bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new primate model of hypophyseal dysfunction
Authors: Kawabata Teppei , Suga Hidetaka , Takeuchi Kazuhito , Nagata Yuichi , Sakakibara Mayu , Ushida Kaori , Ozone Chikafumi , Enomoto Atsushi , Kawamoto Ikuo , Itagaki Iori , Tsuchiya Hideaki , Arima Hiroshi , Wakabayashi Toshihiko 
Published: May 2021

AbstractFor pituitary regenerative medicine, the creation of a hypophyseal model in monkeys is necessary to conduct future preclinical studies; however, previous studies reported that hypophysectomy in monkeys is not always safe or satisfactory. This study aimed to create a hypophyseal dysfunction model in a cynomolgus monkey using a safer surgical technique and establish the protocol of pituitary hormone replacement therapy for this model. Surgical resection of the pituitary gland of a 7.8-year-old healthy adult cynomolgus male monkey weighing 5.45 kg was performed to create a hypophyseal dysfunction model for future regenerative studies. Endoscopic transoral transsphenoidal surgery was used to perform hypophysectomy under navigation support. These procedures were useful for confirming total removal of the pituitary gland without additional bone removal and preventing complications such as cerebrospinal fluid leakage. Total removal was confirmed by pathological examination and computed tomography. Hypopituitarism was verified with endocrinological examinations including stimulation tests. Postoperatively, the monkey’s general condition of hypopituitarism was treated with hormone replacement therapy, resulting in long-term survival. The success of a minimally invasive and safe surgical method and long-term survival indicate the creation of a hypophyseal dysfunction model in a cynomolgus monkey; hence, this protocol can be employed in the future.
Entrapment of glucose oxidase within gold converts it to a general monosaccharide-oxidase
Authors: Baruch-Shpigler Yael , Avnir David 
Published: May 2021

AbstractWe report that entrapping glucose oxidase (GOx) within metallic gold, expands its activity to become an oxidase for monosaccharides that do not have a natural enzyme with that activity—fructose and xylose—and that this entrapment also removes the enantioselectivity, rendering this enzyme capable of oxidizing the “wrong” l-enantiomer of glucose. These observations suggest that in this biomaterial adsorptive interactions of the outer regions of the protein with the gold cage, pull apart and widen the tunnel between the two monomeric units of GOx, to a degree that its stereoselectivity is compromised; then, the active sites which are more versatile than currently attributed to, are free and capable of acting on the foreign sugars. To test this proposition, we entrapped in gold l-asparaginase, which is also a dimeric enzyme (a dimer of tight dimers), and found, again, that this metallic biomaterial widens the activity of that enzyme, to include the D-amino acid counter enantiomer as well. Detailed kinetic analyses for all substrates are provided for the gold bio-composites, including determination of the difference between the activation energies towards two opposite enantiomers.
A validated model for predicting live birth after embryo transfer
Authors: Awadalla Michael S. , Bendikson Kristin A. , Ho Jacqueline R. , McGinnis Lynda K. , Ahmady Ali 
Published: May 2021

AbstractAccurately predicting the probability of live birth and multiple gestations is important for determining a safe number of embryos to transfer after in vitro fertilization. We developed a model that can be fit to individual clinic data for predicting singleton, twin, and total live birth rates after human embryo transfer. The predicted and observed rates of singleton and twin deliveries were compared in a tenfold cross-validation study using data from a single clinic. The model presented accounts for patient age, embryo stage (cleavage or blastocyst), type of transfer cycle (fresh or frozen) and uterine/universal factors. The standardized errors for rates of singleton and twin deliveries were normally distributed and the mean errors were not significantly different from zero (all p > 0.05). The live birth rates per embryo varied from as high as 43% for fresh blastocysts in the 35-year-old age group to as low as 1% for frozen cleavage stage embryos in the 43-year-old age group. This quantitative model or a simplified version can be used for clinics to generate and analyze their own data to guide the number of embryos to transfer to limit the risk of multiple gestations.
A radiomics-based model to classify the etiology of liver cirrhosis using gadoxetic acid-enhanced MRI
Authors: Elkilany Aboelyazid , Fehrenbach Uli , Auer Timo Alexander , Müller Tobias , Schöning Wenzel , Hamm Bernd , Geisel Dominik 
Published: May 2021

AbstractThe implementation of radiomics in radiology is gaining interest due to its wide range of applications. To develop a radiomics-based model for classifying the etiology of liver cirrhosis using gadoxetic acid-enhanced MRI, 248 patients with a known etiology of liver cirrhosis who underwent 306 gadoxetic acid-enhanced MRI examinations were included in the analysis. MRI examinations were classified into 6 groups according to the etiology of liver cirrhosis: alcoholic cirrhosis, viral hepatitis, cholestatic liver disease, nonalcoholic steatohepatitis (NASH), autoimmune hepatitis, and other. MRI examinations were randomized into training and testing subsets. Radiomics features were extracted from regions of interest segmented in the hepatobiliary phase images. The fivefold cross-validated models (2-dimensional—(2D) and 3-dimensional—(3D) based) differentiating cholestatic cirrhosis from noncholestatic etiologies had the best accuracy (87.5%, 85.6%), sensitivity (97.6%, 95.6%), predictive value (0.883, 0.877), and area under curve (AUC) (0.960, 0.910). The AUC was larger in the 2D-model for viral hepatitis, cholestatic cirrhosis, and NASH-associated cirrhosis (P-value of 0.05, 0.05, 0.87, respectively). In alcoholic cirrhosis, the AUC for the 3D model was larger (P = 0.01). The overall intra-class correlation coefficient (ICC) estimates and their 95% confident intervals (CI) for all features combined was 0.68 (CI 0.56–0.87) for 2D and 0.71 (CI 0.61–0.93) for 3D measurements suggesting moderate reliability. Radiomics-based analysis of hepatobiliary phase images of gadoxetic acid-enhanced MRI may be a promising noninvasive method for identifying the etiology of liver cirrhosis with better performance of the 2D- compared with the 3D-generated models.
Electrical behaviour and evolutionary computation in thin films of bovine brain microtubules
Authors: Vissol-Gaudin Eléonore , Pearson Chris , Groves Chris , Zeze Dagou A. , Cantiello Horacio F. , Cantero María del Rocio , Petty Michael C. 
Published: May 2021

AbstractWe report on the electrical behaviour of thin films of bovine brain microtubules (MTs). For samples in both their dried and hydrated states, the measured currents reveal a power law dependence on the applied DC voltage. We attribute this to the injection of space-charge from the metallic electrode(s). The MTs are thought to form a complex electrical network, which can be manipulated with an applied voltage. This feature has been exploited to undertake some experiments on the use of the MT mesh as a medium for computation. We show that it is possible to evolve MT films into binary classifiers following an evolution in materio approach. The accuracy of the system is, on average, similar to that of early carbon nanotube classifiers developed using the same methodology.
IGF1R and Src inhibition induce synergistic cytotoxicity in HNSCC through inhibition of FAK
Authors: Lehman Christine E. , Spencer Adam , Hall Sarah , Shaw Jeremy J. P. , Wulfkuhle Julia , Petricoin Emanuel F. , Bekiranov Stefan , Jameson Mark J. , Gioeli Daniel 
Published: May 2021

AbstractHead and neck cancer is the sixth most common cancer worldwide with a 5-year survival of only 65%. Targeting compensatory signaling pathways may improve therapeutic responses and combat resistance. Utilizing reverse phase protein arrays (RPPA) to assess the proteome and explore mechanisms of synergistic growth inhibition in HNSCC cell lines treated with IGF1R and Src inhibitors, BMS754807 and dasatinib, respectively, we identified focal adhesion signaling as a critical node. Focal Adhesion Kinase (FAK) and Paxillin phosphorylation were decreased as early as 15 min after treatment, and treatment with a FAK inhibitor, PF-562,271, was sufficient to decrease viability in vitro. Treatment of 3D spheroids demonstrated robust cytotoxicity suggesting that the combination of BMS754807 and dasatinib is effective in multiple experimental models. Furthermore, treatment with BMS754807 and dasatinib significantly decreased cell motility, migration, and invasion in multiple HNSCC cell lines. Most strikingly, treatment with BMS754807 and dasatinib, or a FAK inhibitor alone, significantly increased cleaved-PARP in human ex-vivo HNSCC patient tissues demonstrating a potential clinical utility for targeting FAK or the combined targeting of the IGF1R with Src. This ex-vivo result further confirms FAK as a vital signaling node of this combinatorial treatment and demonstrates therapeutic potential for targeting FAK in HNSCC patients.
A systematic review and meta-analysis on correlation of weather with COVID-19
Authors: Majumder Poulami , Ray Partha Pratim 
Published: May 2021

AbstractThis study presents a systematic review and meta-analysis over the findings of significance of correlations between weather parameters (temperature, humidity, rainfall, ultra violet radiation, wind speed) and COVID-19. The meta-analysis was performed by using ‘meta’ package in R studio. We found significant correlation between temperature (0.11 [95% CI 0.01–0.22], 0.22 [95% CI, 0.16–0.28] for fixed effect death rate and incidence, respectively), humidity (0.14 [95% CI 0.07–0.20] for fixed effect incidence) and wind speed (0.58 [95% CI 0.49–0.66] for fixed effect incidence) with the death rate and incidence of COVID-19 (p < 0.01). The study included 11 articles that carried extensive research work on more than 110 country-wise data set. Thus, we can show that weather can be considered as an important element regarding the correlation with COVID-19.
Decline in influenza cases in Mexico after the implementation of public health measures for COVID-19
Authors: Arellanos-Soto Daniel , Padilla-Rivas Gerardo , Ramos-Jimenez Javier , Galan-Huerta Kame , Lozano-Sepulveda Sonia , Martinez-Acuña Natalia , Treviño-Garza Consuelo , Montes-de-Oca-Luna Roberto , de-la-O-Cavazos Manuel , Rivas-Estilla Ana Maria 
Published: May 2021

AbstractMexico took swift action and has strictly followed mitigation measures to prevent the spread of coronavirus disease, COVID-19. In this study we compared influenza activity indicators in our country after the implementation of public health measures for COVID-19. We compared indicators of influenza activity in 2020 before and after public health measures were taken to reduce COVID-19 with the corresponding indicators from three preceding years and the immediate one, and the potential decrease in seasonal influenza cases/deaths. Nationwide surveillance data revealed a drastic decline in influenza diagnosis in outpatient clinics and public hospitals, influenza positivity rates of clinical specimens, and confirmed severe cases during the following 10 weeks of 2020 as lockdown activities and control measures were established compared with the same period of 2019. Our results suggest that the measures taken for COVID-19 were effective in reducing the spread of other viral respiratory diseases as influenza in our country.
Dissection of the anti-Candida albicans mannan immune response using synthetic oligomannosides reveals unique properties of β-1,2 mannotriose protective epitopes
Authors: Sendid Boualem , Lecointe Karine , Collot Mayeul , Danzé Pierre-Marie , Damiens Sébastien , Drucbert Anne-Sophie , Fradin Chantal , Vilcot Jean-Pierre , Grenouillet Frédéric , Dubar Faustine , de Ruyck Jérôme , Jawhara Samir , Mallet Jean-Maurice , Poulain Daniel 
Published: May 2021

AbstractCandida albicans mannan consists of a large repertoire of oligomannosides with different types of mannose linkages and chain lengths, which act as individual epitopes with more or less overlapping antibody specificities. Although anti-C. albicans mannan antibody levels are monitored for diagnostic purposes nothing is known about the qualitative distribution of these antibodies in terms of epitope specificity. We addressed this question using a bank of previously synthesized biotin sulfone tagged oligomannosides (BSTOs) of α and β anomery complemented with a synthetic β-mannotriose described as a protective epitope. The reactivity of these BSTOs was analyzed with IgM isotype monoclonal antibodies (MAbs) of known specificity, polyclonal sera from patients colonized or infected with C. albicans, and mannose binding lectin (MBL). Surface plasmon resonance (SPR) and multiple analyte profiling (MAP) were used. Both methods confirmed the usual reactivity of MAbs against either α or β linkages, excepted for MAb B6.1 (protective epitope) reacting with β-Man whereas the corresponding BSTO reacted with anti-α-Man. These results were confirmed in western blots with native C. albicans antigens. Using patients’ sera in MAP, a significant correlation was observed between the detection of anti-mannan antibodies recognizing β- and α-Man epitopes and detection of antibodies against β-linked mannotriose suggesting that this epitope also reacts with human polyclonal antibodies of both specificities. By contrast, the reactivity of human sera with other α- and β-linked BSTOs clearly differed according to their colonized or infected status. In these cases, the establishment of an α/β ratio was extremely discriminant. Finally SPR with MBL, an important lectin of innate immunity to C. albicans, classically known to interact with α-mannose, also interacted in an unexpected way with the protective epitope. These cumulative data suggest that structure/activity investigations of the finely tuned C. albicans anti-mannose immune response are worthwhile to increase our basic knowledge and for translation in medicine.
Derivation of stationary distributions of biochemical reaction networks via structure transformation
Authors: Hong Hyukpyo , Kim Jinsu , Ali Al-Radhawi M. , Sontag Eduardo D. , Kim Jae Kyoung 
Published: May 2021

AbstractLong-term behaviors of biochemical reaction networks (BRNs) are described by steady states in deterministic models and stationary distributions in stochastic models. Unlike deterministic steady states, stationary distributions capturing inherent fluctuations of reactions are extremely difficult to derive analytically due to the curse of dimensionality. Here, we develop a method to derive analytic stationary distributions from deterministic steady states by transforming BRNs to have a special dynamic property, called complex balancing. Specifically, we merge nodes and edges of BRNs to match in- and out-flows of each node. This allows us to derive the stationary distributions of a large class of BRNs, including autophosphorylation networks of EGFR, PAK1, and Aurora B kinase and a genetic toggle switch. This reveals the unique properties of their stochastic dynamics such as robustness, sensitivity, and multi-modality. Importantly, we provide a user-friendly computational package, CASTANET, that automatically derives symbolic expressions of the stationary distributions of BRNs to understand their long-term stochasticity.
Integrated genomics and comprehensive validation reveal drivers of genomic evolution in esophageal adenocarcinoma
Authors: Kumar Subodh , Buon Leutz , Talluri Srikanth , Roncador Marco , Liao Chengcheng , Zhao Jiangning , Shi Jialan , Chakraborty Chandraditya , Gonzalez Gabriel , Tai Yu-Tzu , Prabhala Rao , Samur Mehmet K. , Munshi Nikhil C. , Shammas Masood A. 
Published: May 2021

AbstractEsophageal adenocarcinoma (EAC) is associated with a marked genomic instability, which underlies disease progression and development of resistance to treatment. In this study, we used an integrated genomics approach to identify a genomic instability signature. Here we show that elevated expression of this signature correlates with poor survival in EAC as well as three other cancers. Knockout and overexpression screens establish the relevance of these genes to genomic instability. Indepth evaluation of three genes (TTK, TPX2 and RAD54B) confirms their role in genomic instability and tumor growth. Mutational signatures identified by whole genome sequencing and functional studies demonstrate that DNA damage and homologous recombination are common mechanisms of genomic instability induced by these genes. Our data suggest that the inhibitors of TTK and possibly other genes identified in this study have potential to inhibit/reduce growth and spontaneous as well as chemotherapy-induced genomic instability in EAC and possibly other cancers.
Seismic evidence for a thermochemical mantle plume underplating the lithosphere of the Ontong Java Plateau
Authors: Isse Takehi , Suetsugu Daisuke , Ishikawa Akira , Shiobara Hajime , Sugioka Hiroko , Ito Aki , Kawano Yuki , Yoshizawa Kazunori , Ishihara Yasushi , Tanaka Satoru , Obayashi Masayuki , Tonegawa Takashi , Yoshimitsu Junko 
Published: May 2021

AbstractThe Ontong Java Plateau in the western Pacific Ocean is the world’s largest oceanic plateau. It was formed 122 million years ago by a massive volcanic event that significantly affected Earth’s environment. The cause of the magmatic event remains controversial because the upper mantle structure beneath the plateau is poorly known. Here we use passive seismic data obtained through seafloor observations, alongside existing seismic data, to determine the three-dimensional radially anisotropic shear wave velocity to depths of up to 300 km. We find that the lithosphere–asthenosphere boundary is approximately 40 km deeper beneath the centre of the Ontong Java Plateau than beneath the surrounding seafloor. Based on our results and petrological and rheological constraints, we propose that the lithosphere–asthenosphere boundary has deepened as a result of underplating of dehydrated residual material beneath the pre-existing lithosphere during formation of the Ontong Java Plateau by a thermochemical mantle plume.
Circular RNAs as microRNA sponges: evidence and controversies
Authors: Jarlstad Olesen Morten T. , S. Kristensen Lasse 
Published: May 2021

Abstract
Gene expression in eukaryotic cells is a complex process encompassing several layers of regulation at the transcriptional and post-transcriptional levels. At the post-transcriptional level, microRNAs (miRs) are key regulatory molecules that function by binding directly to mRNAs. This generally leads to less efficient translation of the target mRNAs. More recently, an additional layer of gene regulation has been discovered, as other molecules, including circular RNAs (circRNAs), may bind to miRs and thereby function as sponges or decoys resulting in increased expression of the corresponding miR target genes. The circRNAs constitute a large class of mainly non-coding RNAs, which have been extensively studied in recent years, in particular in the cancer research field where many circRNAs have been proposed to function as miR sponges. Here, we briefly describe miR-mediated gene regulation and the extra layer of regulation that is imposed by the circRNAs. We describe techniques and methodologies that are commonly used to investigate potential miR sponging properties of circRNAs and discuss major pitfalls and controversies within this relatively new research field.
Introduction to bioprinting of in vitro cancer models
Authors: Yi Hee-Gyeong 
Published: May 2021

Abstract
Cancer models are essential in cancer research and for new drug development pipelines. However, conventional cancer tissue models have failed to capture the human cancer physiology, thus hindering drug discovery. The major challenge is the establishment of physiologically relevant cancer models that reflect the complexity of the tumor microenvironment (TME). The TME is a highly complex milieu composed of diverse factors that are associated with cancer progression and metastasis, as well as with the development of cancer resistance to therapeutics. To emulate the TME, 3D bioprinting has emerged as a way to create engineered cancer tissue models. Bioprinted cancer tissue models have the potential to recapitulate cancer pathology and increased drug resistance in an organ-mimicking 3D environment. This review overviews the bioprinting technologies used for the engineering of cancer tissue models and provides a future perspective on bioprinting to further advance cancer research.
Production of proteins and commodity chemicals using engineered Bacillus subtilis platform strain
Authors: Zhang Quanwei , Wu Yaokang , Gong Mengyue , Zhang Hongzhi , Liu Yanfeng , Lv Xueqin , Li Jianghua , Du Guocheng , Liu Long 
Published: May 2021

Abstract
Currently, increasing demand of biochemicals produced from renewable resources has motivated researchers to seek microbial production strategies instead of traditional chemical methods. As a microbial platform, Bacillus subtilis possesses many advantages including the generally recognized safe status, clear metabolic networks, short growth cycle, mature genetic editing methods and efficient protein secretion systems. Engineered B. subtilis strains are being increasingly used in laboratory research and in industry for the production of valuable proteins and other chemicals. In this review, we first describe the recent advances of bioinformatics strategies during the research and applications of B. subtilis. Secondly, the applications of B. subtilis in enzymes and recombinant proteins production are summarized. Further, the recent progress in employing metabolic engineering and synthetic biology strategies in B. subtilis platform strain to produce commodity chemicals is systematically introduced and compared. Finally, the major limitations for the further development of B. subtilis platform strain and possible future directions for its research are also discussed.
Face hallucination based on cluster consistent dictionary learning
Authors: Li Minqi , He Xiangjian , Lam Kin‐Man , Zhang Kaibing , Jing Junfeng 
Published: May 2021

AbstractFace hallucination is a super‐resolution technique specially designed to reconstruct high‐resolution faces from low‐resolution faces. Most state‐of‐the‐art algorithms leverage position‐patch prior knowledge of human faces to better super‐resolve face images. However, most of them assume the training face dataset is sufficiently large, well cropped or aligned. This paper, proposes a novel example‐based face hallucination method, based on cluster consistent dictionary learning with the assumption that human faces have similar facial structures. In this method, the paired face image patches are firstly labelled as face areas including eyes, nose, mouth and other parts, as well as non‐face areas without requiring the training face images cropped and aligned. Then, the training patches are clustered according their labels and textures. The cluster consistent dictionary is learned to represent the low‐resolution patches and the high‐resolution patches. Finally, the high‐resolution patches of the input low‐resolution face image can be efficiently generated by using the adjusted anchored neighbourhood regression. As utilizing the labelled facial parts prior knowledge, the proposed method represents more details in the reconstruction. Experimental results demonstrate that the authors' algorithm outperforms many state‐of‐the‐art techniques for face hallucination under different datasets.