bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthesis runs counter to directional folding of a nascent protein domain
Authors: Chen Xiuqi , Rajasekaran Nandakumar , Liu Kaixian , Kaiser Christian M. 
Published: October 2020

AbstractFolding of individual domains in large proteins during translation helps to avoid otherwise prevalent inter-domain misfolding. How folding intermediates observed in vitro for the majority of proteins relate to co-translational folding remains unclear. Combining in vivo and single-molecule experiments, we followed the co-translational folding of the G-domain, encompassing the first 293 amino acids of elongation factor G. Surprisingly, the domain remains unfolded until it is fully synthesized, without collapsing into molten globule-like states or forming stable intermediates. Upon fully emerging from the ribosome, the G-domain transitions to its stable native structure via folding intermediates. Our results suggest a strictly sequential folding pathway initiating from the C-terminus. Folding and synthesis thus proceed in opposite directions. The folding mechanism is likely imposed by the final structure and might have evolved to ensure efficient, timely folding of a highly abundant and essential protein.
Suppression of phase transitions and glass phase signatures in mixed cation halide perovskites
Authors: Simenas Mantas , Balciunas Sergejus , Wilson Jacob N. , Svirskas Sarunas , Kinka Martynas , Garbaras Andrius , Kalendra Vidmantas , Gagor Anna , Szewczyk Daria , Sieradzki Adam , Maczka Miroslaw , Samulionis Vytautas , Walsh Aron , Grigalaitis Robertas , Banys Juras 
Published: October 2020

AbstractCation engineering provides a route to control the structure and properties of hybrid halide perovskites, which has resulted in the highest performance solar cells based on mixtures of Cs, methylammonium, and formamidinium. Here, we present a multi-technique experimental and theoretical study of structural phase transitions, structural phases and dipolar dynamics in the mixed methylammonium/dimethylammonium MA1-xDMAxPbBr3 hybrid perovskites (0 ≤ x ≤ 1). Our results demonstrate a significant suppression of the structural phase transitions, enhanced disorder and stabilization of the cubic phase even for a small amount of dimethylammonium cations. As the dimethylammonium concentration approaches the solubility limit in MAPbBr3, we observe the disappearance of the structural phase transitions and indications of a glassy dipolar phase. We also reveal a significant tunability of the dielectric permittivity upon mixing of the molecular cations that arises from frustrated electric dipoles.
Rational design of a robust aluminum metal-organic framework for multi-purpose water-sorption-driven heat allocations
Authors: Cho Kyung Ho , Borges D. Damasceno , Lee U-Hwang , Lee Ji Sun , Yoon Ji Woong , Cho Sung June , Park Jaedeuk , Lombardo Walter , Moon Dohyun , Sapienza Alessio , Maurin Guillaume , Chang Jong-San 
Published: October 2020

AbstractAdsorption-driven heat transfer technology using water as working fluid is a promising eco-friendly strategy to address the exponential increase of global energy demands for cooling and heating purposes. Here we present the water sorption properties of a porous aluminum carboxylate metal-organic framework, [Al(OH)(C6H3NO4)]·nH2O, KMF-1, discovered by a joint computational predictive and experimental approaches, which exhibits step-like sorption isotherms, record volumetric working capacity (0.36 mL mL−1) and specific energy capacity (263 kWh m−3) under cooling working conditions, very high coefficient of performances of 0.75 (cooling) and 1.74 (heating) together with low driving temperature below 70 °C which allows the exploitation of solar heat, high cycling stability and remarkable heat storage capacity (348 kWh m−3). This level of performances makes this porous material as a unique and ideal multi-purpose water adsorbent to tackle the challenges of thermal energy storage and its further efficient exploitation for both cooling and heating applications.
Pre-existing Helicobacter pylori serum IgG enhances the vibriocidal antibody response to CVD 103-HgR live oral cholera vaccine in Malian adults
Authors: Muhsen Khitam , Sow Samba O. , Tapia Milagritos D. , Haidara Fadima C. , Reymann Mardi , Asato Valeria , Chen Wilbur H. , Pasetti Marcela F. , Levine Myron M. 
Published: October 2020

AbstractAccumulating evidence indicates that persistent Helicobacter pylori gastric infection influences immune responses to oral enteric vaccines. We studied the association between pre-existing H. pylori serum IgG and serum pepsinogens levels (PGs) as markers of gastric inflammation and the immune response to single-dose live oral cholera vaccine CVD 103-HgR in Malian adults. Baseline sera obtained during a phase 2 safety/immunogenicity clinical trial of cholera vaccine CVD 103-HgR among 93 healthy Malian adults were tested for H. pylori IgG antibodies and PGI and PGII levels using enzyme linked immunosorbent assays. Overall 74/93 (80%) vaccine recipients were H. pylori IgG seropositive at baseline. Vibriocidal antibody seroconversion (≥ fourfold increase 14 days following administration of CVD 103-HgR compared to baseline) among vaccine recipients was 56%. However, vibriocidal antibody seroconversion was markedly higher among H. pylori seropositives than seronegatives 64% vs. 26% (p = 0.004); adjusted relative risk: 2.20 (95% confidence intervals 1.00–4.80; p = 0.049). Among H. pylori seropositive vaccine recipients, there were no significant associations between PGI, PGII and PGI:PGII levels and vibriocidal seroconversion. The enhanced seroconversion to oral cholera vaccine CVD 103-HgR among H. pylori seropositive African adults provides further evidence of the immunomodulating impact of H. pylori on oral vaccine immunogenicity.
TrkA inhibitor promotes motor functional regeneration of recurrent laryngeal nerve by suppression of sensory nerve regeneration
Authors: Suzuki Hiroshi , Araki Koji , Matsui Toshiyasu , Tanaka Yuya , Uno Kosuke , Tomifuji Masayuki , Yamashita Taku , Satoh Yasushi , Kobayashi Yasushi , Shiotani Akihiro 
Published: October 2020

AbstractRecurrent laryngeal nerve (RLN) injury, in which hoarseness and dysphagia arise as a result of impaired vocal fold movement, is a serious complication. Misdirected regeneration is an issue for functional regeneration. In this study, we demonstrated the effect of TrkA inhibitors, which blocks the NGF-TrkA pathway that acts on the sensory/automatic nerves thus preventing misdirected regeneration among motor and sensory nerves, and thereby promoting the regeneration of motor neurons to achieve functional recovery. RLN axotomy rat models were used in this study, in which cut ends of the nerve were bridged with polyglycolic acid-collagen tube with and without TrkA inhibitor (TrkAi) infiltration. Our study revealed significant improvement in motor nerve fiber regeneration and function, in assessment of vocal fold movement, myelinated nerve regeneration, compound muscle action potential, and prevention of laryngeal muscle atrophy. Retrograde labeling demonstrated fewer labeled neurons in the vagus ganglion, which confirmed reduced misdirected regeneration among motor and sensory fibers, and a change in distribution of the labeled neurons in the nucleus ambiguus. Our study demonstrated that TrkAi have a strong potential for clinical application in the treatment of RLN injury.
Prediction of creep failure time using machine learning
Authors: Biswas Soumyajyoti , Fernandez Castellanos David , Zaiser Michael 
Published: October 2020

AbstractA subcritical load on a disordered material can induce creep damage. The creep rate in this case exhibits three temporal regimes viz. an initial decelerating regime followed by a steady-state regime and a stage of accelerating creep that ultimately leads to catastrophic breakdown. Due to the statistical regularities in the creep rate, the time evolution of creep rate has often been used to predict residual lifetime until catastrophic breakdown. However, in disordered samples, these efforts met with limited success. Nevertheless, it is clear that as the failure is approached, the damage become increasingly spatially correlated, and the spatio-temporal patterns of acoustic emission, which serve as a proxy for damage accumulation activity, are likely to mirror such correlations. However, due to the high dimensionality of the data and the complex nature of the correlations it is not straightforward to identify the said correlations and thereby the precursory signals of failure. Here we use supervised machine learning to estimate the remaining time to failure of samples of disordered materials. The machine learning algorithm uses as input the temporal signal provided by a mesoscale elastoplastic model for the evolution of creep damage in disordered solids. Machine learning algorithms are well-suited for assessing the proximity to failure from the time series of the acoustic emissions of sheared samples. We show that materials are relatively more predictable for higher disorder while are relatively less predictable for larger system sizes. We find that machine learning predictions, in the vast majority of cases, perform substantially better than other prediction approaches proposed in the literature.
Five-year trajectories of multimorbidity patterns in an elderly Mediterranean population using Hidden Markov Models
Authors: Violán Concepción , Fernández-Bertolín Sergio , Guisado-Clavero Marina , Foguet-Boreu Quintí , Valderas Jose M. , Vidal Manzano Josep , Roso-Llorach Albert , Cabrera-Bean Margarita 
Published: October 2020

AbstractThis study aimed to analyse the trajectories and mortality of multimorbidity patterns in patients aged 65 to 99 years in Catalonia (Spain). Five year (2012–2016) data of 916,619 participants from a primary care, population-based electronic health record database (Information System for Research in Primary Care, SIDIAP) were included in this retrospective cohort study. Individual longitudinal trajectories were modelled with a Hidden Markov Model across multimorbidity patterns. We computed the mortality hazard using Cox regression models to estimate survival in multimorbidity patterns. Ten multimorbidity patterns were originally identified and two more states (death and drop-outs) were subsequently added. At baseline, the most frequent cluster was theNon-Specific Pattern(42%), and the least frequent theMultisystem Pattern(1.6%).Most participants stayed in the same cluster over the 5 year follow-up period, from 92.1% in theNervous, Musculoskeletalpattern to 59.2% in theCardio-Circulatory and Renalpattern. The highest mortality rates were observed for patterns that included cardio-circulatory diseases:Cardio-Circulatory and Renal(37.1%);Nervous, Digestive and Circulatory(31.8%); andCardio-Circulatory, Mental, Respiratory and Genitourinary(28.8%). This study demonstrates the feasibility of characterizing multimorbidity patterns along time. Multimorbidity trajectories were generally stable, although changes in specific multimorbidity patterns were observed. The Hidden Markov Model is useful for modelling transitions across multimorbidity patterns and mortality risk. Our findings suggest that health interventions targeting specific multimorbidity patterns may reduce mortality in patients with multimorbidity.
Identifying the sources of structural sensitivity in partially specified biological models
Authors: Adamson Matthew W. , Morozov Andrew Yu. 
Published: October 2020

AbstractBiological systems are characterised by a high degree of uncertainty and complexity, which implies that exact mathematical equations to describe biological processes cannot generally be justified. Moreover, models can exhibit sensitivity to the precise formulations of their component functions—a property known as structural sensitivity. Structural sensitivity can be revealed and quantified by considering partially specified models with uncertain functions, but this goes beyond well-established, parameter-based sensitivity analysis, and currently presents a mathematical challenge. Here we build upon previous work in this direction by addressing the crucial question of identifying the processes which act as the major sources of model uncertainty and those which are less influential. To achieve this goal, we introduce two related concepts: (1) the gradient of structural sensitivity, accounting for errors made in specifying unknown functions, and (2) the partial degree of sensitivity with respect to each function, a global measure of the uncertainty due to possible variation of the given function while the others are kept fixed. We propose an iterative framework of experiments and analysis to inform a heuristic reduction of structural sensitivity in a model. To demonstrate the framework introduced, we investigate the sources of structural sensitivity in a tritrophic food chain model.
How attitudes generated by humanoid robots shape human brain activity
Authors: Di Cesare G. , Vannucci F. , Rea F. , Sciutti A. , Sandini G. 
Published: October 2020

AbstractDuring interpersonal interactions, people perform actions with different forms of vitality, communicating their positive or negative attitude toward others. For example, a handshake can be “soft” or “vigorous”, a caress can be ‘kind’ or ‘rushed’. While previous studies have shown that the dorso-central insula is a key area for the processing of human vitality forms, there is no information on the perception of vitality forms generated by a humanoid robot. In this study, two fMRI experiments were conducted in order to investigate whether and how the observation of actions generated by a humanoid robot (iCub) with low and fast velocities (Study 1) or replicating gentle and rude human forms (Study 2) may convey vitality forms eliciting the activation of the dorso-central insula. These studies showed that the observation of robotic actions, generated with low and high velocities, resulted in activation of the parieto-frontal circuit typically involved in the recognition and the execution of human actions but not of the insula (Study 1). Most interestingly, the observation of robotic actions, generated by replicating gentle and rude human vitality forms, produced a BOLD signal increase in the dorso-central insula (Study 2). In conclusion, these data highlight the selective role of dorso-central insula in the processing of vitality forms opening future perspectives on the perception and understanding of actions performed by humanoid robots.
Investigation of a new graphene strain sensor based on surface plasmon resonance
Authors: Ma Zenghong , Chen Zijian , Xu Jian , Li Weiping , Zhang Lian , Wang Lei 
Published: October 2020

AbstractThe high confinement of surface plasmon polaritons in graphene nanostructures at infrared frequencies can enhance the light-matter interactions, which open up intriguing possibilities for the sensing. Strain sensors have attracted much attention due to their unique electromechanical properties. In this paper, a surface plasmon resonance based graphene strain sensor is presented. The considered sensing platform consists of arrays of graphene ribbons placed on a flexible substrate which enables efficient coupling of an electromagnetic field into localized surface plasmons. When the strain stretching is applied to the configuration, the localized surface plasmon resonance frequency sensitively shift. The strain is then detected by measuring the frequency shifts of the localized plasmon resonances. This provides a new optical method for graphene strain sensing. Our results show that the tensile direction is the key parameter for strain sensing. Besides, the sensitivity and the figure of merit were calculated to evaluate the performance of the proposed sensor. The calculated figure of merit can be up to two orders of magnitude, which could be potentially useful from a practical point of view.
Direct stimulation of ERBB2 highlights a novel cytostatic signaling pathway driven by the receptor Thr701 phosphorylation
Authors: Gaviraghi Marco , Rabellino Andrea , Andolfo Annapaola , Brand Matthias , Brombin Chiara , Bagnato Paola , De Feudis Giuseppina , Raimondi Andrea , Locatelli Alberta , Tosoni Daniela , Mazza Davide , Gianni Luca , Tonon Giovanni , Yarden Yosef , Tacchetti Carlo , Daniele Tiziana 
Published: October 2020

AbstractERBB2 is a ligand-less tyrosine kinase receptor expressed at very low levels in normal tissues; when overexpressed, it is involved in malignant transformation and tumorigenesis in several carcinomas. In cancer cells, ERBB2 represents the preferred partner of other members of the ERBB receptor family, leading to stronger oncogenic signals, by promoting both ERK and AKT activation. The identification of the specific signaling downstream of ERBB2 has been impaired by the lack of a ligand and of an efficient way to selectively activate the receptor. In this paper, we found that antibodies (Abs) targeting different epitopes on the ERBB2 extracellular domain foster the activation of ERBB2 homodimers, and surprisingly induce a unique cytostatic signaling cascade promoting an ERK-dependent ERBB2 Thr701 phosphorylation, leading to AKT de-phosphorylation, via PP2A Ser/Thr phosphatases. Furthermore, the immunophilin Cyclophilin A plays a crucial role in this pathway, acting as a negative modulator of AKT de-phosphorylation, possibly by competing with Ser/Thr phosphatases for binding to AKT. Altogether, our data show that Ab recognizing ERBB2 extracellular domain function as receptor agonists, promoting ERBB2 homodimer activation, leading to an anti-proliferative signaling. Thus, the ultimate outcome of ERBB2 activity might depend on the dimerization status: pro-oncogenic in the hetero-, and anti-oncogenic in the homo-dimeric form.
Describing fluctuating indoor aerosol dust measurements with application to house dust mite allergens
Authors: van Boven F. E. , de Jong N. W. , Loomans M. G. L. C. , Braunstahl G. J. , Gerth van Wijk R. , Arends L. R. 
Published: October 2020

AbstractMeasuring house dust mite aeroallergen concentrations is essential in understanding mite allergen exposure. Physically, the aerolized house dust mite faeces are part of indoor particulate matter. We studied the statistical ways of summarizing measurements of fluctuating mite aeroallergen exposure inside homes through indoor particulate matter. To study emissions from beddings, we measured the time-related airborne dust concentration after shaking a duvet. Analysis was performed both by a method based on the estimated mean and by a non-linear model. Twenty-eight studies reported a sum of concentrations; only one also reported the peak. In our four experiments on shaking a duvet (245 to 275 measurements each), the peak value was two to four times higher than the mean. The mean-based and non-linear models both predicted the sum of concentrations exactly. A 1% upper prediction bound and the non-linear model predicted the peak emission rate moderately well (64 to 92%, and 63 to 93%, respectively). Mean levels of indoor particulate matter measurements differ substantially from peak concentrations. The use of the mean is only sufficient to predict the sum of concentrations. We suggest that, mite aeroallergen measurements should include information on the peak as well as the mean.
Predicting toxins found in toxin–antitoxin systems with a role in host-induced Burkholderia pseudomallei persistence
Authors: Ross Brittany N. , Thiriot Joseph D. , Wilson Shane M. , Torres Alfredo G. 
Published: October 2020

AbstractBurkholderia pseudomallei (Bpm) is a bacterial pathogen that causes Melioidosis, a disease with up to 40% mortality and an infection relapse of 15–23% despite antibiotic treatment. Ineffective clearance of Bpm by antibiotics is believed to be due to persistence, a hibernation-like survival mechanism modulated, in part, by toxin–antitoxin systems (TAS). Several organisms possess a repertoire of TASs but defining environmental cues eliciting their activity is hindered by laborious in vitro experiments, especially when there are many toxins with redundant function. Here, we identified which of 103 proteins in Bpm that share features found in toxins of the TAS and repurposed transcriptional data to identify which ones play a role in surviving intracellular host defenses. Putative toxins with the strongest transcriptional response were found to have low conservation between Bpm strains, while toxins that were constitutively expressed were highly conserved. Further examination of highly conserved toxins BPSS0899, BPSS1321, and BPSL1494 showed that they were functional, and their mutation led to reduce survival within macrophages and reduced in vivo persistence-associated pathology (abscesses) during treatment, but did not affect macrophages persistence. These findings highlight the utility of a data-driven approach to select putative toxins and suggests a selective role for some TAS in host survival.
Altered metabolomic profiling of overweight and obese adolescents after combined training is associated with reduced insulin resistance
Authors: Duft Renata G. , Castro Alex , Bonfante Ivan L. P. , Lopes Wendell A. , da Silva Larissa R. , Chacon-Mikahil Mara P. T. , Leite Neiva , Cavaglieri Cláudia R. 
Published: October 2020

AbstractExercise training and a healthy diet are the main non-pharmacological strategies for treating chronic conditions, such as obesity and insulin resistance (IR), in adolescents. However, the isolated metabolic changes caused by exercise training without dietary intervention have not yet been established. We investigated how combined training (CT) without dietary intervention altered the concentrations of serum metabolites, biochemical, anthropometric and functional parameters in overweight and obese adolescents. Thirty-seven adolescents (14.6 ± 1.05 years), of both sexes, were randomly assigned to the control group (CG, n = 19) or the training group (TG, n = 18). The CT was composed by resistance training and aerobic training performed in the same session (~ 60 min), three times a week, for 12 weeks. All assessments were performed pre and post-intervention. Metabolomics analyses were conducted using nuclear magnetic resonance spectroscopy (1H NMR) in a 600 MHz spectrometer. There was a decrease in body weight (BW), body mass index (BMI), waist circumference (WC), % body fat (%BF), fasting glucose, insulin levels, and insulin resistance (IR), by HOMA-IR, in the TG. An increase in fat-free mass (FFM) was also observed in the CG. The metabolic changes were given mainly by changes in the levels of metabolites 2-oxoisocaproate (↓TG), 3-hydroxyisobutyrate (↑CG and ↓TG), glucose (↓TG), glutamine (↓CG and ↑TG) and pyruvate (↓TG). These findings demonstrate the positive effects of CT program without dietary intervention on metabolomic profile, body composition, biochemical markers, and glucose metabolism in overweight and obese adolescents.