bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of alexithymia on the management of Latin American patients with asthma: A cross-sectional study
Authors: Vanegas Emanuel , Felix Miguel , Ramon German D , López Jove Orlando , Matos Benavides Edgar Emilio , Tinoco-Morán Iván , Bernstein Jonathan A , Cherrez-Ojeda Iván 
Published: June 2020

Objectives: In asthmatic patients, studies suggest that alexithymia leads to negative consequences and emotions that can affect physical, psychological, and social aspects of life. We designed this study to determine the frequency of alexithymia in Latin American patients with asthma, as well as to understand how this personality trait and each of its components interact with asthma severity and demographic variables, and their implications on treatment adherence and disease control under such setting. Methods: We conducted a cross-sectional study, involving 265 Latin American patients with asthma. Patient demographics and clinical characteristics were reported. The presence of alexithymia, asthma severity, and control, as well as treatment adherence, was analyzed. To assess the presence of alexithymia, the 20-item Toronto Alexithymia Scale was used. For the statistical analyses, we performed Kendall’s tau-b correlation coefficient, chi-square tests for association, and one-way analysis of variance. Results: A total of 265 patients participated in the study with a gender distribution of 69.4% female and an average age of 54.7 years. In total, 30.2% of individuals presented alexithymia. There was a statistically significant correlation between educational level and 20-item Toronto Alexithymia Scale categories ( p < .001), as well as a higher proportion of severe (35.1%, p = .001) and uncontrolled (50.0%, p = .185) asthma in patients with alexithymia. A higher proportion of patients with some level of non-adherence was seen on those with uncontrolled asthma (68.5%, p = .008). Conclusion: Our results suggest that in our sample, 3 in 10 Latin American asthma patients have alexithymia, and such mental condition is more common in those individuals with lower educational levels. Individuals with alexithymia present with severe asthma more frequently than do patients with possible or no alexithymia and are also more likely to have their disease uncontrolled.
Risk factors for transplant-associated thrombotic microangiopathy and mortality in a pediatric cohort
Authors: Schoettler Michelle , Lehmann Leslie E. , Margossian Steven , Lee Maia , Kean Leslie S. , Kao Pei-Chi , Ma Clement , Duncan Christine N. 
Published: June 2020

Abstract
Transplant-associated thrombotic microangiopathy (TA-TMA) is a well-recognized complication of hematopoietic cell transplantation (HCT). Diagnosis is challenging and in the absence of a tissue biopsy, TA-TMA is provisionally diagnosed by meeting clinical criteria. In this study, we describe the prevalence, outcomes, and risk factors for meeting 2 different diagnostic criteria for TA-TMA and for increased transplant-related mortality (TRM). In this retrospective study of 307 pediatric HCT patients, records were reviewed for the first 100 days after HCT. Patients who were diagnosed with TA-TMA by a provider during this time were included. In addition, the Cho et al criteria (2010) and Jodele et al (2014) TA-TMA criteria were applied retrospectively. Eight patients (2.6%) were diagnosed with TA-TMA by their provider. However, on retrospective review, 20% and 36% met the Cho and Jodele criteria for TA-TMA, respectively. Overall survival was significantly worse (P &lt; .0001) and TRM was significantly higher in patients who met criteria for TA-TMA (MC-TA-TMA) (P &lt; .0001). After controlling for comorbid conditions, MC-TA-TMA (hazard ratio [HR], 10.9; P = .0001) and grade 3/4 acute graft-versus-host-disease (aGVHD) (HR 3.5; P = .01) remained independently associated with increased TRM. Among allogeneic HCT recipients, features associated with an increased risk for MC-TA-TMA included ≥2 HCT, concurrent grade 3/4 aGVHD and concurrent infections. Among patients who MC-TA-TMA, LDH ≥2 times the upper limit of normal (P = .001), the need for ≥2 antihypertensive medications (P &lt; .0001), and acute kidney injury (P = .003) were associated with significantly increased TRM.
Ethyl pyruvate protects against sepsis-associated encephalopathy through inhibiting the NLRP3 inflammasome
Authors: Zhong Xiaoli , Xie Lingli , Yang Xiaolong , Liang Fang , Yang Yanliang , Tong Jianbin , Zhong Yanjun , Zhao Kai , Tang Yiting , Yuan Chuang 
Published: June 2020

Abstract
Background
With the advance of antibiotics and life support therapy, the mortality of sepsis has been decreasing in recent years. However, the incidence of sepsis-associated encephalopathy (SAE), a common complication of sepsis, is still high. There are few effective therapies to treat clinical SAE. We previously found that ethyl pyruvate (EP), a metabolite derivative, is able to effectively inhibit the NLRP3 inflammasome activation. Administration of ethyl pyruvate protects mice against polymicrobial sepsis in cecal ligation and puncture (CLP) model. The aim of present study is to investigate if ethyl pyruvate is able to attenuate SAE.

Methods
After CLP, C57BL/6 mice were intraperitoneally or intrathecally injected with saline or ethyl pyruvate using the sham-operated mice as control. New Object Recognition (NOR) and Morris Water Maze (MWM) were conducted to determine the cognitive function. Brain pathology was assessed via immunohistochemistry. To investigate the mechanisms by which ethyl pyruvate prevent SAE, the activation of NLRP3 in the hippocampus and the microglia were determined using western blotting, and cognitive function, microglia activation, and neurogenesis were assessed using WT, Nlrp3−/− and Asc−/− mice in the sublethal CLP model. In addition, Nlrp3−/− and Asc−/− mice treated with saline or ethyl pyruvate were subjected to CLP.

Results
Ethyl pyruvate treatment significantly attenuated CLP-induced cognitive decline, microglia activation, and impaired neurogenesis. In addition, EP significantly decreased the NLRP3 level in the hippocampus of the CLP mice, and inhibited the cleavage of IL-1β induced by NLRP3 inflammsome in microglia. NLRP3 and ASC deficiency demonstrated similar protective effects against SAE. Nlrp3−/− and Asc−/− mice significantly improved cognitive function and brain pathology when compared with WT mice in the CLP models. Moreover, ethyl pyruvate did not have additional effects against SAE in Nlrp3−/− and Asc−/− mice.

Conclusion
The results demonstrated that ethyl pyruvate confers protection against SAE through inhibiting the NLRP3 inflammasome.
Multidimensional assessment of the effects of erenumab in chronic migraine patients with previous unsuccessful preventive treatments: a comprehensive real-world experience
Authors: Russo Antonio , Silvestro Marcello , Scotto di Clemente Fabrizio , Trojsi Francesca , Bisecco Alvino , Bonavita Simona , Tessitore Alessandro , Tedeschi Gioacchino 
Published: June 2020

Abstract
Background
erenumab was safe and effective in clinical trials for the prevention of migraine. However, real-life data are still lacking. Here we report the clinical experience from an Italian real-world setting using erenumab in patients with chronic migraine experiencing previous unsuccessful preventive treatments.

Methods
Seventy patients with chronic migraine and failure to ≥4 migraine preventive medication classes initially received monthly erenumab 70 mg s.c. Patients without a clinically meaningful improvement, considered as a > 30% reduction in headache days per month, after ≥3 months of therapy switched to monthly erenumab 140 mg. At the first administration and after 3 and 6 months, patients underwent extensive interviews to assess clinical parameters of disease severity and migraine-related disability and impact, and validated questionnaires to explore depression/anxiety, sleep, and quality of life (QoL). Finally, the Pain Catastrophizing Scale, Allodynia Symptom Checklist-12 and MIGraine attacks-Subjective COGnitive impairments scale (MIG-SCOG) were administered.

Results
70% of patients were “responders” after the third administration of erenumab 70 mg, whereas 30% switched to erenumab 140 mg; 29% (6 pts) responded after the sixth administration. The headache-day frequency was reduced from 21.1 ± 0.7 to 11.4 ± 0.9 days after the third administration (p < 0.001) and to 8.9 ± 0.7 days after the sixth administration (p < 0.001). 53% and 70% of patients, respectively, showed a reduction of ≥50% of headache days/month after the third and the sixth administrations.
Also improved were headache pain severity, migraine-related disability, and impact on daily living, QoL, pain catastrophizing and allodynia (all p < 0.001), quality of sleep, symptoms of depression or anxiety (p < 0.05) but not MIG-SCOG. There were no new adverse event signals.

Conclusion
These real-world data support monthly erenumab 70 or 140 mg s.c. as a safe and effective preventive treatment to reduce headache frequency and severity in chronic migraine patients experiencing previous unsuccessful preventive treatments.
Gradient Engineered Light Absorption Layer for Enhanced Carrier Separation Efficiency in Perovskite Solar Cells
Authors: Wu Gaozhu , Zhu Qing , Zhang Teng , Zou Ziqi , Wang Weiping , Cao Yiyan , Kong Lijing , Zheng Xuanli , Wu Yaping , Li Xu , Wu Zhiming , Kang Junyong 
Published: June 2020

AbstractCarrier transport behavior in the perovskite light absorption layer significantly impacts the performance of perovskite solar cells (PSCs). In this work, reduced carrier recombination losses were achieved by the design of a band structure in perovskite materials. An ultrathin (PbI2/PbBr2)n film with a gradient thickness ratio was deposited as the lead halide precursor layer by a thermal evaporation method, and PSCs with a gradient band structure in the perovskite absorption layer were fabricated by a two-step method in ambient atmosphere. For comparison, PSCs with homogeneous perovskite materials of MAPbI3 and MAPbIxBr3 − x were fabricated as well. It is found that the gradient type-II band structure greatly reduces the carrier lifetime and enhances the carrier separation efficiency. As a result, the PSCs with a gradient band structure exhibit an average power conversion efficiency of 17.5%, which is 1–2% higher than that of traditional PSCs. This work provides a novel method for developing high-efficiency PSCs.
Successful single-stage transperitoneal laparoscopic ureterolithotomy in a solitary functioning renal unit with multiple large ureteric calculi along its entire length
Authors: Kamath Sheshang U. , Kaddu Deepak , Patil Bhushan , Patwardhan Sujata K. 
Published: June 2020

AbstractBackgroundLaparoscopic ureterolithotomy bridges the gap between open and endourologic procedures as it is minimally invasive and overcomes a few of the disadvantages of open ureterolithotomy. We report a case of a solitary functioning renal unit with at least 12 large ureteric calculi coursing along the entire length of the ureter and involving the renal pelvis presenting with obstructive uropathy which was subsequently successfully managed with laparoscopic ureterolithotomy.Case presentationA 50-year-old male patient presented with obstructive uropathy with CT suggestive of solitary functioning right kidney with right ureter showing at least 13 large ureteric calculi and large renal pelvic calculi. Right transperitoneal laparoscopic ureterolithotomy was performed. All the renal and ureteric calculi were successfully removed.ConclusionThus, laparoscopic ureterolithotomy with only three ports can be used to remove any burden of calculi along the course of the entire urinary tract being successful in a single stage with minimal morbidity.
Amino acid encoding for deep learning applications
Authors: ElAbd Hesham , Bromberg Yana , Hoarfrost Adrienne , Lenz Tobias , Franke Andre , Wendorff Mareike 
Published: June 2020

Abstract
Background
The number of applications of deep learning algorithms in bioinformatics is increasing as they usually achieve superior performance over classical approaches, especially, when bigger training datasets are available. In deep learning applications, discrete data, e.g. words or n-grams in language, or amino acids or nucleotides in bioinformatics, are generally represented as a continuous vector through an embedding matrix. Recently, learning this embedding matrix directly from the data as part of the continuous iteration of the model to optimize the target prediction – a process called ‘end-to-end learning’ – has led to state-of-the-art results in many fields. Although usage of embeddings is well described in the bioinformatics literature, the potential of end-to-end learning for single amino acids, as compared to more classical manually-curated encoding strategies, has not been systematically addressed. To this end, we compared classical encoding matrices, namely one-hot, VHSE8 and BLOSUM62, to end-to-end learning of amino acid embeddings for two different prediction tasks using three widely used architectures, namely recurrent neural networks (RNN), convolutional neural networks (CNN), and the hybrid CNN-RNN.

Results
By using different deep learning architectures, we show that end-to-end learning is on par with classical encodings for embeddings of the same dimension even when limited training data is available, and might allow for a reduction in the embedding dimension without performance loss, which is critical when deploying the models to devices with limited computational capacities. We found that the embedding dimension is a major factor in controlling the model performance. Surprisingly, we observed that deep learning models are capable of learning from random vectors of appropriate dimension.

Conclusion
Our study shows that end-to-end learning is a flexible and powerful method for amino acid encoding. Further, due to the flexibility of deep learning systems, amino acid encoding schemes should be benchmarked against random vectors of the same dimension to disentangle the information content provided by the encoding scheme from the distinguishability effect provided by the scheme.
PPAI: a web server for predicting protein-aptamer interactions
Authors: Li Jianwei , Ma Xiaoyu , Li Xichuan , Gu Junhua 
Published: June 2020

Abstract
Background
The interactions between proteins and aptamers are prevalent in organisms and play an important role in various life activities. Thanks to the rapid accumulation of protein-aptamer interaction data, it is necessary and feasible to construct an accurate and effective computational model to predict aptamers binding to certain interested proteins and protein-aptamer interactions, which is beneficial for understanding mechanisms of protein-aptamer interactions and improving aptamer-based therapies.

Results
In this study, a novel web server named PPAI is developed to predict aptamers and protein-aptamer interactions with key sequence features of proteins/aptamers and a machine learning framework integrated adaboost and random forest. A new method for extracting several key sequence features of both proteins and aptamers is presented, where the features for proteins are extracted from amino acid composition, pseudo-amino acid composition, grouped amino acid composition, C/T/D composition and sequence-order-coupling number, while the features for aptamers are extracted from nucleotide composition, pseudo-nucleotide composition (PseKNC) and normalized Moreau-Broto autocorrelation coefficient. On the basis of these feature sets and balanced the samples with SMOTE algorithm, we validate the performance of PPAI by the independent test set. The results demonstrate that the Area Under Curve (AUC) is 0.907 for prediction of aptamer, while the AUC reaches 0.871 for prediction of protein-aptamer interactions.

Conclusion
These results indicate that PPAI can query aptamers and proteins, predict aptamers and predict protein-aptamer interactions in batch mode precisely and efficiently, which would be a novel bioinformatics tool for the research of protein-aptamer interactions. PPAI web-server is freely available at http://39.96.85.9/PPAI.
Genome-wide identification and characterisation of Aquaporins in Nicotiana tabacum and their relationships with other Solanaceae species
Authors: De Rosa Annamaria , Watson-Lazowski Alexander , Evans John R. , Groszmann Michael 
Published: June 2020

Abstract
Background
Cellular membranes are dynamic structures, continuously adjusting their composition, allowing plants to respond to developmental signals, stresses, and changing environments. To facilitate transmembrane transport of substrates, plant membranes are embedded with both active and passive transporters. Aquaporins (AQPs) constitute a major family of membrane spanning channel proteins that selectively facilitate the passive bidirectional passage of substrates across biological membranes at an astonishing 108 molecules per second. AQPs are the most diversified in the plant kingdom, comprising of five major subfamilies that differ in temporal and spatial gene expression, subcellular protein localisation, substrate specificity, and post-translational regulatory mechanisms; collectively providing a dynamic transportation network spanning the entire plant. Plant AQPs can transport a range of solutes essential for numerous plant processes including, water relations, growth and development, stress responses, root nutrient uptake, and photosynthesis. The ability to manipulate AQPs towards improving plant productivity, is reliant on expanding our insight into the diversity and functional roles of AQPs.

Results
We characterised the AQP family from Nicotiana tabacum (NtAQPs; tobacco), a popular model system capable of scaling from the laboratory to the field. Tobacco is closely related to major economic crops (e.g. tomato, potato, eggplant and peppers) and itself has new commercial applications. Tobacco harbours 76 AQPs making it the second largest characterised AQP family. These fall into five distinct subfamilies, for which we characterised phylogenetic relationships, gene structures, protein sequences, selectivity filter compositions, sub-cellular localisation, and tissue-specific expression. We also identified the AQPs from tobacco’s parental genomes (N. sylvestris and N. tomentosiformis), allowing us to characterise the evolutionary history of the NtAQP family. Assigning orthology to tomato and potato AQPs allowed for cross-species comparisons of conservation in protein structures, gene expression, and potential physiological roles.

Conclusions
This study provides a comprehensive characterisation of the tobacco AQP family, and strengthens the current knowledge of AQP biology. The refined gene/protein models, tissue-specific expression analysis, and cross-species comparisons, provide valuable insight into the evolutionary history and likely physiological roles of NtAQPs and their Solanaceae orthologs. Collectively, these results will support future functional studies and help transfer basic research to applied agriculture.
Interactive effects of elevated CO2 concentration and combined heat and drought stress on tomato photosynthesis
Authors: Zhou Rong , Yu Xiaqing , Wen Junqin , Jensen Nikolaj Bjerring , dos Santos Thayna Mendanha , Wu Zhen , Rosenqvist Eva , Ottosen Carl-Otto 
Published: June 2020

Abstract
Background
Extreme weather events are predicted to increase, such as combined heat and drought. The CO2 concentration ([CO2]) is predicted to approximately double by 2100. We aim to explore how tomato physiology, especially photosynthesis, is affected by combined heat and drought under elevated [CO2] (e [CO2]).

Results
Two genotypes, ‘OuBei’ (‘OB’, Solanum lycopersicum) and ‘LA2093’ (S. pimpinellifolium) were grown at a [CO2] (atmospheric [CO2], 400 ppm) and e [CO2] (800 ppm), respectively. The 27-days-old seedlings were treated at 1) a [CO2], 2) a [CO2] + combined stress, 3) e [CO2] and 4) e [CO2] + combined stress, followed by recovery. The PN (net photosynthetic rate) increased at e [CO2] as compared with a [CO2] and combined stress inhibited the PN. Combined stress decreased the Fv/Fm (maximum quantum efficiency of photosystem II) of ‘OB’ at e [CO2] and that of ‘LA2093’ in regardless of [CO2]. Genotypic difference was observed in the e [CO2] effect on the gas exchange, carbohydrate accumulation, pigment content and dry matter accumulation.

Conclusions
Short-term combined stress caused reversible damage on tomato while the e [CO2] alleviated the damage on photosynthesis. However, the e [CO2] cannot be always assumed have positive effects on plant growth during stress due to increased water consumption. This study provided insights into the physiological effects of e [CO2] on tomato growth under combined stress and contributed to tomato breeding and management under climate change.
A blood RNA transcript signature for TB exposure in household contacts
Authors: Kwan Philip Kam Weng , Periaswamy Balamurugan , De Sessions Paola Florez , Lin Wenwei , Molton James S. , Naftalin Claire M. , Naim Ahmad Nazri Mohamed , Hibberd Martin L. , Paton Nicholas I. 
Published: June 2020

Abstract
Background
Current tools for diagnosing latent TB infection (LTBI) detect immunological memory of past exposure but are unable to determine whether exposure is recent. We sought to identify a whole-blood transcriptome signature of recent TB exposure.

Methods
We studied household contacts of TB patients; healthy volunteers without recent history of TB exposure; and patients with active TB. We performed whole-blood RNA sequencing (in all), an interferon gamma release assay (IGRA; in contacts and healthy controls) and PET/MRI lung scans (in contacts only). We evaluated differentially-expressed genes in household contacts (log2 fold change ≥1 versus healthy controls; false-discovery rate < 0.05); compared these to differentially-expressed genes seen in the active TB group; and assessed the association of a composite gene expression score to independent exposure/treatment/immunological variables.

Results
There were 186 differentially-expressed genes in household contacts (n = 26, age 22–66, 46% male) compared with healthy controls (n = 5, age 29–38, 100% male). Of these genes, 141 (76%) were also differentially expressed in active TB (n = 14, age 27–69, 71% male). The exposure signature included genes from inflammatory response, type I interferon signalling and neutrophil-mediated immunity pathways; and genes such as BATF2 and SCARF1 known to be associated with incipient TB. The composite gene-expression score was higher in IGRA-positive contacts (P = 0.04) but not related to time from exposure, isoniazid prophylaxis, or abnormalities on PET/MRI (all P > 0.19).

Conclusions
Transcriptomics can detect TB exposure and, with further development, may be an approach of value for epidemiological research and targeting public health interventions.