bluuebunny/crossref_metadata_2025_split huggingface dataset:
New approach to investigate Common Variable Immunodeficiency patients using spectrochemical analysis of blood
Authors: Callery Emma L. , Morais Camilo L. M. , Paraskevaidi Maria , Brusic Vladimir , Vijayadurai Pavaladurai , Anantharachagan Ariharan , Martin Francis L. , Rowbottom Anthony W. 
Published: May 2019

AbstractCommon variable immune deficiency (CVID) is a primary immunodeficiency disease, characterized by hypogammaglobulinemia, recurrent infections and various complications. The clinical heterogeneity of CVID has hindered identification of an underlying immune defect; diagnosis relies on clinical judgement, alongside evidence-based criteria. The lack of pathognomonic clinical or laboratory features leads to average diagnostic delays of 5 years or more from the onset. Vibrational spectroscopic techniques such as Fourier-transform infrared (FTIR) spectroscopy have recently gained increasing clinical importance, being rapid-, non-invasive and inexpensive methods to obtain information on the content of biological samples. This has led us to apply FTIR spectroscopy to the investigation of blood samples from a cohort of CVID patients; revealing spectral features capable of stratifying CVID patients from healthy controls with sensitivities and specificities of 97% and 93%, respectively for serum, and 94% and 95%, respectively for plasma. Furthermore we identified several discriminating spectral biomarkers; wavenumbers in regions indicative of nucleic acids (984 cm−1, 1053 cm−1, 1084 cm−1, 1115 cm−1, 1528 cm−1, 1639 cm−1), and a collagen-associated biomarker (1528 cm−1), which may represent future candidate biomarkers and provide new knowledge on the aetiology of CVID. This proof-of-concept study provides a basis for developing a novel diagnostic tool for CVID.
Simultaneous assessment of cell morphology and adhesion using aluminum nanoslit-based plasmonic biosensing chips
Authors: Hou Hsien-San , Lee Kuang-Li , Wang Chen-Hung , Hsieh Tung-Han , Sun Juan-Jie , Wei Pei-Kuen , Cheng Ji-Yen 
Published: May 2019

AbstractA variety of physiological and pathological processes rely on cell adhesion, which is most often tracked by changes in cellular morphology. We previously reported a novel gold nanoslit-based biosensor that is capable of real-time and label-free monitoring of cell morphological changes and cell viability. However, the preparation of gold biosensors is inefficient, complicated and costly. Recently, nanostructure-based aluminum (Al) sensors have been introduced for biosensing applications. The Al-based sensor has a longer decay length and is capable of analyzing large-sized mass such as cells. Here, we developed two types of double-layer Al nanoslit-based plasmonic biosensors, which were nanofabricated and used to evaluate the correlation between metastatic potency and adhesion of lung cancer and melanoma cell lines. Cell adhesion was determined by Fano resonance signals that were induced by binding of the cells to the nanoslit. The peak and dip of the Fano resonance spectrum respectively reflected long- and short-range cellular changes, allowing us to simultaneously detect and distinguish between focal adhesion and cell spreading. Also, the Al nanoslit-based biosensor chips were used to evaluate the inhibitory effects of drugs on cancer cell spreading. We are the first to report the use of double layer Al nanoslit-based biosensors for detection of cell behavior, and such devices may become powerful tools for anti-metastasis drug screening in the future.
Decomposing motion that changes over time into task-relevant and task-irrelevant components in a data-driven manner: application to motor adaptation in whole-body movements
Authors: Furuki Daisuke , Takiyama Ken 
Published: May 2019

AbstractMotor variability is inevitable in human body movements and has been addressed from various perspectives in motor neuroscience and biomechanics: it may originate from variability in neural activities, or it may reflect a large number of degrees of freedom inherent in our body movements. How to evaluate motor variability is thus a fundamental question. Previous methods have quantified (at least) two striking features of motor variability: smaller variability in the task-relevant dimension than in the task-irrelevant dimension and a low-dimensional structure often referred to as synergy or principal components. However, the previous methods cannot be used to quantify these features simultaneously and are applicable only under certain limited conditions (e.g., one method does not consider how the motion changes over time, and another does not consider how each motion is relevant to performance). Here, we propose a flexible and straightforward machine learning technique for quantifying task-relevant variability, task-irrelevant variability, and the relevance of each principal component to task performance while considering how the motion changes over time and its relevance to task performance in a data-driven manner. Our method reveals the following novel property: in motor adaptation, the modulation of these different aspects of motor variability differs depending on the perturbation schedule.
Human adipose stromal-vascular fraction self-organizes to form vascularized adipose tissue in 3D cultures
Authors: Muller Sandra , Ader Isabelle , Creff Justine , Leménager Hélène , Achard Pauline , Casteilla Louis , Sensebé Luc , Carrière Audrey , Deschaseaux Frédéric 
Published: May 2019

AbstractNative human subcutaneous adipose tissue (AT) is well organized into unilocular adipocytes interspersed within dense vascularization. This structure is completely lost under standard culture conditions and may impair the comparison with native tissue. Here, we developed a 3-D model of human white AT reminiscent of the cellular architecture foundin vivo. Starting with adipose progenitors derived from the stromal-vascular fraction of human subcutaneous white AT, we generated spheroids in which endogenous endothelial cells self-assembled to form highly organized endothelial networks among stromal cells. Using an optimized adipogenic differentiation medium to preserve endothelial cells, we obtained densely vascularized spheroids containing mature adipocytes with unilocular lipid vacuoles.In vivostudy showed that when differentiated spheroids were transplanted in immune-deficient mice, endothelial cells within the spheroids connected to the recipient circulatory system, forming chimeric vessels. In addition, adipocytes of human origin were still observed in transplanted mice. We therefore have developed anin vitromodel of vascularized human AT-like organoids that constitute an excellent tool and model for any study of human AT.
Contaminated feed-borne Bacillus cereus aggravates respiratory distress post avian influenza virus H9N2 infection by inducing pneumonia
Authors: Zhang Qiang , Zuo Zonghui , Guo Yongxia , Zhang Tianyuan , Han Zhenhai , Huang Shujian , Karama Musafiri , Saleemi Muhammad Kashif , Khan Ahrar , He Cheng 
Published: May 2019

AbstractAvian influenza virussubtype H9N2 is identified in chickens with respiratory disease whileBacillus cereus(B. cereus) has been frequently isolated from chicken feed in China. However, the roles of co-infection with these two pathogens remain unclear. In the present study, SPF chicks were intragastrically administered with 108 CFU/mL ofB. cereusfor 7 days and then inoculated intranasally with 100 EID50of H9N2 three days later. Alternatively, chickens were initially inoculated with H9N2 and then withB. cereusfor one week. Post administration, typical respiratory distress persisted for 5 days in both co-infection groups. Gizzard erosions developed in the groupsB. cereus/H9N2 andB. cereusgroup on 7thday while in group H9N2/B. cereuson 14thday. More importantly, both air-sac lesions and lung damage increased significantly in the co-infection group. Significant inflammatory changes were observed in theB. cereusgroup from day 7 to day 21. Moreover, higher loads of H9N2 virus were found in the co-infected groups than in the H9N2 group. Newcastle Disease Virus (NDV) specific antibodies were decreased significantly in the H9N2/B. cereusgroup compared to theB. cereusand theB. cereus/H9N2 groups. Nonspecific IgA titers were reduced significantly in theB. cereusgroup and the H9N2/B. cereusgroup compared to the control group. In addition to this, lower lymphocyte proliferation was found in the con-infection groups and the H9N2 group. Hence, feed-borneB. cereuscontamination potentially exacerbates gizzard ulceration and aggravates H9N2-induced respiratory distress by inhibiting antibody-mediated immunity and pathogen clearance. Thus controlling theB. cereuscontamination in poultry feed is immediately needed.
The impact of differences in plasma glucose between glucose oxidase and hexokinase methods on estimated gestational diabetes mellitus prevalence
Authors: Dickson Lynnsay M. , Buchmann Eckhart J. , Janse Van Rensburg Charl , Norris Shane A. 
Published: May 2019

AbstractWe evaluated the extent of measurement discordance between glucose oxidase and hexokinase laboratory methods and the effect of this on estimated gestational diabetes mellitus (GDM) prevalence in a routine clinical setting. 592 consecutive urban African women were screened for GDM. Paired venous specimens were submitted to two independent calibrated laboratories that used either method to measure plasma glucose concentrations. World Health Organisation diagnostic criteria were applied. GDM prevalence determined by the glucose oxidase and hexokinase methods was 6.9% and 5.1% respectively. The overall GDM prevalence was 9%. Only 34% of GDM positive diagnoses were common to both laboratory methods. Bland Altman plots identified a bias of 0.2 mmol/l between laboratory methods. Plasma glucose concentrations measured by the glucose oxidase method were more platykurtic in distribution. Low diagnostic agreement between laboratory methods was further indicated by a Cohen’s kappa of 0.48 (p < 0.001). Reports of GDM prevalence using either the glucose oxidase or hexokinase laboratory methods may not be truly interchangeable or directly comparable.
Extraction of Multi-Labelled Movement Information from the Raw HD-sEMG Image with Time-Domain Depth
Authors: Olsson Alexander E. , Sager Paulina , Andersson Elin , Björkman Anders , Malešević Nebojša , Antfolk Christian 
Published: May 2019

AbstractIn contemporary muscle-computer interfaces for upper limb prosthetics there is often a trade-off between control robustness and range of executable movements. As a very low movement error rate is necessary in practical applications, this often results in a quite severe limitation of controllability; a problem growing ever more salient as the mechanical sophistication of multifunctional myoelectric prostheses continues to improve. A possible remedy for this could come from the use of multi-label machine learning methods, where complex movements can be expressed as the superposition of several simpler movements. Here, we investigate this claim by applying a multi-labeled classification scheme in the form of a deep convolutional neural network (CNN) to high density surface electromyography (HD-sEMG) recordings. We use 16 independent labels to model the movements of the hand and forearm state, representing its major degrees of freedom. By training the neural network on 16 × 8 sEMG image sequences 24 samples long with a sampling rate of 2048 Hz to detect these labels, we achieved a mean exact match rate of 78.7% and a mean Hamming loss of 2.9% across 14 healthy test subjects. With this, we demonstrate the feasibility of highly versatile and responsive sEMG control interfaces without loss of accuracy.
A comprehensive analysis of the Lactuca sativa, L. transcriptome during different stages of the compatible interaction with Rhizoctonia solani
Authors: Verwaaijen Bart , Wibberg Daniel , Winkler Anika , Zrenner Rita , Bednarz Hanna , Niehaus Karsten , Grosch Rita , Pühler Alfred , Schlüter Andreas 
Published: May 2019

AbstractThe leafy green vegetableLactuca sativa, L. is susceptible to the soil-born fungusRhizoctonia solaniAG1-IB. In a previous study, we reported on the transcriptional response ofR. solaniAG1-IB (isolate 7/3/14) during the interspecies interaction withL. sativacv. Tizian by means of RNA sequencing. Here we present theL. sativatranscriptome and metabolome from the same experimental approach. Three distinct interaction zones were sampled and compared to a blank (non-inoculated) sample: symptomless zone 1, zone 2 showing light brown discoloration, and a dark brown zone 3 characterized by necrotic lesions. Throughout the interaction, we observed a massive reprogramming of theL. sativatranscriptome, with 9231 unique genes matching the threshold criteria for differential expression. The lettuce transcriptome of the light brown zone 2 presents the most dissimilar profile compared to the uninoculated zone 4, marking the main stage of interaction. Transcripts putatively encoding several essential proteins that are involved in maintaining jasmonic acid and auxin homeostasis were found to be negatively regulated. These and other indicator transcripts mark a potentially inadequate defence response, leading to a compatible interaction. KEGG pathway mapping and GC-MS metabolome data revealed large changes in amino acid, lignin and hemicellulose related pathways and related metabolites.
σ54 (σL) plays a central role in carbon metabolism in the industrially relevant Clostridium beijerinckii
Authors: Hocq Rémi , Bouilloux-Lafont Maxime , Lopes Ferreira Nicolas , Wasels François 
Published: May 2019

AbstractThe solventogenic C. beijerinckii DSM 6423, a microorganism that naturally produces isopropanol and butanol, was previously modified by random mutagenesis. In this work, one of the resulting mutants was characterized. This strain, selected with allyl alcohol and designated as the AA mutant, shows a dominant production of acids, a severely diminished butanol synthesis capacity, and produces acetone instead of isopropanol. Interestingly, this solvent-deficient strain was also found to have a limited consumption of two carbohydrates and to be still able to form spores, highlighting its particular phenotype. Sequencing of the AA mutant revealed point mutations in several genes including CIBE_0767 (sigL), which encodes the σ54 sigma factor. Complementation with wild-type sigL fully restored solvent production and sugar assimilation and RT-qPCR analyses revealed its transcriptional control of several genes related to solventogensis, demonstrating the central role of σ54 in C. beijerinckii DSM 6423. Comparative genomics analysis suggested that this function is conserved at the species level, and this hypothesis was further confirmed through the deletion of sigL in the model strain C. beijerinckii NCIMB 8052.
The role of atom tunneling in gas-phase reactions in planet-forming disks
Authors: Meisner J. , Kamp I. , Thi W.-F. , Kästner J. 
Published: May 2019

Context.Chemical Gas-phase reactions of simple molecules have been recently revised to include atom tunneling at very low temperatures. This paper investigates the impact of the increased reaction rate constant due to tunneling effects on planet-forming disks.Aims.Our aim is to quantify the astrophysical implications of atom tunneling for simple molecules that are frequently used to infer disk structure information or to define the initial conditions for planet (atmosphere) formation.Methods.We quantify the tunneling effect on reaction rate constants by using H2+ OH → H2O + H as a scholarly example in comparison to previous UMIST2012 rate constants. In a chemical network with 1299 reactions, we identify all chemical reactions that could show tunneling effects. We devise a simple formulation of reaction rate constants that overestimates tunneling and screen a standard T Tauri disk model for changes in species abundances. For those reactions found to be relevant, we find values of the most recent literature for the rate constants including tunneling and compare the resulting disk chemistry to the standard disk model(s), a T Tauri and a Herbig disk.Results.The rate constants in the UMIST2012 database in many cases already capture tunneling effects implicitly, as seen in the curvature of the Arrhenius plots of some reactions at low temperature. A rigorous screening procedure identified three neutral-neutral reactions where atom tunneling could change simple molecule abundances. However, by adopting recent values of the rate constants of these reactions and due to the layered structure of planet-forming disks, the effects are limited to a small region between the ion-molecule dominated regime and the ice reservoirs where cold (<250 K) neutral-neutral chemistry dominates. Abundances of water close to the midplane snowline can increase by a factor of two at most compared to previous results with UMIST2012 rates. Observables from the disk surface, such as high excitation (>500 K) water line fluxes, decrease by 60% at most when tunneling effects are explicitly excluded. On the other hand, disk midplane quantities relevant for planet formation such as the C-to-O ratio and also the ice-to-rock ratio are clearly affected by these gas-phase tunneling effects.
Penumbral microjets at high spatial and temporal resolution
Authors: Rouppe van der Voort Luc H. M. , Drews Ainar 
Published: May 2019

Context. Sunspot observations in chromospheric spectral lines have revealed short-lived linear bright transients that are commonly referred to as penumbral microjets (PMJs). Details on the origin and physical nature of PMJs are to a large extend still unknown.
Aims. We aim to characterize the dynamical nature of PMJs to provide guidance for future modeling efforts.
Methods. We analyzed high spatial (0.̋1) and temporal resolution (1 s) Ca II H filtergram (0.1 nm bandwidth) observations of a sunspot that were obtained on two consecutive days with the Swedish 1 m Solar Telescope.
Results. We find that PMJs appear to be the rapid brightening of an already existing (faint) fibril. The rapid brightening is the fast increase (typically less than 10 s) in intensity over significant length (several hundreds of kilometers) of the existing fibril. For most PMJs, no clear root or source from where the brightening appears to originate can be identified. After the fast onset, about half of the PMJs have tops that move with an apparent velocity of between 5 and 14 km s−1, most of them upward. No significant motion of the top is observed in the other PMJs. About one-third of the PMJs split into two parallel and coevolving linear features during the later phases of their lifetimes.
Conclusions. We conclude that mass flows can play only a limited role in the onset phase of PMJs. It is more likely that we see the effect of a fast heating front.
Lipid Peroxidation, Protein Oxidation, Gelatinases, and Their Inhibitors in a Group of Adults with Obesity
Authors: Caimi Gregorio , Canino Baldassare , Montana Maria , Urso Caterina , Calandrino Vincenzo , Presti Rosalia Lo , Hopps Eugenia 
Published: May 2019

AbstractThe association between obesity and cardiovascular diseases has a multifactorial pathogenesis, including the synthesis of inflammatory molecules, the increase in oxidative stress and the dysregulation of the matrix metalloprotease (MMP) concentration and activity. In a group of adults with obesity, divided in 2 subgroups according to the body mass index (BMI), we examined lipid peroxidation, expressed as thiobarbituric acid-reactive substances (TBARS), protein oxidation, expressed as protein carbonyl groups (PCs), plasma gelatinases (MMP-2 and MMP-9), and their tissue inhibitors (TIMP-1 and TIMP-2). In the whole group, as well as in the 2 subgroups (with BMI 30–35 or BMI>35) of obese subjects, we observed an increase in TBARS, PCs, MMP-2, and MMP-9, and also TIMP-1 and TIMP-2 in comparison with the control group. A positive correlation between TBARS and PCs emerged in obese subjects and persisted after dividing obese subjects according to BMI. The correlation between MMP-2 and TIMP-2 was not statistically significant, while a significant correlation was present between MMP-9 and TIMP-1. The correlations between the markers of oxidative stress (TBARS and PCs) and those of the MMP/TIMP profile indicated a more marked influence of protein oxidation on MMPs and TIMPs in comparison with TBARS. The innovative aspect of our study was the simultaneous evaluation of oxidative stress markers and MMP/TIMP profile in adult obese subjects. We observed significant alterations and correlations that may negatively influence the clinical course of the disease.
Analysis of Immediate versus Delayed Sternal Reconstruction with Pectoralis Major Advancement Versus Turnover Muscle Flaps
Authors: Kamel George N. , Jacobson Joshua , Rizzo Amanda M. , Kinkhabwala Corin , Lalezar Frank , Draper Lawrence , Tepper Oren M. , Garfein Evan S. , Weichman Katie E. 
Published: May 2019

Abstract
Background The pectoralis major muscle flap is a versatile reconstructive option for deep sternal wound infections (DSWI). The timing and surgical technique of bilateral pectoralis major muscle advancement flaps versus unilateral pectoralis major muscle turnover and unilateral pectoralis major muscle advancement flap on patient outcomes remain to be elucidated. The purpose of this investigation was to compare timing, immediate versus delayed reconstruction, and the surgical technique in patients with deep sternal wounds infections on patient outcomes.
Methods A retrospective review of patients who underwent sternal reconstruction with pectoralis major muscle was conducted. Patients diagnosed with DSWI after undergoing cardiac surgery were included for analysis. Patients were divided by flap timing and flap type for analyses. Bivariate tests were performed to compare patient clinical characteristics. Outcomes of interest were rates of postoperative complications, same admission mortality, reoperation, readmission, operating room time, and length of stay.
Results A total of 88 patients were included for analyses (n = 57 bilateral advancement, n = 31 unilateral advancement with unilateral turnover; n = 62 immediate, and n = 26 delayed). Baseline characteristics did not differ between groups of flap type or timing. When postoperative complication rates were compared, the rate of tissue necrosis was significantly greater in patients with unilateral advancement with unilateral turnover flaps (n = 6 [19.4%]) compared with bilateral advancement flaps (n = 2 [3.5%]; p = 0.021). Mortality during admission did not differ with respect to flap type but differed significantly with respect to flap timing (immediate n = 7 [11.3%], delayed n = 9 [34.6%]; p = 0.015). Length of stay differed significantly by both type and timing (type: bilateral advancement = 26.9 ± 22.6 days, unilateral turnover = 38.0 ± 26.7 days, p = 0.042; timing: immediate = 26.8 ± 22.1 days, delayed = 40.2 ± 27.8, p = 0.019).
Conclusion Patients who underwent pectoralis major muscle advancement flaps had lower incidence of tissue necrosis. Furthermore, the timing of immediate sternal reconstruction was associated with a decreased hospital length of stay.