bluuebunny/crossref_metadata_2025_split huggingface dataset:
Domain-specific cues improve robustness of deep learning-based segmentation of CT volumes
Authors: Kloenne Marie , Niehaus Sebastian , Lampe Leonie , Merola Alberto , Reinelt Janis , Roeder Ingo , Scherf Nico 
Published: July 2020

AbstractMachine learning has considerably improved medical image analysis in the past years. Although data-driven approaches are intrinsically adaptive and thus, generic, they often do not perform the same way on data from different imaging modalities. In particular computed tomography (CT) data poses many challenges to medical image segmentation based on convolutional neural networks (CNNs), mostly due to the broad dynamic range of intensities and the varying number of recorded slices of CT volumes. In this paper, we address these issues with a framework that adds domain-specific data preprocessing and augmentation to state-of-the-art CNN architectures. Our major focus is to stabilise the prediction performance over samples as a mandatory requirement for use in automated and semi-automated workflows in the clinical environment. To validate the architecture-independent effects of our approach we compare a neural architecture based on dilated convolutions for parallel multi-scale processing (a modified Mixed-Scale Dense Network: MS-D Net) to traditional scaling operations (a modified U-Net). Finally, we show that an ensemble model combines the strengths across different individual methods. Our framework is simple to implement into existing deep learning pipelines for CT analysis. It performs well on a range of tasks such as liver and kidney segmentation, without significant differences in prediction performance on strongly differing volume sizes and varying slice thickness. Thus our framework is an essential step towards performing robust segmentation of unknown real-world samples.
Immunosuppressive properties of cytochalasin B-induced membrane vesicles of mesenchymal stem cells: comparing with extracellular vesicles derived from mesenchymal stem cells
Authors: Gomzikova M. O. , Aimaletdinov A. M. , Bondar O. V. , Starostina I. G. , Gorshkova N. V. , Neustroeva O. A. , Kletukhina S. K. , Kurbangaleeva S. V. , Vorobev V. V. , Garanina E. E. , Persson J. L. , Jeyapalan J. , Mongan N. P. , Khaiboullina S. F. , Rizvanov A. A. 
Published: July 2020

AbstractExtracellular vesicles derived from mesenchymal stem cells (MSCs) represent a novel approach for regenerative and immunosuppressive therapy. Recently, cytochalasin B-induced microvesicles (CIMVs) were shown to be effective drug delivery mediators. However, little is known about their immunological properties. We propose that the immunophenotype and molecular composition of these vesicles could contribute to the therapeutic efficacy of CIMVs. To address this issue, CIMVs were generated from murine MSC (CIMVs-MSCs) and their cytokine content and surface marker expression determined. For the first time, we show that CIMVs-MSCs retain parental MSCs phenotype (Sca-1+, CD49e+, CD44+, CD45−). Also, CIMVs-MSCs contained a cytokine repertoire reflective of the parental MSCs, including IL-1β, IL-2, IL-3, IL-4, IL-5, IL-6, IL-9, IL-10, IL-12(p40), IL-13, IL-17, CCL2, CCL3, CCL4, CCL5, CCL11, G-CSF, GM-CSF and TNF-α. Next, we evaluated the immune-modulating properties of CIMVs-MSCs in vivo using standard preclinical tests. MSCs and CIMVs-MSCs reduced serum levels of anti-sheep red blood cell antibody and have limited effects on neutrophil and peritoneal macrophage activity. We compared the immunomodulatory effect of MSCs, CIMVs and EVs. We observed no immunosuppression in mice pretreated with natural EVs, whereas MSCs and CIMVs-MSCs suppressed antibody production in vivo. Additionally, we have investigated the biodistribution of CIMVs-MSCs in vivo and demonstrated that CIMVs-MSCs localized in liver, lung, brain, heart, spleen and kidneys 48 h after intravenous injection and can be detected 14 days after subcutaneous and intramuscular injection. Collectively our data demonstrates immunomodulatory efficacy of CIMVs and supports their further preclinical testing as an effective therapeutic delivery modality.
Avocado (Persea americana) pulp improves cardiovascular and autonomic recovery following submaximal running: a crossover, randomized, double-blind and placebo-controlled trial
Authors: Sousa Fernando H. , Valenti Vitor E. , Pereira Leticia C. , Bueno Rafaela R. , Prates Sara , Akimoto Amanda N. , Kaviani Mojtaba , Garner David M. , Amaral Joice A. T. , de Abreu Luiz Carlos 
Published: July 2020

AbstractPrevious studies have demonstrated that regular avocado consumption presents advantageous effects on cardiovascular system. However, little attention has been paid to the use of avocado as a dietary supplement, in particular, for individuals involved in physical exercise training. Therefore, this study aims to evaluate the effect of acute avocado pulp intake on cardiovascular and autonomic recovery subsequent to moderate exercise. Using a crossover, randomized, double-blind and placebo-controlled trial design, 16 healthy female adults underwent two protocols: Avocado pulp (600 mg in capsule) and placebo (600 mg starch in capsule). After the ingestion of Avocado pulp or placebo, the subjects were seated for 60 min at rest, followed by running on a treadmill at a submaximal level and then remained seated for 60 min during recovery from the exercise. Heart rate (HR), heart rate variability (HRV) [rMSSD, SD1, HF (ms2)] and skin conductance were evaluated before and during exercise, as well as during recovery. HR, systolic blood pressure, HRV and skin conductance recovered faster when subjects were given avocado pulp prior to exercise. In conclusion, avocado pulp improved cardiovascular and autonomic recovery after exercise, suggesting a reduced risk of cardiovascular events after exertion. The current results support the beneficial effects of ingestion of avocado prior to submaximal treadmill running.
Evaluation of enhanced recovery after surgery program components implemented in laparoscopic appendectomy: prospective randomized clinical study
Authors: Nechay Taras , Sazhin Alexander , Titkova Svetlana , Tyagunov Alexander , Anurov Mikhail , Melnikov-Makarchuk Kirill , Tyagunov Anton 
Published: July 2020

Abstract
Background
Laparoscopic appendectomy (LA) is a widely used surgical procedure. Patients often suffer from considerable postoperative pain and indigestion, which prolongs their in-hospital stay. Almost 10% of patients develop postoperative complications. The enhanced recovery after surgery (ERAS) program has proven its efficacy in elective surgery and could hypothetically improve LA outcomes. Currently, there is no ERAS program for LA.

Methods
A modified ERAS (mERAS) protocol was studied in a prospective, randomized nonblinded clinical trial. The mERAS group consisted of 50 patients; the control group, of 54 patients. The mERAS protocol included a patient information brochure; minimizing drain use; local anesthesia; low-pressure pneumoperitoneum; early mobilization and oral diet. The primary outcome was postoperative length of stay (pLOS).

Results
Modified protocol reduced median pLOS to 1.25 days vs 2 days in the controls (p < 0.0001). Twenty-one (42%) mERAS patients and 4 (7.4%) controls were discharged within 24 h (p < 0.001) after surgery; 0 readmissions were reported. Postoperative pain intensity assessed on the visual analogue scale was significantly lower in the mERAS group [mERAS vs control 0 h, 2 h, 6 h, 12 h and 24 h after surgery: 2.33 ± 2.12 vs 4.19 ± 2.08 (p < 0.0001), 2.27 ± 1.91 vs 4.02 ± 1.89 (p < 0.0001), 2.28 ± 1.98 vs 3.70 ± 1.57 (p = 0.0001), 1.98 ± 1.72 vs 3.43 ± 1.54 (p < 0.0001) and 1.80 ± 1.74 vs 3.00 ± 1.27 (p = 0.032), respectively)]. The severity of shoulder and neck pain was lower but its incidence was similar. Peristalsis recovery was achieved earlier in the study group (median (min–max))—mERAS 7 (2–34) h vs control 11 (3–43) h; p = 0.009) but did not affect the time of the first flatus 23 (2–72) h vs 29 (6–70) h, respectively; p = 0.499).

Conclusions
The modified ERAS program for LA has advantages over the traditional approach.

Registration
This trial was registered at ClinicalTrials.gov as NCT03754777 (27/11/2018).
Incidence and impact of extra-pulmonary organ failures on hospital mortality in acute exacerbation of idiopathic pulmonary fibrosis
Authors: Zhuang Yi , Zhou Ying , Qiu Xiaohua , Xiao Yonglong , Cai Hourong , Dai Jinghong 
Published: July 2020

AbstractTo evaluate hospital mortality and associated risk factors for acute exacerbations of idiopathic pulmonary fibrosis (AEIPF). Emphases were put on incidence and impact of extra-pulmonary organ failures. Patients diagnosed with AEIPF from July 2014 to September 2018 were enrolled. Clinical data were collected. Acute physiology and chronic health evaluation II (APACHE II) and simplified acute physiological score II (SAPS II) were calculated. Extra-pulmonary organ failures were diagnosed upon criteria of sequential organ failure assessment (SOFA). Forty-five patients with AEIPF were included. Eighteen patients (40.0%) developed extra-pulmonary organ failures, and 25 patients (55.6%) died during hospitalization. Serum C-reactive protein (CRP) (p = 0.001), SAPS II (p = 0.004), SOFA (p = 0.001) were higher, whereas arterial oxygen pressure (PaO2)/ fractional inspired oxygen (FiO2) (p = 0.001) was lower in non-survivors than survivors. More non-survivors developed extra-pulmonary organ failures than survivors (p = 0.002). After adjustment, elevated serum CRP (OR 1.038, p = 0.049) and extra-pulmonary organ failure (OR 13.126, p = 0.016) were independent predictors of hospital mortality in AEIPF. AEIPF had high hospital mortality and occurrence of extra-pulmonary organ failure was common. Elevated serum CRP and extra-pulmonary organ failure had predictive values for mortality.
An in vitro methodology for discovering broadly-neutralizing monoclonal antibodies
Authors: Ahmadi Shirin , Pucca Manuela B. , Jürgensen Jonas A. , Janke Rahel , Ledsgaard Line , Schoof Erwin M. , Sørensen Christoffer V. , Çalışkan Figen , Laustsen Andreas H. 
Published: July 2020

AbstractBroadly-neutralizing monoclonal antibodies are of high therapeutic utility against infectious diseases caused by bacteria and viruses, as well as different types of intoxications. Snakebite envenoming is one such debilitating pathology, which is currently treated with polyclonal antibodies derived from immunized animals. For the development of novel envenoming therapies based on monoclonal antibodies with improved therapeutic benefits, new discovery approaches for broadly-neutralizing antibodies are needed. Here, we present a methodology based on phage display technology and a cross-panning strategy that enables the selection of cross-reactive monoclonal antibodies that can broadly neutralize toxins from different snake species. This simple in vitro methodology is immediately useful for the development of broadly-neutralizing (polyvalent) recombinant antivenoms with broad species coverage, but may also find application in the development of broadly-neutralizing antibodies against bacterial, viral, and parasitic agents that are known for evading therapy via resistance mechanisms and antigen variation.
The effect of social media on well-being differs from adolescent to adolescent
Authors: Beyens Ine , Pouwels J. Loes , van Driel Irene I. , Keijsers Loes , Valkenburg Patti M. 
Published: July 2020

AbstractThe question whether social media use benefits or undermines adolescents’ well-being is an important societal concern. Previous empirical studies have mostly established across-the-board effects among (sub)populations of adolescents. As a result, it is still an open question whether the effects are unique for each individual adolescent. We sampled adolescents’ experiences six times per day for one week to quantify differences in their susceptibility to the effects of social media on their momentary affective well-being. Rigorous analyses of 2,155 real-time assessments showed that the association between social media use and affective well-being differs strongly across adolescents: While 44% did not feel better or worse after passive social media use, 46% felt better, and 10% felt worse. Our results imply that person-specific effects can no longer be ignored in research, as well as in prevention and intervention programs.
Conservation and divergence in NaChBac and NaV1.7 pharmacology reveals novel drug interaction mechanisms
Authors: Zhu Wandi , Li Tianbo , Silva Jonathan R. , Chen Jun 
Published: July 2020

AbstractVoltage-gated Na+ (NaV) channels regulate homeostasis in bacteria and control membrane electrical excitability in mammals. Compared to their mammalian counterparts, bacterial NaV channels possess a simpler, fourfold symmetric structure and have facilitated studies of the structural basis of channel gating. However, the pharmacology of bacterial NaV remains largely unexplored. Here we systematically screened 39 NaV modulators on a bacterial channel (NaChBac) and characterized a selection of compounds on NaChBac and a mammalian channel (human NaV1.7). We found that while many compounds interact with both channels, they exhibit distinct functional effects. For example, the local anesthetics ambroxol and lidocaine block both NaV1.7 and NaChBac but affect activation and inactivation of the two channels to different extents. The voltage-sensing domain targeting toxin BDS-I increases NaV1.7 but decreases NaChBac peak currents. The pore binding toxins aconitine and veratridine block peak currents of NaV1.7 and shift activation (aconitine) and inactivation (veratridine) respectively. In NaChBac, they block the peak current by binding to the pore residue F224. Nonetheless, aconitine has no effect on activation or inactivation, while veratridine only modulates activation of NaChBac. The conservation and divergence in the pharmacology of bacterial and mammalian NaV channels provide insights into the molecular basis of channel gating and will facilitate organism-specific drug discovery.
The effect of commercial functional food with probiotics on microorganisms from early carious lesions
Authors: Angarita-Díaz María del Pilar , Arias Johanna C. , Bedoya-Correa Claudia , Cepeda María J. , Arboleda María F. , Chacón Juan M. , Leal Yenny 
Published: July 2020

AbstractCaries rates in school-age children are still high enough to be the cause of serious concern for health systems in different countries. The biotechnology strategies studied to decrease these rates include the consumption of probiotics—available via a variety of functional foods obtainable on the market—that are able to inhibit bacteria associated with this disease. In this vein, the purpose of this study was to determine the effect of these foods on the growth of microorganisms in early carious lesions in children aged between 6 and 12. In the first phase, an agar well diffusion method was applied to selected foods, available in supermarkets, which contain probiotics that have already been shown to inhibit Streptococcusmutans (ATCC 25175), and to lower the pH in liquid culture media. In a second phase, these foods (n = 4) were examined in terms of their ability to inhibit the microorganisms in contact with early carious lesions in children and to reduce the pH of mixed cultures combined with the food. The results revealed that, of the foods tested, three inhibit the growth of microorganisms in carious lesions and, at the same time, lower the pH of the culture by more than 2.5 units. The food with the highest inhibitory capacity (14 mm, IQR 13–14) showed a similar effect among patients (P > 0.05), which together with the fact that its sugar concentration is less than 10%, makes it an ideal candidate for clinical study.
Cognitive–Linguistic Functions in Adults With Epilepsy: Preliminary Electrophysiological and Behavioral Findings
Authors: Dutta Manaswita , Murray Laura L. , Miller Wendy , Innis Isaiah , Newman Sharlene 
Published: July 2020

Purpose

Cognition and language difficulties are frequently reported in both children and adults with epilepsy. The majority of the existing research has focused on pediatric epilepsy, documenting impairments in learning, academics, and social–emotional functioning. In comparison, language deficits in younger and older adults with epilepsy have received less empirical attention. Given recently identified limitations in the extant literature regarding assessing epilepsy-related language problems in adults (
Dutta et al., 2018
), the current exploratory study described in this research note investigated the cognitive–linguistic abilities of adults with focal or generalized types of epilepsy.

Method
Twelve participants with epilepsy and 11 age- and education-matched healthy controls completed a cognitive–linguistic test battery. Event-related potential (ERP) procedures were also employed to assess the integrity of neural activity supporting psycholinguistic processing in both groups using a lexical decision task.

Results
No significant performance differences between epilepsy and healthy control groups were noted on basic language tasks; however, group differences were evident on the more complex language measures, including spoken discourse. Even though both groups performed the lexical decision task similarly in terms of accuracy, individuals with epilepsy demonstrated longer reaction times and some atypical ERP characteristics compared to controls.

Conclusion
The cognitive–linguistic assessment and ERP findings suggested that, compared to neurotypical adults, individuals with epilepsy demonstrate slower processing times and greater difficulty with high-level language and spoken discourse production, despite performing within typical limits on basic language tests. Preliminary results from this research are significant in providing new knowledge about language functioning in adults with epilepsy.
Estimation of Subglottal Pressure From Neck Surface Vibration in Patients With Voice Disorders
Authors: Marks Katherine L. , Lin Jonathan Z. , Burns James A. , Hron Tiffiny A. , Hillman Robert E. , Mehta Daryush D. 
Published: July 2020

PurposeGiven the established linear relationship between neck surface vibration magnitude and mean subglottal pressure (Ps) in vocally healthy speakers, the purpose of this study was to better understand the impact of the presence of a voice disorder on this baseline relationship.MethodData were obtained from participants with voice disorders representing a variety of glottal conditions, including phonotraumatic vocal hyperfunction, nonphonotraumatic vocal hyperfunction, and unilateral vocal fold paralysis. Participants were asked to repeat /p/-vowel syllable strings from loud-to-soft loudness levels in multiple vowel contexts (/pa/, /pi/, /pu/) and pitch levels (comfortable, higher than comfortable, lower than comfortable). Three statistical metrics were computed to analyze the regression line between neck surface accelerometer (ACC) signal magnitude and Ps within and across pitch, vowel, and voice disorder category: coefficient of determination (r2), slope, and intercept. Three linear mixed-effects models were used to evaluate the impact of voice disorder category, pitch level, and vowel context on the relationship between ACC signal magnitude and Ps.ResultsThe relationship between ACC signal magnitude and Ps was statistically different in patients with voice disorders than in vocally healthy controls; patients exhibited higher levels of Ps given similar values of ACC signal magnitude. Negligible effects were found for pitch condition within each voice disorder category, and negligible-to-small effects were found for vowel context. The mean of patient-specificr2values was .63, ranging from .13 to .92.ConclusionsThe baseline, linear relationship between ACC signal magnitude and Ps is affected by the presence of a voice disorder, with the relationship being participant-specific. Further work is needed to improve ACC-based prediction of Ps, across treatment, and during naturalistic speech production.
Cobalt and copper abundances in 56 Galactic bulge red giants
Authors: Ernandes H. , Barbuy B. , Friaça A. C. S. , Hill V. , Zoccali M. , Minniti D. , Renzini A. , Ortolani S. 
Published: July 2020

Context. The Milky Way bulge is an important tracer of the early formation and chemical enrichment of the Galaxy. The abundances of different iron-peak elements in field bulge stars can give information on the nucleosynthesis processes that took place in the earliest supernovae. Cobalt (Z = 27) and copper (Z = 29) are particularly interesting.
Aims. We aim to identify the nucleosynthesis processes responsible for the formation of the iron-peak elements Co and Cu.
Methods. We derived abundances of the iron-peak elements cobalt and copper in 56 bulge giants, 13 of which were red clump stars. High-resolution spectra were obtained using FLAMES-UVES at the ESO Very Large Telescope by our group in 2000–2002, which appears to be the highest quality sample of optical high-resolution data on bulge red giants obtained in the literature to date. Over the years we have derived the abundances of C, N, O, Na, Al, Mg; the iron-group elements Mn and Zn; and neutron-capture elements. In the present work we derive abundances of the iron-peak elements cobalt and copper. We also compute chemodynamical evolution models to interpret the observed behaviour of these elements as a function of iron.
Results. The sample stars show mean values of [Co/Fe] ~ 0.0 at all metallicities, and [Cu/Fe] ~ 0.0 for [Fe/H] ≥−0.8 and decreasing towards lower metallicities with a behaviour of a secondary element.
Conclusions. We conclude that [Co/Fe] varies in lockstep with [Fe/H], which indicates that it should be produced in the alpha-rich freezeout mechanism in massive stars. Instead [Cu/Fe] follows the behaviour of a secondary element towards lower metallicities, indicating its production in the weak s-process nucleosynthesis in He-burning and later stages. The chemodynamical models presented here confirm the behaviour of these two elements (i.e. [Co/Fe] vs. [Fe/H] ~constant and [Cu/Fe] decreasing with decreasing metallicities).
Applications of neutron reflectometry in biology
Authors: Gerelli Yuri 
Published: July 2020

Over the last 10 years, neutron reflectometry (NR) has emerged as a powerful technique for the investigation of biologically relevant thin films. The great advantage of NR with respect to many other surface-sensitive techniques is its sub-nanometer resolution that enables structural characterizations at the molecular level. In the case of bio-relevant samples, NR is non-destructive and can be used to probe thin films at buried interfaces or enclosed in bulky sample environment equipment. Moreover, recent advances in biomolecular deutera-tion enabled new labeling strategies to highlight certain structural features and to resolve with better accuracy the location of chemically similar molecules within a thin film.
In this chapter I will describe some applications of NR to bio-relevant samples and discuss some of the data analysis approaches available for biological thin films. In particular, examples on the structural characterization of biomembranes, protein films and protein-lipid interactions will be described.