bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dual Effects of Nanoviricides Platform Technology Based NV-CoV-2 Biomimetic Polymer Against COVID-19
Authors: Diwan Anil , Chakraborty Ashok , Chiniga Vijetha , Arora Vinod , Holkar Preetam , Thakur Yogesh , Tatake Jay , Barton Randall , Holkar Neelam , Pond Bethany 
Published: November 2021

AbstractRemdesivir (RDV) is the only antiviral drug so far approved for COVID-19 therapy by the FDA. However its efficacy is limited in vivo due to its low stability in presence of plasma. This paper compared the stability of RDV encapsulated with our platform technology based polymer NV-387 (NV-CoV-2), in presence of plasma in vitro and in vivo. Furthermore, a non- clinical pharmacology studies of NV-CoV-2 (Polymer) and NV-CoV-2-R (Polymer encapsulated Remdesivir) in both NL-63 infected and uninfected rats were done. In an in vitro cell culture model experiment, antiviral activity of NV-CoV-2 and NV-CoV-2-R are also compared with RDV.The results are (i) NV-CoV-2 polymer encapsulation protects RDV from plasma- mediated catabolism in vitro and in vivo, too. (ii) Body weight measurements of the normal (uninfected) rats after administration of the test materials (NV-CoV-2, and NV-CoV-2-R) show no toxic effects on them. (iii) NL-63 infected rats body weights and their survival length were like uninfected rats after treatment with NV-CoV-2 and NV-CoV-2-R, and the efficacy as an antiviral regimen were found in the order as below: NV-CoV-2-R > NV-CoV-2 > RDV.In brief, our platform technology based NV-387-encapsulated-RDV (NV-CoV-2-R) drug has a dual effect on coronaviruses. First, NV-CoV-2 itself as an antiviral regimen. Secondly, RDV is protected from plasma-mediated degradation in transit, rendering altogether the safest and an efficient regimen against COVID-19.
Figbird: A probabilistic method for filling gaps in genome assemblies
Authors: Tarafder Sumit , Islam Mazharul , Shatabda Swakkhar , Rahman Atif 
Published: November 2021

AbstractMotivationAdvances in sequencing technologies have led to sequencing of genomes of a multitude of organisms. However, draft genomes of many of these organisms contain a large number of gaps due to repeats in genomes, low sequencing coverage and limitations in sequencing technologies. Although there exist several tools for filling gaps, many of these do not utilize all information relevant to gap filling.ResultsHere, we present a probabilistic method for filling gaps in draft genome assemblies using second generation reads based on a generative model for sequencing that takes into account information on insert sizes and sequencing errors. Our method is based on the expectation-maximization (EM) algorithm unlike the graph based methods adopted in the literature. Experiments on real biological datasets show that this novel approach can fill up large portions of gaps with small number of errors and misassemblies compared to other state of the art gap filling tools.Availability and ImplementationThe method is implemented using C++ in a software named “Filling Gaps by Iterative Read Distribution (Figbird)”, which is available at: https://github.com/SumitTarafder/Figbird.Contactatif@cse.buet.ac.bdSupplementary informationSupplementary data are available at Bioinformatics online.
A dysmorphic mouse model reveals developmental interactions of chondrocranium and dermatocranium
Authors: Motch Perrine Susan M. , Pitirri M. Kathleen , Durham Emily L. , Kawasaki Mizuho , Zheng Hao , Chen Danny Z. , Kawasaki Kazuhiko , Richtsmeier Joan T. 
Published: November 2021

AbstractThe cranial endo- and dermal skeletons, which comprise the vertebrate skull, evolved independently over 470 million years ago and form separately during embryogenesis. In mammals, much of the cartilaginous chondrocranium is transient, undergoing endochondral ossification or disappearing, so its role in skull morphogenesis is not well studied and it remains an enigmatic structure. We provide complete three-dimensional (3D) reconstructions of the laboratory mouse chondrocranium from embryonic day 13.5 through 17.5 using a novel methodology of uncertainty-guided segmentation of phosphotungstic enhanced 3D microcomputed tomography images with sparse annotation. We evaluate the embryonic mouse chondrocranium and dermatocranium in 3D and delineate the effects of a Fgfr2 variant on embryonic chondrocranial cartilages and on the association with forming dermal bones using the Fgfr2cC342Y/+ Crouzon syndrome mouse. We show that the dermatocranium develops outside of and in shapes that conform to the chondrocranium. Results reveal direct effects of the Fgfr2 variant on embryonic cartilage, on chondrocranium morphology, and on the association between chondrocranium and dermatocranium development. Histologically we observe a trend of relatively more chondrocytes, larger chondrocytes, and/or more matrix in the Fgfr2cC342Y/+ embryos at all timepoints before the chondrocranium begins to disintegrate at E16.5. The chondrocrania and forming dermatocrania of Fgfr2cC342Y/+ embryos are relatively large, but a contrasting trend begins at E16.5 and continues into early postnatal (P0 and P2) timepoints, with the skulls of older Fgfr2cC342Y/+ mice reduced in most dimensions compared to Fgfr2c+/+ littermates. Our findings have implications for the study and treatment of human craniofacial disease, for understanding the impact of chondrocranial morphology on skull growth, and potentially on the evolution of skull morphology.
A fully automated FAIMS-DIA proteomic pipeline for high-throughput characterization of iPSC-derived neurons
Authors: Reilly Luke , Peng Lirong , Lara Erika , Ramos Daniel , Fernandopulle Michael , Pantazis Caroline B. , Stadler Julia , Santiana Marianita , Dadu Anant , Iben James , Faghri Faraz , Nalls Mike A. , Coon Steven L. , Narayan Priyanka , Singleton Andrew B. , Cookson Mark R. , Ward Michael E. , Qi Yue A. 
Published: November 2021

AbstractFully automated proteomic pipelines have the potential to achieve deep coverage of cellular proteomes with high throughput and scalability. However, it is important to evaluate performance, including both reproducibility and ability to provide meaningful levels of biological insight. Here, we present an approach combining high field asymmetric waveform ion mobility spectrometer (FAIMS) interface and data independent acquisition (DIA) proteomics approach developed as part of the induced pluripotent stem cell (iPSC) Neurodegenerative Disease Initiative (iNDI), a large-scale effort to understand how inherited diseases may manifest in neuronal cells. Our FAIMS-DIA approach identified more than 8000 proteins per mass spectrometry (MS) acquisition as well as superior total identification, reproducibility, and accuracy compared to other existing DIA methods. Next, we applied this approach to perform a longitudinal proteomic profiling of the differentiation of iPSC-derived neurons from the KOLF2.1J parental line used in iNDI. This analysis demonstrated a steady increase in expression of mature cortical neuron markers over the course of neuron differentiation. We validated the performance of our proteomics pipeline by comparing it to single cell RNA-Seq datasets obtained in parallel, confirming expression of key markers and cell type annotations. An interactive webapp of this temporal data is available for aligned-UMAP visualization and data browsing (https://share.streamlit.io/anant-droid/singlecellumap). In summary, we report an extensively optimized and validated proteomic pipeline that will be suitable for large-scale studies such as iNDI.
Spectral organ fingerprints for intraoperative tissue classification with hyperspectral imaging
Authors: Studier-Fischer A. , Seidlitz S. , Sellner J. , Wiesenfarth M. , Ayala L. , Özdemir B. , Odenthal J. , Knödler S. , Kowalewski K.F. , Haney C.M. , Camplisson I. , Dietrich M. , Schmidt K. , Salg G.A. , Kenngott H.G. , Adler T.J. , Schreck N. , Kopp-Schneider A. , Maier-Hein K. , Maier-Hein L. , Müller-Stich B.P. , Nickel F. 
Published: November 2021

AbstractVisual discrimination of tissue during surgery can be challenging since different tissues appear similar to the human eye. Hyperspectral imaging (HSI) removes this limitation by associating each pixel with high-dimensional spectral information. While previous work has shown its general potential to discriminate tissue, clinical translation has been limited due to the method’s current lack of robustness and generalizability. Specifically, it had been unknown whether variability in spectral reflectance is primarily explained by tissue type rather than the recorded individual or specific acquisition conditions. The contribution of this work is threefold: (1) Based on an annotated medical HSI data set (9,059 images from 46 pigs), we present a tissue atlas featuring spectral fingerprints of 20 different porcine organs and tissue types. (2) Using the principle of mixed model analysis, we show that the greatest source of variability related to HSI images is the organ under observation. (3) We show that HSI-based fully-automatic tissue differentiation of 20 organ classes with deep neural networks is possible with high accuracy (> 95 %). We conclude from our study that automatic tissue discrimination based on HSI data is feasible and could thus aid in intraoperative decision making and pave the way for context-aware computer-assisted surgery systems and autonomous robotics.
Secondary DNA transfer on denim using a human blood analogue
Authors: Ridings Rebecca , Gabriel Alon , Elliott Colin I. , Shafer Aaron B.A. 
Published: November 2021

AbstractDNA quantification technology has increased in accuracy and sensitivity, now allowing for detection and profiling of trace DNA. Secondary DNA transfer occurs when DNA is deposited via an intermediary source (e.g. clothing, tools, utensils). Multiple courtrooms have now seen secondary transfer introduced as an explanation for DNA being present at a crime scene, but sparse experimental studies mean expert opinions are often limited. Here, we used bovine blood and indigo denim substrates to quantify the amount of secondary DNA transfer and quality of STRs under three different physical contact scenarios: passive, pressure, and friction. We showed that the DNA transfer was highest under a friction scenario, followed by pressure and passive treatments. The STR profiles showed a similar, albeit less pronounced trend, with correctly scored alleles and genotype completeness being highest under a friction scenario, followed by pressure and passive. DNA on the primary substrate showed a decrease in concentration and genotype completeness both immediately and at 24 hours, suggestive of a loss of DNA during the primary transfer. The majority of secondary transfer samples amplified less than 50% of STR loci regardless of contact type. This study showed that while DNA transfer is common between denim, this is not manifested in full STR profiles. We discuss the possible technical solutions to partial profiles from trace DNA, and more broadly the ubiquity of secondary DNA transfer.
Genetic perturbation enhances functional heterogeneity in alkaline phosphatase
Authors: Sakuma Morito , Honda Shingo , Ueno Hiroshi , Miyazaki Kentaro , Tokuriki Nobuhiko , Noji Hiroyuki 
Published: November 2021

AbstractEnzymes inherently exhibit molecule-to-molecule heterogeneity in catalytic activity or function, which underlies the acquisition of new functions in evolutionary processes. However, correlations between the functional heterogeneity of an enzyme and its multi-functionality or promiscuity remain elusive. In addition, the modulation of functional heterogeneity upon genetic perturbation is currently unexplored. Here, we quantitatively analyzed functional heterogeneity in the wild-type and 69 single-point mutants of Escherichia coli alkaline phosphatase (AP) by employing single-molecule assay with a femtoliter reactor array device. Most mutant enzymes exhibited higher functional heterogeneity than the wild-type enzyme, irrespective of catalytic activity. These results indicated that the wild-type AP minimizes functional heterogeneity, and single-point mutations can significantly expand the span of functional heterogeneity in AP. Moreover, we identified a clear correlation between functional heterogeneity and promiscuous activities. These findings suggest that enzymes can acquire greater functional heterogeneity following marginal genetic perturbations that concomitantly promote catalytic promiscuity.
A novel semi-supervised self-training method based on resampling for Twitter fake account identification
Authors: Zeng Ziming , Li Tingting , Sun Shouqiang , Sun Jingjing , Yin Jie 
Published: November 2021

PurposeTwitter fake accounts refer to bot accounts created by third-party organizations to influence public opinion, commercial propaganda or impersonate others. The effective identification of bot accounts is conducive to accurately judge the disseminated information for the public. However, in actual fake account identification, it is expensive and inefficient to manually label Twitter accounts, and the labeled data are usually unbalanced in classes. To this end, the authors propose a novel framework to solve these problems.Design/methodology/approachIn the proposed framework, the authors introduce the concept of semi-supervised self-training learning and apply it to the real Twitter account data set from Kaggle. Specifically, the authors first train the classifier in the initial small amount of labeled account data, then use the trained classifier to automatically label large-scale unlabeled account data. Next, iteratively select high confidence instances from unlabeled data to expand the labeled data. Finally, an expanded Twitter account training set is obtained. It is worth mentioning that the resampling technique is integrated into the self-training process, and the data class is balanced at the initial stage of the self-training iteration.FindingsThe proposed framework effectively improves labeling efficiency and reduces the influence of class imbalance. It shows excellent identification results on 6 different base classifiers, especially for the initial small-scale labeled Twitter accounts.Originality/valueThis paper provides novel insights in identifying Twitter fake accounts. First, the authors take the lead in introducing a self-training method to automatically label Twitter accounts from the semi-supervised background. Second, the resampling technique is integrated into the self-training process to effectively reduce the influence of class imbalance on the identification effect.
Blockchain: an EOM approach to reconciliation in banking
Authors: R Vedapradha , Ravi Hariharan 
Published: November 2021

PurposeThe study aim is to evaluate the contribution of Blockchain technology (Cryptobanking) using expected operating model (EOM) to address the pain points in reconciliation at middle and back-office operational levels in assessing the significance of this technology on return on investment.Design/methodology/approachA structured questionnaire was designed to collect primary data using a stratified sampling method from 120 respondents working in leading Investment banks operating in the geographical locality of urban Bangalore. Demographic variables, accounting variables, data reporting variables, approach variables, variables of EOM were considered to validate the hypothesis with the help of statistical tools, namely ANOVA, and Multiple Stepwise Regression Analysis.FindingsThe results obtained confirm that there is significant difference in reconciliation with implementation of an innovative business process. Financial analysis is the highest predictor of ROI when integrated with technology as the adapted Blockchain innovation in reconciliation is the most influencing factor in enhancing, improving ROI playing a pivotal role in the Investment banks.Originality/valueBlockchain technology (Cryptobanking) facilitates in transforming the reconciliation process of these banks with improved operational efficiency. Blockchain and settlement platforms offer inter-organization solutions facilitating in the reconciliation of various transactions in real-time through a trust-based network in the form of digital settlements with better consortiums.
Cryptocurrency: usability perspective versus volatility threat
Authors: Khan Ruby , Hakami Tahani Ali 
Published: November 2021

PurposeThe objective of this study is to examine the nature of cryptocurrencies, risks involved in using it due to its volatile nature, advantages, disadvantages and its functions as money.Design/methodology/approachThis is an inductive approach to a descriptive analysis (Qualitative research). In order to come to an adequate conclusion, we reviewed several studies and articles previously published in this field related to our research questions, and then explored the nature of Cryptocurrencies, their advantages and disadvantages, risks associated with cryptocurrency usage and their user-friendliness in Saudi Arabia.FindingsThe findings of this study reveal that anonymity and concealment are important aspects of cryptocurrencies. This system does not follow a transparent process that can make it parallel to conventional fiat currency.Research limitations/implicationsAlthough this study focuses on the issue of trust, it fails to recognize more technological factors hampering its transaction mechanism instead of enhancing it, owing to a lack of facts and knowledge.Practical implicationsLike conventional transaction system users must sign their crypto transactions that others must duly verify easily. Once a promise is made, one will not be able to back out of it until it is protected from revocation by the signer.Originality/valueIn comparison with reviewed literature, this study focuses more on the issue of volatility, which accounts for the fact that cryptocurrency has not been accepted as a permanent tool of monetary policy. Additionally, the study finds that the Saudi public is largely pessimistic toward such currencies.
When microbial biotechnology meets material engineering
Authors: Hernández‐Arriaga Ana M. , Campano Cristina , Rivero‐Buceta Virginia , Prieto M. Auxiliadora 
Published: November 2021

SummaryBacterial biopolymers such as bacterial cellulose (BC), alginate or polyhydroxyalkanotes (PHAs) have aroused the interest of researchers in many fields, for instance biomedicine and packaging, due to their being biodegradable, biocompatible and renewable. Their properties can easily be tuned by means of microbial biotechnology strategies combined with materials science. This provides them with highly diverse properties, conferring them non‐native features. Herein we highlight the enormous structural diversity of these macromolecules, how are they produced, as well as their wide range of potential applications in our daily lives. The emergence of new technologies, such as synthetic biology, enables the creation of next‐generation‐advanced materials presenting smart functional properties, for example the ability to sense and respond to stimuli as well as the capacity for self‐repair. All this has given rise to the recent emergence of biohybrid materials, in which a synthetic component is brought to life with living organisms. Two different subfields have recently garnered particular attention: hybrid living materials (HLMs), such as encapsulation or bioprinting, and engineered living materials (ELMs), in which the material is created bottom‐up with the use of microbial biotechnology tools. Early studies showed the strong potential of alginate and PHAs as HLMs, whilst BC constituted the most currently promising material for the creation of ELMs.
Circulating cytokines associated with clinical outcomes in advanced non‐small cell lung cancer patients who received chemoimmunotherapy
Authors: Shi Yuequan , Liu Xiaoyan , Du Juan , Zhang Dongming , Liu Jia , Chen Minjiang , Zhao Jing , Zhong Wei , Xu Yan , Wang Mengzhao 
Published: November 2021

AbstractBackgroundPretreatment and on‐treatment plasma cytokine levels in predicting clinical benefit in patients with advanced non‐small cell lung cancer (NSCLC) treated with anti‐programmed death‐1 (PD‐1)‐based chemotherapy is still a matter of debate.MethodsWe measured 12 kind of plasma cytokines in patients with stage III/IV NSCLC before and during treatment with anti‐PD‐1 based chemotherapy. Associations with best overall response, and survival including progression‐free survival (PFS) and overall survival (OS) were assessed using Chi‐square test and Kaplan–Meier plots with log‐rank test, respectively. Logistic regression and Cox regression were used to determine independent risk factors.ResultsOf a total of 60 patients, high‐level of pretreatment interleukin‐2 was associated with longer PFS (log rank p = 0.049), while high‐level of pretreatment interleukin‐8 was associated with shorter OS (log rank p = 0.006). Increased on‐treatment interleukin‐1β (IL‐1β) was associated with both better response (odds ratio [OR] 6.233, 95% confidential interval [CI]: 1.451–26.344, p = 0.013) and longer PFS (hazard ratio [HR] 0.305, 95% CI: 0.127–0.730, p = 0.008). On the contrary, increased on‐treatment interleukin‐6 (IL‐6) was associated with a worse response (OR 0.015, 95% CI: 0.001–0.400, p = 0.012), worse PFS (HR 2.639, 95% CI: 1.163–5.991, p = 0.020) and worse OS (HR 2.742, 95% CI: 1.063–7.074, p = 0.037). Increased interferon‐γ (IFN‐γ) was found to be associated with better PFS (HR 0.336, 95% CI: 0.153–0.745, p = 0.007).ConclusionsIn patients with advanced NSCLC who received chemoimmunotherapy, on‐treatment increased IL‐1β and IFN‐γ may serve as positive indicator of efficacy, while on‐treatment increased IL‐6 might play a predictive role of worse clinical outcome.
Repeated cocaine or methamphetamine treatment alters astrocytic CRF2 and GLAST expression in the ventral midbrain
Authors: Sharpe Amanda L. , Trzeciak Marta , Eliason Nicole L. , Blankenship Harris E. , Byrd Bre' Ana M. , Douglas Phillip D. , Freeman Willard M. , Beckstead Michael J. 
Published: November 2021

AbstractDopamine neurons in the substantia nigra (SN) and ventral tegmental area (VTA) play a central role in the reinforcing properties of abused drugs including methamphetamine and cocaine. Chronic effects of psychostimulants in the SN/VTA also involve non‐dopaminergic transmitters, including glutamate and the stress‐related peptide corticotropin‐releasing factor (CRF). In the SN/VTA, astrocytes express a variety of membrane‐bound neurotransmitter receptors and transporters that influence neurotransmission. CRF receptor type 2 (CRF2) activity in the VTA is important for stress‐induced relapse and drug‐seeking behaviour, but the localization of its effects is incompletely understood. Here, we first identified CRF2 transcript in astrocytes of the SN/VTA using RNA‐Seq in Aldh1l1;NuTRAP mice and confirmed it using in situ hybridization (RNAscope) in wild‐type mice. We then used immunofluorescence to quantify the astrocytic marker protein S100β, glial‐specific glutamate/aspartate transporter GLAST, and CRF2 in the SN/VTA following 12 days of treatment (i.p.) with methamphetamine (3 mg/kg), cocaine (10 mg/kg), or saline. We observed a significant decrease in GLAST immunofluorescence in brains of psychostimulant treated mice compared with saline controls. In addition, we observed increased labelling of CRF2 in drug treated groups, a decrease in the number of S100β positive cells, and an increase of co‐staining of CRF2 with both S100β and tyrosine hydroxylase (dopamine neurons). Our results suggest a significant interaction between CRF2, GLAST, and astrocytes in the midbrain that emerges with repeated exposure to psychostimulants. These findings provide rationale for future investigation of astrocyte‐based strategies for altering cellular and circuit function in response to stress and drug exposure.