bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spontaneous Mutations in HIV-1 Gag, protease, RT p66 in the first replication cycle and how they appear: Insights from anin vitroBSL2 assay on mutation rates and types
Authors: Yeo Joshua Yi , Koh Darius Wen-Shuo , Yap Ping , Goh Ghin-Ray , Gan Samuel Ken-En 
Published: June 2019

AbstractWhile drug resistant mutations in HIV-1 is largely credited to its error prone HIV-1 RT, host proteins such as deaminases may also play a role generating mutations. Many HIV-1 RT mutationalin vitrostudies utilize reporter genes (LacZ) as template, leaving out the possible contribution of HIV codon usage and gene-specific effects. To address this gap, we studied HIV-1 RT mutation rates and bias on its own Gag, protease, and RT p66 genes in anin-vitroselection pressure free system. We found rare clinical mutations with a general avoidance of crucial functional sites in the background mutations rates for Gag, protease and RT p66 at 4.71 x 10−5, 6.03 x 10−5, and 7.09 x 10−5mutations/bp respectively. Gag and p66 genes showed a large number of ‘A to G’ hypermutations likely due to cellular adenosine deaminases. Comparisons with silently mutated p66 sequences showed an increase in mutation rates (1.88 x 10−4mutations/bp) and that ‘A to G’ mutations occurred in regions reminiscent of ADAR neighbour preferences. Mutational free energies by the ‘A to G’ mutations revealed an avoidance of destabilizing effects with the natural p66 gene codon usage providing barriers to ADAR effects. Our study demonstrates the importance of studying mutation emergence in HIV genes to understand how fast drug resistance can emerge, sometimes with contributions of host deaminases, providing transferable applications to how new viral diseases and drug resistances can emerge.
Transcriptome responses of intestinal epithelial cells induced by membrane vesicles ofListeria monocytogenesunveil novel insights into the host-pathogen cross talk
Authors: Karthikeyan Raman , Gayathri Pratapa , Gunasekaran Paramasamy , Jagannadham Medicharla V. , Rajendhran Jeyaprakash 
Published: June 2019

AbstractMembrane vesicles (MVs) serve as a vital source of virulence factors in many pathogenic organisms. The release of MVs byListeria monocytogenesis only recently recognized, but its role in the pathogenesis is poorly understood. Here, we investigated the role of MVs ofL. monocytogenesin virulence and host interactions. Proteomic analyses of whole cells and MVs ofL. monocytogeneswere performed using LC/MS/MS. A total of 1376 and 456 proteins were identified in theL. monocytogenescells and MVs, respectively. Also, we have found that MVs contains active pore-forming listeriolysin (LLO), internalin B (inlB), phosphatidylinositol-specific phospholipase C (PI-PLC-A). We have previously reported that MVs ofL. monocytogenescan infect and induce cytotoxicity in Caco-2 cells. In this study, we report the transcriptome response of Caco-2 cells upon infection with MVs as well asL. monocytogenes. In particular, we observed the up-regulation of autophagy-related genes in the early phase of infection with MVs. Transcription of inflammatory cytokines (CCL2, CXCL6, CXCL8, CXCL15, CXCL5, CXCL10) peaked at four h of infection. A large number of differentially expressed genes was associated with actin cytoskeleton rearrangement, autophagy, cell cycle arrest, and induction of oxidative stress. At a later time point, transcriptional programs generated upon infection with MVs point toward to evade innate immune signals, by modulating the expression of anti-inflammatory genes. KEGG pathway enrichment analysis revealed that MVs induce several signaling pathways such as PI3k-Akt signaling pathway, mitogen-activated protein kinase (MAPK) pathway, NOD-like receptor signaling pathway, cAMP signaling pathway, TNF, and NF-kB signaling pathway. Moreover, MVs induced the expression of cell cycle regulatory genes, which may result in the ability to prolong host cell survival, thus protecting the replicative niche forL. monocytogenes. Notably, we identified several non-coding RNAs (ncRNAs) are regulated during infection, suggesting that an early manipulation of the host gene expression may be essential forL. monocytogenespersistence and replication in host cells.
Human Endometrial Transcriptome and Progesterone Receptor Cistrome Reveal Important Pathways and Epithelial Regulators
Authors: Chi Ru-pin Alicia , Wang Tianyuan , Adams Nyssa , Wu San-pin , Young Steven L. , Spencer Thomas E. , DeMayo Francesco 
Published: June 2019

ABSTRACTContextPoor uterine receptivity is one major factor leading to pregnancy loss and infertility. Understanding the molecular events governing successful implantation is hence critical in combating infertility.ObjectiveTo define PGR-regulated molecular mechanisms and epithelial roles in receptivity.DesignRNA-seq and PGR-ChIP-seq were conducted in parallel to identify PGR-regulated pathways during the WOI in endometrium of fertile women.SettingEndometrial biopsies from the proliferative and mid-secretory phases were analyzed.Patients or Other ParticipantsParticipants were fertile, reproductive aged (18-37) women with normal cycle length; and without any history of dysmenorrhea, infertility, or irregular cycles. In total, 42 endometrial biopsies obtained from 42 women were analyzed in this study.InterventionsThere were no interventions during this study.Main Outcome MeasuresHere we measured the alterations in gene expression and PGR occupancy in the genome during the WOI, based on the hypothesis that PGR binds uterine chromatin cycle-dependently to regulate genes involved in uterine cell differentiation and function.Results653 genes were identified with regulated PGR binding and differential expression during the WOI. These were involved in regulating inflammatory response, xenobiotic metabolism, EMT, cell death, interleukin/STAT signaling, estrogen response, and MTORC1 response. Transcriptome of the epithelium identified 3,052 DEGs, of which 658 were uniquely regulated. Transcription factors IRF8 and MEF2C were found to be regulated in the epithelium during the WOI at the protein level, suggesting potentially important functions that are previously unrecognized.ConclusionPGR binds the genomic regions of genes regulating critical processes in uterine receptivity and function.PrécisUsing a combination of RNA-seq and PGR ChIP-seq, novel signaling pathways and epithelial regulators were identified in the endometrium of fertile women during the window of implantation.
In Depth Flow Inspection Using Dynamic Laser Speckle Temporal Statistics
Authors: Golberg Mark , Califa Ran , Polani Sagi , Garcia Javier , Zalevsky Zeev 
Published: June 2019

AbstractWe present novel optical approach based on statistical analysis of temporal laser speckle patterns for tissue in-depth flow characteristics. An ability to distinguish between Brownian motion of particles and laminar flow is well proved. The main steps in the post processing algorithm and the in-vivo and in-vitro experimental results are presented and demonstrated.
Cardiac contraction velocity has evolved to match heart rate with body size through variation in β-cardiac myosin sequence
Authors: Johnson Chloe A. , McGreig Jake E. , Vera Carlos D. , Mulvihill Dan P. , Ridout Martin , Leinwand Leslie A. , Wass Mark N. , Geeves Michael A. 
Published: June 2019

AbstractHeart rate and the maximum velocity of contraction of striated muscle are inversely related to species size. As mammals evolve to different sizes, adaptations are required such as slower contracting heart and skeletal muscles. Analysis of the motor domain of β-myosin from 67 mammals from two clades identifies 14 sites, out of 800, strongly associated with body mass (p<0.01) but not with the clade (p>0.05). Nine of these sites were mutated in the human β-myosin to make it resemble the rat sequence. Biochemical analysis revealed that the rat-human β-myosin chimera functioned like the native rat myosin with a two fold increase in both motility and in the rate of ADP release from the actin.myosin cross-bridge (the step that limits contraction velocity). Both clades use the same small set of amino acids to adjust contraction velocity, suggesting a limited number of ways in which velocity can be manipulated.
Strategizing in English hospitals: accounting, practical coping and strategic intent
Authors: Begkos Christos , Llewellyn Sue , Walshe Kieran 
Published: June 2019

PurposeThe purpose of this paper is to investigate the intricate ways in which accounting is implicated in the unfolding of strategizing in a pluralistic setting. The authors treat strategizing as a practical coping mechanism which begins in response to a problem and unfolds over time into an episode. This approach enables the authors to explore strategizing pathways and the ways they can mobilise accounting to advance from practical coping to explicit strategic intent.Design/methodology/approachThe authors conducted semi-structured interviews with Clinical Directors, Business Managers and Finance personnel at three NHS hospitals. Documents were also collected, such as business cases and financial reports. The authors employed theories on strategizing agency, episodes and practical coping to select examples of strategizing and indicate how strategizing is constructed and performed. The authors present the results of this qualitative analysis in three strategizing narratives.FindingsThe analysis highlights how Clinical Directors’ strategizing with accounting, in response to their financial problems, can take on contesting, conforming and circumventing modes. As the strategizing pathway unfolds, accounting acts as an obligatory passage point through which Clinical Directors pursue their strategic intent. Along each pathway the authors identify, first, where practical coping takes on a clear strategic intent and, second, whether this emergent strategy proves efficacious.Originality/valueThe authors contribute to the nascent body of accounting and strategizing studies through seeing strategizing with accounting, not as the formulation of explicit organisational strategy as “done” in board rooms and strategy meetings, but as an impromptu response to a critical financial problem within a localised organisational setting. In response to a problem, actors may realise their immanent strategizing through their engagement with accounting practices.
Adaptive motion planning framework by learning from demonstration
Authors: Li Xiao , Cheng Hongtai , Liang Xiaoxiao 
Published: June 2019

PurposeLearning from demonstration (LfD) provides an intuitive way for non-expert persons to teach robots new skills. However, the learned motion is typically fixed for a given scenario, which brings serious adaptiveness problem for robots operating in the unstructured environment, such as avoiding an obstacle which is not presented during original demonstrations. Therefore, the robot should be able to learn and execute new behaviors to accommodate the changing environment. To achieve this goal, this paper aims to propose an improved LfD method which is enhanced by an adaptive motion planning technique.Design/methodology/approachThe LfD is based on GMM/GMR method, which can transform original off-line demonstrations into a compressed probabilistic model and recover robot motion based on the distributions. The central idea of this paper is to reshape the probabilistic model according to on-line observation, which is realized by the process of re-sampling, data partition, data reorganization and motion re-planning. The re-planned motions are not unique. A criterion is proposed to evaluate the fitness of each motion and optimize among the candidates.FindingsThe proposed method is implemented in a robotic rope disentangling task. The results show that the robot is able to complete its task while avoiding randomly distributed obstacles and thereby verify the effectiveness of the proposed method. The main contributions of the proposed method are avoiding unforeseen obstacles in the unstructured environment and maintaining crucial aspects of the motion which guarantee to accomplish a skill/task successfully.Originality/valueTraditional methods are intrinsically based on motion planning technique and treat the off-line training data asa prioriprobability. The paper proposes a novel data-driven solution to achieve motion planning for LfD. When the environment changes, the off-line training data are revised according to external constraints and reorganized to generate new motion. Compared to traditional methods, the novel data-driven solution is concise and efficient.
Developing specific involvement strategies within a psychologically informed planned environment: a service evaluation
Authors: Greenacre Karine , Paez Rebecca 
Published: June 2019

PurposeThe purpose of this paper is to apply current understanding of service user involvement (SUI) to forensic practice with reference to the benefits and drawbacks. Specifically, it discusses models of SUI and their application to a psychologically informed planned environment (PIPE) located in a Category C male prison.Design/methodology/approachDrawing upon residents’ experiences, the evaluation reflects on the contribution of cultural, environmental and political factors to the success or failure of SUI within the PIPE service.FindingsThe evaluation will review current systems and explore ways of improving and strengthening strategies by referring to the “whole systems approach” to SUI (Wright, 2006).Originality/valueThe evaluation makes recommendations for local and national SUI within PIPE services.
SEC approves amendments to the NYSE’s substantial stockholder issuance rule and 20 per cent rule for shareholder approval of certain private offerings
Authors: Hoffman Justin , Dworaczyk Jude 
Published: June 2019

Purpose
To explain recent amendments by the US Securities and Exchange Commission (the SEC) to Sections 312.03(b) relating to issuances of securities to substantial stockholders (the Substantial Stockholder Issuance Rule) and 312.03(c) (the 20 Per cent Rule) of the New York Stock Exchange’s (the NYSE) Listed Company Manual to change the definition of “market value” for purposes of the 20 Per cent Rule and eliminate the requirement for shareholder approval of certain private issuances at a price less than book value but greater than market value.

Design/methodology/approach
This article provides background on the purpose and policy behind the Substantial Stockholder Issuance Rule and the 20 Per cent Rule and summarizes the provisions of each rule, both before and after the recent SEC amendments thereto. This article then highlights the most important changes to the Substantial Stockholder Issuance Rule and the 20 Per cent Rule and explains the implications thereof for NYSE-listed issuers.

Findings
The amended Substantial Stockholder Issuance Rule and the 20 Per cent Rule provide NYSE-listed issuers greater flexibility in structuring transactions involving private placements of equity and will likely reduce the number of such transactions requiring a shareholder vote.

Originality/value
Practical guidance from experienced corporate finance and capital markets lawyers.
Mergers in higher education institutions: a proposal of a novel conceptual model
Authors: Sułkowski Łukasz , Fijałkowska Justyna , Dzimińska Małgorzata 
Published: June 2019

PurposeThe macroeconomic changes as well as the challenges facing universities nowadays result in the transfer and adaptation of various concepts and organizational methods from enterprises to universities. One of such solutions is mergers. Even though there are a very large number of practical examples of university mergers in the world, at the same time there is a shortage of frameworks that would help manage mergers. The purpose of this paper is to present key areas of focus in HEIs’ consolidation processes and the creation of the conceptual model of the universities’ mergers.Design/methodology/approachIn this paper synthesis, the inductive approach for model development and case study description were used. The analysis and findings were based on the systematic literature review taken out from management and public policy areas. The new public management and public value governance approaches as well as strategic and process theories of mergers were applied. The descriptive approach to management was used as well.FindingsFormulation of a Conceptual Model of Universities’ Mergers and ten principles of effective management of universities’ mergers that cover the entire process, from planning, through implementation, to integration.Research limitations/implicationsThere is a need to verify the proposed inductive model of universities’ mergers through further qualitative and mixed-methods research studies.Practical implicationsThe paper offers a significant opportunity for practical application of the presented content, because it indicates how the know-how from one (business) sector can be valuable for the future of another sector (the over-fragmented sector of higher education).Originality/valueThis study presents the key areas of focus in HEIs’ consolidation processes and proposes a novel Conceptual Model of Universities’ Mergers. It concludes with the principles of effective management of universities’ mergers.
Diagnostic accuracy of procalcitonin for the early diagnosis of anastomotic leakage after colorectal surgery: a meta‐analysis
Authors: Su'a Bruce , Tutone Senitila , MacFater Wiremu , Barazanchi Ahmed , Xia Weisi , Zeng Irene , Hill Andrew G. 
Published: June 2019

BackgroundAnastomotic leakage (AL) is a dreaded complication following colorectal surgery. Procalcitonin is one of many biomarkers studied and research has suggested that it has improved accuracy for the diagnosis of AL compared with other inflammatory biomarkers such as C‐reactive protein. This meta‐analysis was conducted to evaluate the accuracy of procalcitonin in the early diagnosis of AL following colorectal surgery.MethodsMEDLINE, Embase and PubMed were searched for studies evaluating procalcitonin in the context of AL following colorectal surgery in the elective setting. The literature was reviewed using the Preferred Reporting Items for Systematic Review and Meta‐Analysis (PRISMA) statement. Quality of the studies was assessed using the Quality Assessment Diagnostic Accuracy Studies (QUADAS)‐2 tool. Meta analyses were conducted using area under the receiver operating characteristic curves for day 3, 4 and 5 post‐surgery as a diagnostic test to detect AL.ResultsA total of eight studies were analysed. Results showed that the highest diagnostic accuracy for procalcitonin is on day 5 post surgery. The reported optimal cut‐off values ranged from 0.25 to 680 ng/mL from postoperative day 3 to 5, with reported negative predictive values ranging from 95% to 100%, and positive predictive values of up to 34%. The highest area under the receiver operating characteristic curve was 0.88 on postoperative day 5.ConclusionProcalcitonin is a useful negative test for AL following elective colorectal surgery. However, as an isolated test, it is not useful in detecting AL.
Single‐strain regression analysis evaluating disc potencies of flumequine and enrofloxacin for testing Aeromonas sobria and Vibrio anguillarum
Authors: Kronvall Göran , Baron Sandrine , Larvor Emeline , Rudas–Villarreal Casandra , Hobson Jonathan , Smith Peter 
Published: June 2019

Two quite different disc contents are used for antimicrobial susceptibility testing of two fluoroquinolone drugs, flumequine and enrofloxacin, in the disc diffusion test, 30 and 5 µg, respectively. Using the SRA method, single‐strain regression analysis, we studied the impact of disc content when testing two relevant bacterial species, Aeromonas sobria and Vibrio anguillarum. There were no major differences between the antimicrobial regression lines for the two species. Wild‐type strains produced acceptable zones of inhibition over a wide range of disc contents. The flumequine 30 µg disc should be lowered in its drug content. No rational reasons for choosing so different disc contents for the two antimicrobials were apparent. At present, the choice of disc content for new antimicrobials are outside the realm of clinical microbiologists. It is recommended that reference authorities, such as EUCAST, CLSI and USCAST, are consulted for the choice of disc contents in the future.
Isolation of antibiotic‐resistant gram‐negative organisms from donor respiratory culture does not impact non‐lung solid organ recipient management
Authors: Benamu Esther , Pereira Marcus R. , Taimur Sarah , Jacobs Samantha E. , Friedman Amy L. , Jenkins Stephen G. , Herold Betsy C. , Pellett Madan Rebecca 
Published: June 2019

AbstractBackgroundMultidrug‐resistant (MDR) and extensively drug‐resistant (XDR) gram‐negative bacteria may be transmitted from organ donors to solid organ transplant recipients and are associated with poor outcomes post‐transplant.MethodsWe reported the prevalence of MDR/XDR gram‐negative respiratory colonization among 702 deceased organ donors in the New York City area from 2011 to 2014 and performed chart reviews for a subset of recipients to determine whether donor respiratory culture results were predictive of subsequent recipient infection or used to guide post‐transplant antimicrobial therapy.ResultsFifty donors (7% of the cohort) had MDR or XDR gram‐negative bacteria isolated from endotracheal aspirate or bronchoalveolar lavage culture. Organs from these 50 donors were transplanted into 120 recipients; chart review was performed for 89 of these recipients (38 kidney, 32 liver, 11 heart, 6 kidney/pancreas, 1 liver/kidney, 1 lung). None of the 89 recipients of organs from donors with MDR/XDR gram‐negative respiratory colonization were reported to have a donor‐derived infection post‐transplant, and chart review for the 88 non‐lung recipients indicated that peri‐transplant antibiotics were not adjusted specifically for donor respiratory culture results.ConclusionThese results suggest that donor respiratory culture results are not predictive of post‐transplant infection in non‐lung recipients and are unlikely to impact post‐transplant management.