bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduced numbers of T cells and B cells correlates with persistent SARS-CoV-2 presence in non-severe COVID-19 patients
Authors: Liu Bing , Han Junyan , Cheng Xiaohuan , Yu Long , Zhang Li , Wang Wei , Ni Lan , Wei Chaojie , Huang Yafei , Cheng Zhenshun 
Published: October 2020

AbstractCOVID-19 has been widely spreading. We aimed to examine adaptive immune cells in non-severe patients with persistent SARS-CoV-2 shedding. 37 non-severe patients with persistent SARS-CoV-2 presence that were transferred to Zhongnan hospital of Wuhan University were retrospectively recruited to the PP (persistently positive) group, which was further allocated to PPP group (n = 19) and PPN group (n = 18), according to their testing results after 7 days (N = negative). Epidemiological, demographic, clinical and laboratory data were collected and analyzed. Data from age- and sex-matched non-severe patients at disease onset (PA [positive on admission] patients, n = 37), and lymphocyte subpopulation measurements from matched 54 healthy subjects were extracted for comparison (HC). Compared with PA patients, PP patients had much improved laboratory findings. The absolute numbers of CD3+ T cells, CD4+ T cells, and NK cells were significantly higher in PP group than that in PA group, and were comparable to that in healthy controls. PPP subgroup had markedly reduced B cells and T cells compared to PPN group and healthy subjects. Finally, paired results of these lymphocyte subpopulations from 10 PPN patients demonstrated that the number of T cells and B cells significantly increased when the SARS-CoV-2 tests turned negative. Persistent SARS-CoV-2 presence in non-severe COVID-19 patients is associated with reduced numbers of adaptive immune cells. Monitoring lymphocyte subpopulations could be clinically meaningful in identifying fully recovered COVID-19 patients.
Autonomous materials discovery driven by Gaussian process regression with inhomogeneous measurement noise and anisotropic kernels
Authors: Noack Marcus M. , Doerk Gregory S. , Li Ruipeng , Streit Jason K. , Vaia Richard A. , Yager Kevin G. , Fukuto Masafumi 
Published: October 2020

AbstractA majority of experimental disciplines face the challenge of exploring large and high-dimensional parameter spaces in search of new scientific discoveries. Materials science is no exception; the wide variety of synthesis, processing, and environmental conditions that influence material properties gives rise to particularly vast parameter spaces. Recent advances have led to an increase in the efficiency of materials discovery by increasingly automating the exploration processes. Methods for autonomous experimentation have become more sophisticated recently, allowing for multi-dimensional parameter spaces to be explored efficiently and with minimal human intervention, thereby liberating the scientists to focus on interpretations and big-picture decisions. Gaussian process regression (GPR) techniques have emerged as the method of choice for steering many classes of experiments. We have recently demonstrated the positive impact of GPR-driven decision-making algorithms on autonomously-steered experiments at a synchrotron beamline. However, due to the complexity of the experiments, GPR often cannot be used in its most basic form, but rather has to be tuned to account for the special requirements of the experiments. Two requirements seem to be of particular importance, namely inhomogeneous measurement noise (input-dependent or non-i.i.d.) and anisotropic kernel functions, which are the two concepts that we tackle in this paper. Our synthetic and experimental tests demonstrate the importance of both concepts for experiments in materials science and the benefits that result from including them in the autonomous decision-making process.
Robot-assisted radical prostatectomy with clipless intrafascial neurovascular bundle-sparing approach: surgical technique and one-year functional and oncologic outcomes
Authors: Shin Tae Young , Lee Yong Seong 
Published: October 2020

AbstractVarious neurovascular bundle-sparing techniques have been introduced to maximize recovery of erectile function after robot-assisted radical prostatectomy (RARP). The clipless intrafascial neurovascular bundle-sparing technique aims to preserve periprostatic structures and neurovascular bundles as much as possible by avoiding clipping of the vascular pedicles. This study reports 1-year functional and oncologic outcomes and postoperative complications in 105 patients with intact preoperative erectile function who underwent a modified clipless intrafascial neurovascular bundle-sparing RARP. Intact erectile function was defined as score ≥ 21 on the Sexual Health Inventory for Men questionnaire or ability to have sexual intercourse. Median follow-up was 26.5 months (IQR 15.25–48). Postoperative erectile function recovery rates were 71.4%, 81.9%, 88.6%, 92.4%, and 94.3% at 1, 3, 6, 9, and 12 months, respectively. The rate of positive surgical margins was 16.2% overall and 11.8% in patients with stage pT2 disease. The biochemical recurrence rate was 6.7% overall. The modified clipless intrafascial neurovascular bundle-sparing technique is safe and feasible and can achieve excellent recovery of erectile function after RARP. Further large-scale prospective comparative studies are warranted.
Sisters in structure but different in character, some benzaldehyde and cinnamaldehyde derivatives differentially tune Aspergillus flavus secondary metabolism
Authors: Bisceglie Franco , Degola Francesca , Rogolino Dominga , Giannelli Gianluigi , Orsoni Nicolò , Spadola Giorgio , Pioli Marianna , Restivo Francesco M. , Carcelli Mauro , Pelosi Giorgio 
Published: October 2020

AbstractGreat are the expectations for a new generation of antimicrobials, and strenuous are the research efforts towards the exploration of diverse molecular scaffolds—possibly of natural origin – aimed at the synthesis of new compounds against the spread of hazardous fungi. Also high but winding are the paths leading to the definition of biological targets specifically fitting the drug’s structural characteristics. The present study is addressed to inspect differential biological behaviours of cinnamaldehyde and benzaldehyde thiosemicarbazone scaffolds, exploiting the secondary metabolism of the mycotoxigenic phytopathogen Aspergillus flavus. Interestingly, owing to modifications on the parent chemical scaffold, some thiosemicarbazones displayed an increased specificity against one or more developmental processes (conidia germination, aflatoxin biosynthesis, sclerotia production) of A. flavus biology. Through the comparative analysis of results, the ligand-based screening strategy here described has allowed us to delineate which modifications are more promising for distinct purposes: from the control of mycotoxins contamination in food and feed commodities, to the environmental management of microbial pathogens, to the investigation of specific structure–activity features for new generation drug discovery.
Wireless, non-invasive, wearable device for continuous remote monitoring of hemodynamic parameters in a swine model of controlled hemorrhagic shock
Authors: Nachman Dean , Constantini Keren , Poris Gal , Wagnert-Avraham Linn , Gertz S. David , Littman Romi , Kabakov Eli , Eisenkraft Arik , Gepner Yftach 
Published: October 2020

AbstractAccurate and continuous monitoring of critically ill patients is frequently achieved using invasive catheters, which is technically complex. Our purpose was to evaluate the validity and accuracy of a photoplethysmography (PPG)-based remote monitoring device compared to invasive methods of arterial line (AL) and Swan-Ganz (SG) catheters in a swine model of controlled hemorrhagic shock. Following a baseline phase, hemorrhagic shock was induced in 11 pigs by bleeding 35% of their blood volume, followed by a post-bleeding follow-up phase. Animals were monitored concomitantly by the PPG device, an AL and a SG catheter, for a median period of 447 min. Heart rate (HR), systolic and diastolic blood pressure (SBP and DBP, respectively), and cardiac output (CO) were recorded continuously. The complete data set consisted of 1312 paired observations. Correlations between the PPG-based technique and the invasive methods were significant (p < 0.001) during baseline, bleeding and follow-up phases for HR (r = 0.90–0.98), SBP (r = 0.90–0.94), DBP (r = 0.89–0.93), and CO (r = 0.76–0.90). Intraclass correlations for all phases combined were 0.96, 0.92, 0.93 and 0.87 for HR, SBP, DBP and CO, respectively. Correlations for changes in CO, SBP and DBP were significant (p < 0.001) and strong (r > 0.88), with concordance rates (determined by quadrant plots) of 86%, 66% and 68%, respectively. The novel PPG-based device was accurate and valid compared to existing invasive techniques and might be used for continuous monitoring in several clinical settings following further studies.
Hydrostatic pressure can induce apoptosis of the skin
Authors: Le Tien Minh , Morimoto Naoki , Ly Nhung Thi My , Mitsui Toshihito , Notodihardjo Sharon Claudia , Munisso Maria Chiara , Kakudo Natsuko , Moriyama Hiroyuki , Yamaoka Tetsuji , Kusumoto Kenji 
Published: October 2020

AbstractWe previously showed that high hydrostatic pressure (HHP) treatment at 200 MPa for 10 min induced complete cell death in skin and skin tumors via necrosis. We used this technique to treat a giant congenital melanocytic nevus and reused the inactivated nevus tissue as a dermis autograft. However, skin inactivated by HHP promoted inflammation in a preclinical study using a porcine model. Therefore, in the present study, we explored the pressurization conditions that induce apoptosis of the skin, as apoptotic cells are not believed to promote inflammation, so the engraftment of inactivated skin should be improved. Using a human dermal fibroblast cell line in suspension culture, we found that HHP at 50 MPa for ≥ 36 h completely induced fibroblast cell death via apoptosis based on the morphological changes in transmission electron microscopy, reactive oxygen species elevation, caspase activation and phosphatidylserine membrane translocation. Furthermore, immunohistochemistry with terminal deoxynucleotidyl transferase dUTP nick-end labeling and cleaved caspase-3 showed most cells in the skin inactivated by pressurization to be apoptotic. Consequently, in vivo grafting of apoptosis-induced inactivated skin resulted in successful engraftment and greater dermal cellular density and macrophage infiltration than our existing method. Our finding supports an alternative approach to hydrostatic pressure application.
A brain network that supports consensus-seeking and conflict-resolving of college couples’ shopping interaction
Authors: Jo HanShin , Chen Chiu-Yueh , Chen Der-Yow , Weng Ming-Hung , Kung Chun-Chia 
Published: October 2020

AbstractOne of the typical campus scenes is the social interaction between college couples, and the lesson couples must keep learning is to adapt to each other. This fMRI study investigated the shopping interactions of 30 college couples, one lying inside and the other outside the scanner, beholding the same item from two connected PCs, making preference ratings and subsequent buy/not-buy decisions. The behavioral results showed the clear modulation of significant others’ preferences onto one’s own decisions, and the contrast of the “shop-together vs. shop-alone”, and the “congruent (both liked or disliked the item, 68%) vs. incongruent (one liked but the other disliked, and vice versa)” together trials, both revealed bilateral temporal parietal junction (TPJ) among other reward-related regions, likely reflecting mentalizing during preference harmony. Moreover, when contrasting “own-high/other-low vs. own-low/other-high” incongruent trials, left anterior inferior parietal lobule (l-aIPL) was parametrically mapped, and the “yield (e.g., own-high/not-buy) vs. insist (e.g., own-low/not-buy)” modulation further revealed left lateral-IPL (l-lIPL), together with left TPJ forming a local social decision network that was further constrained by the mediation analysis among left TPJ–lIPL–aIPL. In sum, these results exemplify, via the two-person fMRI, the neural substrate of shopping interactions between couples.
A FDG-PET radiomics signature detects esophageal squamous cell carcinoma patients who do not benefit from chemoradiation
Authors: Li Yimin , Beck Marcus , Päßler Tom , Lili Chen , Hua Wu , Mai Ha Dong , Amthauer Holger , Biebl Matthias , Thuss-Patience Peter C. , Berger Jasmin , Stromberger Carmen , Tinhofer Ingeborg , Kruppa Jochen , Budach Volker , Hofheinz Frank , Lin Qin , Zschaeck Sebastian 
Published: October 2020

AbstractDetection of patients with esophageal squamous cell carcinoma (ESCC) who do not benefit from standard chemoradiation (CRT) is an important medical need. Radiomics using 18-fluorodeoxyglucose (FDG) positron emission tomography (PET) is a promising approach. In this retrospective study of 184 patients with locally advanced ESCC. 152 patients from one center were grouped into a training cohort (n = 100) and an internal validation cohort (n = 52). External validation was performed with 32 patients treated at a second center. Primary endpoint was disease-free survival (DFS), secondary endpoints were overall survival (OS) and local control (LC). FDG-PET radiomics features were selected by Lasso-Cox regression analyses and a separate radiomics signature was calculated for each endpoint. In the training cohort radiomics signatures containing up to four PET derived features were able to identify non-responders in regard of all endpoints (DFS p < 0.001, LC p = 0.003, OS p = 0.001). After successful internal validation of the cutoff values generated by the training cohort for DFS (p = 0.025) and OS (p = 0.002), external validation using these cutoffs was successful for DFS (p = 0.002) but not for the other investigated endpoints. These results suggest that pre-treatment FDG-PET features may be useful to detect patients who do not respond to CRT and could benefit from alternative treatment.
Natural variation in Arabidopsis thaliana rosette area unveils new genes involved in plant development
Authors: González Rubén , Butković Anamarija , Rivarez Mark Paul Selda , Elena Santiago F. 
Published: October 2020

AbstractGrowth is a complex trait influenced by multiple genes that act at different moments during the development of an organism. This makes it difficult to spot its underlying genetic mechanisms. Since plant growth is intimately related to the effective leaf surface area (ELSA), identifying genes controlling this trait will shed light on our understanding of plant growth. To find new genes with a significant contribution to plant growth, here we used the natural variation in Arabidopsis thaliana to perform a genome-wide association study of ELSA. To do this, the projected rosette area of 710 worldwide distributed natural accessions was measured and analyzed using the genome-wide efficient mixed model association algorithm. From this analysis, ten genes were identified having SNPs with a significant association with ELSA. To validate the implication of these genes into A. thaliana growth, six of them were further studied by phenotyping knock-out mutant plants. It was observed that rem1.2, orc1a, ppd1, and mcm4 mutants showed different degrees of reduction in rosette size, thus confirming the role of these genes in plant growth. Our study identified genes already known to be involved in plant growth but also assigned this role, for the first time, to other genes.
A recursive framework for predicting the time-course of drug sensitivity
Authors: Qian Cheng , Emad Amin , Sidiropoulos Nicholas D. 
Published: October 2020

AbstractThe biological processes involved in a drug’s mechanisms of action are oftentimes dynamic, complex and difficult to discern. Time-course gene expression data is a rich source of information that can be used to unravel these complex processes, identify biomarkers of drug sensitivity and predict the response to a drug. However, the majority of previous work has not fully utilized this temporal dimension. In these studies, the gene expression data is either considered at one time-point (before the administration of the drug) or two time-points (before and after the administration of the drug). This is clearly inadequate in modeling dynamic gene–drug interactions, especially for applications such as long-term drug therapy. In this work, we present a novel REcursive Prediction (REP) framework for drug response prediction by taking advantage of time-course gene expression data. Our goal is to predict drug response values at every stage of a long-term treatment, given the expression levels of genes collected in the previous time-points. To this end, REP employs a built-in recursive structure that exploits the intrinsic time-course nature of the data and integrates past values of drug responses for subsequent predictions. It also incorporates tensor completion that can not only alleviate the impact of noise and missing data, but also predict unseen gene expression levels (GEXs). These advantages enable REP to estimate drug response at any stage of a given treatment from some GEXs measured in the beginning of the treatment. Extensive experiments on two datasets corresponding to multiple sclerosis patients treated with interferon are included to showcase the effectiveness of REP.
Phylogenetic diversity shapes salt tolerance in Phragmites australis estuarine populations in East China
Authors: Lambertini Carla , Guo Wen-Yong , Ye Siyuan , Eller Franziska , Guo Xiao , Li Xiu-Zhen , Sorrell Brian K. , Speranza Maria , Brix Hans 
Published: October 2020

AbstractEstuaries are dynamic and selective environments that provide frequent opportunities for the turnover of Phragmites australis populations. We studied Phragmites genetic diversity patterns in three of the major deltas of China, viz. the Yellow River, the Yangtze and the Liaohe, in relation to Phragmites global phylogeography and soil salinity. We found that two distantly related P. australis haplotypes, each with intercontinental distribution, co-occur in these deltas in China. One is European Phragmites (Haplotype O) and is related to P. japonicus; the other (Haplotype P) has its range in East Asia and Australia and is related to the Asian tropical species P. karka. The two haplotypes have differing salt tolerance, with Haplotype O in areas with the highest salinity and Haplotype P in areas with the lowest. Introgressed hybrids of Haplotype P with P. karka, and F1 hybrids with Haplotype O, have higher salt tolerance than Haplotype P. Phylogenetic diversity appears as the factor that better explains population structure and salinity tolerance in these estuaries. Future research may explain whether the two P. australis haplotypes evolved in East Asia, and East Asia is a center of Phragmites diversity, or are introduced and a threat to P. japonicus and P. karka.
Simpler and effective radiological evaluations for modiolar proximity of a slim modiolar cochlear implant electrode
Authors: Lee Sang-Yeon , Han Jin Hee , Carandang Marge , Bae Yun Jung , Choi Byung Yoon 
Published: October 2020

AbstractA new slim modiolar electrode (CI532/632) has been reported to ensure better modiolar proximity than conventional electrodes. Better modiolar proximity has been proposed to yield better electrode discrimination capability and potentially better speech outcomes, necessitating its efficient measurement. Currently, intracochlear positional index (ICPI), the most reliable indicator for evaluating modiolar proximity, has been measured exclusively through ‘metal artifact-less’ cone beam CT. However, popular use of this index is precluded due to lack of cone beam CT in many institutions. Thus, eyes are now on elucidation of easy-to-measure indicators of modiolar proximity derived from conventional CT, which is accessible in all centers. We observed that enhanced tomographic resolution significantly reduces partial volume artifacts, providing better visualization of modiolus-electrode distance. Aided by ultra-high kernel specification with high-resolution index, we developed a novel and easy-to-measure, conventional CT-specific indicator, “modified ICPI”, for evaluation of modiolar proximity. Further, we showed that it closely correlates with the previously proposed parameter of modiolar proximity, the spiral diameter, measured from post-insertion radiograph, reiterating the value of X-ray-based spiral diameter. Through this study, we have taken a step toward the stage of immediate visual feedback regarding modiolar proximity and changes in insertion technique intraoperatively, ensuring optimal modiolar proximity.
Respiration and brain neural dynamics associated with interval timing during odor fear learning in rats
Authors: Dupin Maryne , Garcia Samuel , Messaoudi Belkacem , Doyère Valérie , Mouly Anne-Marie 
Published: October 2020

AbstractIn fear conditioning, where a conditioned stimulus predicts the arrival of an aversive stimulus, the animal encodes the time interval between the two stimuli. Here we monitored respiration to visualize anticipatory behavioral responses in an odor fear conditioning in rats, while recording theta (5–15 Hz) and gamma (40–80 Hz) brain oscillatory activities in the medial prefrontal cortex (mPFC), basolateral amygdala (BLA), dorsomedial striatum (DMS) and olfactory piriform cortex (PIR). We investigated the temporal patterns of respiration frequency and of theta and gamma activity power during the odor-shock interval, comparing two interval durations. We found that akin to respiration patterns, theta temporal curves were modulated by the duration of the odor-shock interval in the four recording sites, and respected scalar property in mPFC and DMS. In contrast, gamma temporal curves were modulated by the interval duration only in the mPFC, and in a manner that did not respect scalar property. This suggests a preferential role for theta rhythm in interval timing. In addition, our data bring the novel idea that the respiratory rhythm might take part in the setting of theta activity dynamics related to timing.
HLA-A alleles including HLA-A29 affect the composition of the gut microbiome: a potential clue to the pathogenesis of birdshot retinochoroidopathy
Authors: Sternes Peter R. , Martin Tammy M. , Paley Michael , Diamond Sarah , Asquith Mark J. , Brown Matthew A. , Rosenbaum James T. 
Published: October 2020

AbstractBirdshot retinochoroidopathy occurs exclusively in individuals who are HLA-A29 positive. The mechanism to account for this association is unknown. The gut microbiome has been causally implicated in many immune-mediated diseases. We hypothesized that HLA-A29 would affect the composition of the gut microbiome, leading to a dysbiosis and immune-mediated eye disease. Fecal and intestinal biopsy samples were obtained from 107 healthy individuals from Portland, Oregon environs, 10 of whom were HLA-A29 positive, undergoing routine colonoscopy. Bacterial profiling was achieved via 16S rRNA metabarcoding. Publicly available whole meta-genome sequencing data from the Human Microbiome Project (HMP), consisting of 298 healthy controls mostly of US origin, were also interrogated. PERMANOVA and sparse partial least squares discriminant analysis (sPLSDA) demonstrated that subjects who were HLA-A29 positive differed in bacterial species composition (beta diversity) compared to HLA-A29 negative subjects in both the Portland (p = 0.019) and HMP cohorts (p = 0.0002). The Portland and HMP cohorts evidenced different subsets of bacterial species associated with HLA-A29 status, likely due to differences in the metagenomic techniques employed. The functional composition of the HMP cohort did not differ overall (p = 0.14) between HLA-A29 positive and negative subjects, although some distinct pathways such as heparan sulfate biosynthesis showed differences. As we and others have shown for various HLA alleles, the HLA allotype impacts the composition of the microbiome. We hypothesize that HLA-A29 may predispose chorioretinitis via an altered gut microbiome.