better guidance for initiative fluid resuscitation for major burns by the TMMU protocol.
Variability in Mammography Quality Assessment After Implementation of Enhancing Quality Using the Inspection Program (EQUIP)
Authors: Funaro Kimberly , Niell Bethany 
Published: January 2021

AbstractObjectiveAnalyze mammography quality and deficiencies, including variability in quality assessment among subspecialized breast radiologists, after implementing the Enhancing Quality Using the Inspection Program (EQUIP).MethodsAfter IRB approval, this single institution study retrospectively queried data prospectively entered into our automated reporting software after implementing EQUIP (October 2017–March 2019). Screening and diagnostic combination (digital mammography with tomosynthesis) mammograms were reviewed by seven breast radiologists. Quality was assessed as excellent, good, adequate, or problems found. Of those with problems found, the deficiency and corrective action were evaluated. The interpreting radiologist, EQUIP radiologist, and performing technologist were recorded. P values were calculated using Fisher exact test and chi-square analyses.ResultsOf 17 312 mammograms, 529 (3%) underwent EQUIP review. Of 43 (8%) with problems found, 23 (53%) did not include sufficient tissue, 9 (21%) had motion degradation, 3 (7%) had artifacts, 2 each (4.7% each) had the nipple not in profile or skin folds, and 4 (9%) were categorized as “other.” Nine (9/529, 1.7%) required recall for repeat imaging. The lead interpreting physician (LIP) was more likely to categorize mammograms as technically inadequate compared to other radiologists (P &lt; 0.00001), and there were also statistically significant differences in how the remaining radiologists stratified cases (P &lt; 0.00001) even when excluding the LIP.ConclusionInsufficient tissue was the most common problem identified in the EQUIP-reviewed mammograms with deficiencies. Significant variability was present among radiologist EQUIP designations. Ongoing review of clinical image quality with EQUIP allows for opportunities to provide corrective feedback.
Gonoactivity of Culex (Culex) (Diptera: Culicidae) Mosquitoes During Winter in Temperate Argentina
Authors: Branda María Florencia , Laurito Magdalena , Visintin Andrés Mario , Almirón Walter Ricardo 
Published: January 2021

Abstract
The subgenus Culex L. includes species involved in summer–autumn arbovirus transmission but studies during winter are scarce in temperate Argentina. Female specimens were collected host-seeking at dry-ice-baited traps during autumn–winter–spring at two sites in Córdoba City during 2016 and 2017. The specimens were morphologically identified and dissected to determine the follicular developmental stage (gonotrophic activity). Females with advanced follicular stages (≥III) were subjected to molecular procedures to confirm or re-identify previous morphological identification. Five species (Culex apicinus Philippi (Diptera: Culicidae), Culex dolosus (Lynch-Arribálzaga) (Diptera: Culicidae), Culex maxi Dyar (Diptera: Culicidae), Culex pipiens pipiens L. (Diptera: Culicidae), and Culex quinquefasciatus Say (Diptera: Culicidae)) were collected and found gonoactive during winter; showing that a high proportion of Culex (Culex) females remain reproductively active during the unfavorable season for mosquito populations. Among them, it is worth noting the collection of Cx. quinquefasciatus, vector of the St. Louis encephalitis virus (endemic in the city), a specimen of Cx. p. pipiens, and a hybrid of Cx. p. pipiens/Cx. quinquefasciatus (during autumn). The study of this community during winter should continue because a high gonoactive female proportion with advanced follicular stages was found: 29.12 and 13.07% in 2016 and 2017, respectively. Local studies such as this one provide evidence about ornithophilic Culex species with active year-round life cycles, species that could favor arbovirus overwintering.
Mechanostimulation: a promising alternative for sustainable agriculture practices
Authors: Ghosh Ritesh , Barbacci Adelin , Leblanc-Fournier Nathalie 
Published: January 2021

AbstractPlants memorize events associated with environmental fluctuations. The integration of environmental signals into molecular memory allows plants to cope with future stressors more efficiently—a phenomenon that is known as ‘priming’. Primed plants are more resilient to environmental stresses than non-primed plants, as they are capable of triggering more robust and faster defence responses. Interestingly, exposure to various forms of mechanical stimuli (e.g. touch, wind, or sound vibration) enhances plants’ basal defence responses and stress tolerance. Thus, mechanostimulation appears to be a potential priming method and a promising alternative to chemical-based priming for sustainable agriculture. According to the currently available method, mechanical treatment needs to be repeated over a month to alter plant growth and defence responses. Such a long treatment protocol restricts its applicability to fast-growing crops. To optimize the protocol for a broad range of crops, we need to understand the molecular mechanisms behind plant mechanoresponses, which are complex and depend on the frequency, intervals, and duration of the mechanical treatment. In this review, we synthesize the molecular underpinnings of plant mechanoperception and signal transduction to gain a mechanistic understanding of the process of mechanostimulated priming.
Of sex and war: carceral feminism and its anti-carceral critique
Authors: Pinto Mattia 
Published: January 2021

Abstract
In the last three decades, wartime sexual violence has become one of the main concerns for feminists engaged with international law. This essay reviews Karen Engle’s monograph on the causes and implications of today’s common-sense narrative about sexual violence in conflict. It shows how Engle’s powerful critique of ‘carceral feminism’ may represent a starting point for a new discussion of sex and war in international law.
Fragmenting Monumentality: Discontinuity and Incompleteness in Mahler’S ‘Der Abschied’
Authors: Deutsch Dan 
Published: January 2021

Abstract
In this article I explore the confluence of Gustav Mahler’s affiliation with a Jewish minority and his approach to musical form and expression. To this end, I devise a theoretical framework that combines Gilles Deleuze and Félix Guattari’s theory of Minor literature with current theories of musical form and analyse selected excerpts from ‘Der Abschied’, the Finale of Mahler’s Das Lied von der Erde (1909). While ‘Der Abschied’ aspires towards monumental expression, it rejects its own realization as a musical monument through musical and textual ambiguities. By means of musical analysis I illustrate how discontinuous and fragmented motion in the musical realm undermines the materialization of apotheotic culminations and negates the interpretative framework of monumentality. Against that background, I then compare Mahler’s formal approach to Kafka’s poetics—the prototype of ‘Minor literature’—and discuss how their ‘Minor works’ concurrently appropriate and subvert the Romantic concept of monumentality and related constructs.
Vibrationally excited HC3N emission in NGC 1068: tracing the recent star formation in the starburst ring
Authors: Rico-Villas F , Martín-Pintado J , González-Alfonso E , Rivilla V M , Martín S , García-Burillo S , Jiménez-Serra I , Sánchez-García M 
Published: January 2021

ABSTRACT
Using the ALMA data, we have studied the HC3N and continuum emission in the starburst pseudo-ring (SB pseudo-ring) and the circumnuclear disc (CND) of the SB/active galactic nucleus (AGN) composite galaxy NGC 1068. We have detected emission from vibrationally excited HC3N (HC3N*) only towards one star-forming region of the SB pseudo-ring. Remarkably, HC3N* was not detected towards the CND despite its large HC3N v = 0 column density. From local thermodynamic equilibrium (LTE) and non-LTE modelling of HC3N*, we obtained a dust temperature (Tdust) of ∼250 K and a density $(n_{\text{H}_2}) \text{ of }6\times 10^5$ cm−3 for this star-forming region. The estimated infrared (IR) luminosity of 5.8 × 108 L⊙ is typical of proto-superstar clusters (proto-SSCs) observed in the SB galaxy NGC 253. We use the continuum emissions at 147 and 350 GHz, along with CO and Pa α, to estimate the ages of other 14 SSCs in the SB pseudo-ring. We find the SSCs to be associated with the region connecting the nuclear bar with the SB pseudo-ring, supporting the inflow scenario. For the CND, our analysis yields Tdust ≤ 100 K and $n_{\text{H}_2}\sim (3\!-\!6)\times 10^5$ cm−3. The very different dust temperatures found for the CND and the proto-SSC indicate that, while the dust in the proto-SSC is being efficiently heated from the inside by the radiation from massive protostars, the CND is being heated externally by the AGN, which in the IR optically thin case can only heat the dust to 56 K. We discuss the implications of the non-detection of HC3N* near the luminous AGN in NGC 1068 on the interpretation of the HC3N* emission observed in the SB/AGN composite galaxies NGC 4418 and Arp 220.
Small-Ncollisional dynamics – V. FromN≲ 10 toN≳ 103
Authors: Barrera Carlos , Leigh Nathan W C , Reinoso Bastián , Stutz Amelia M , Schleicher Dominik 
Published: January 2021

ABSTRACTDirect collisions between finite-sized particles occur commonly in many areas of astrophysics. Such collisions are typically mediated by chaotic, bound gravitational interactions involving small numbers of particles. An important application is stellar collisions, which occur commonly in dense star clusters, and their relevance for the formation of various types of stellar exotica. In this paper, we return to our study of the collision rates and probabilities during small-number chaotic gravitational interactions ($N\, \lesssim$ 10), moving beyond the small-number particle limit and into the realm of larger particle numbers ($N\, \gtrsim$ 103) to test the extent of validity of our analytic model as a function of the particle properties and the number of interacting particles. This is done using direct N-body simulations of stellar collisions in dense star clusters, by varying the relative numbers of particles with different particle masses and radii. We compute the predicted rate of collisions using the mean free path approximation, adopting the point-particle limit and using the sticky-star approximation as our collision criterion. We evaluate its efficacy in the regime where gravitational focusing is important by comparing the theoretical rates to numerical simulations. Using the tools developed in previous papers in this series, in particular Collision Rate Diagrams, we illustrate that our predicted and simulated rates are in excellent agreement, typically consistent with each other to within 1 standard deviation.
Oxidative lesions modulate G-quadruplex stability and structure in the human BCL2 promoter
Authors: Bielskutė Stasė , Plavec Janez , Podbevšek Peter 
Published: January 2021

Abstract
Misregulation of BCL2 expression has been observed with many diseases and is associated with cellular exposure to reactive oxygen species. A region upstream of the P1 promoter in the human BCL2 gene plays a major role in regulating transcription. This G/C-rich region is highly polymorphic and capable of forming G-quadruplex structures. Herein we report that an oxidative event simulated with an 8-oxo-7,8-dihydroguanine (oxoG) substitution within a long G-tract results in a reduction of structural polymorphism. Surprisingly, oxoG within a 25-nt construct boosts thermal stability of the resulting G-quadruplex. This is achieved by distinct hydrogen bonding properties of oxoG, which facilitate formation of an antiparallel basket-type G-quadruplex with a three G-quartet core and a G·oxoG·C base triad. While oxoG has previously been considered detrimental for G-quadruplex formation, its stabilizing effect within a promoter described in this study suggests a potential novel regulatory role of oxidative stress in general and specifically in BCL2 gene transcription.