bluuebunny/crossref_metadata_2025_split huggingface dataset:
Programmable and portable CRISPR-Cas transcriptional activation in bacteria
Authors: Ho Hsing-I , Fang Jennifer , Cheung Jacky , Wang Harris H. 
Published: January 2020

ABSTRACTProgrammable gene activation enables fine-tuned regulation of endogenous and synthetic gene circuits to control cellular behavior. While CRISPR-Cas-mediated gene activation have been extensively developed for eukaryotic systems, similar strategies have been difficult to implement in bacteria. Here, we present a generalizable platform for screening and selection of functional bacterial CRISPR-Cas transcription activators. Using this platform, we identified a novel CRISPR activator, dCas9-AsiA, that could activate gene expression by up to 200-fold across genomic and plasmid targets with diverse promoters after directed evolution. The evolved dCas9-AsiA can simultaneously mediate activation and repression of bacterial regulons inE. coli. We further identified hundreds of promoters with varying basal expression that could be induced by dCas9-AsiA, which provides a rich resource of genetic parts for inducible gene activation. Finally, we show that dCas9-AsiA can be ported to other bacteria of clinical and bioindustrial relevance, thus enabling bacterial CRISPRa in more application areas. This work expands the toolbox for programmable gene regulation in bacteria and provides a useful resource for future engineering of other bacterial CRISPR-based gene regulators.
A suppressor of axillary meristem maturation promotes longevity in flowering plants
Authors: Karami Omid , Rahimi Arezoo , Khan Majid , Bemer Marian , Hazarika Rashmi R. , Mak Patrick , Compier Monique , van Noort Vera , Offringa Remko 
Published: January 2020

AbstractPost embryonic development and growth of flowering plants are for a large part determined by the activity and maturation state of stem cell niches formed in the axils of leaves, the so-called axillary meristems (AMs)1,2. Here we identify a new role for the ArabidopsisAT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED 15(AHL15) gene as a suppressor of AM maturation. Loss ofAHL15function accelerates AM maturation, whereas ectopic expression ofAHL15suppresses AM maturation and promotes longevity in Arabidopsis and tobacco. Together our results indicate thatAHL15expression acts as a key molecular switch, directly downstream of flowering genes (SOC1, FUL) and upstream of GA biosynthesis, in extending the plant’s lifespan by suppressing AM maturation.
The stability flexibility tradeoff and the dark side of detail
Authors: Nassar Matthew R. , Troiani Vanessa 
Published: January 2020

AbstractLearning in dynamic environments requires integrating over stable fluctuations to minimize the impact of noise (stability) but rapidly responding in the face of fundamental changes (flexibility). Achieving one of these goals often requires sacrificing the other to some degree, producing a stability-flexibility tradeoff. Individuals navigate this tradeoff in different ways, with some people learning rapidly (emphasizing flexibility) and others relying more heavily on historical information (emphasizing stability). Despite the prominence of such individual differences in learning tasks, the degree to which they relate to broader characteristics of real-world behavior or pathologies has not been well explored. Here we relate individual differences in learning behavior to self-report measures thought to collectively capture characteristics of the Autism spectrum. We show that that young adults who learn most slowly tend to integrate more effective samples into their beliefs about the world making them more robust to noise (more stability), but are more likely to integrate information from previous contexts (less flexibility). We show that individuals who report paying moreattention to detailtend to use high flexibility and low stability information processing strategies. We demonstrate the robustness of this inverse relationship betweenattention to detailand formation of stable beliefs in a heterogeneous population of children that includes a high proportion of Autism diagnoses. Together, our results highlight thatattention to detailreflects an information processing policy that comes with a substantial downside, namely the ability to integrate data to overcome environmental noise.
A semi-automated machine learning-aided approach to quantitative analysis of centrosomes and microtubule organization
Authors: Sankaran Divya Ganapathi , Hariharan Bharath , Pearson Chad G. 
Published: January 2020

ABSTRACTMicrotubules (MTs) perform important cellular functions including migration, intracellular trafficking, and chromosome segregation. The centrosome, comprised of two centrioles surrounded by the pericentriolar material (PCM), is the cell’s central MT organizing center. The PCM proteins, includingγ-tubulin and Pericentrin, promote MT nucleation and organization. Centrosomes in cancer cells are commonly numerically amplified. However, the question of how amplification of centrosomes alters the MT organization capacity is not well-studied. We developed a quantitative image-processing and machine learning-aided approach for the automated analysis of MT organization. We designed a convolutional neural network-based approach for detecting centrosomes and an automated pipeline for analyzing MT organization around centrosomes, encapsulated in a semi-automatic graphical tool. Using this tool, we analyzed the spatial distribution of PCM proteins, the growing ends of MTs and the total MT density in breast cancer cells. We find that breast cancer cells with supernumerary centrosomes not only have increased PCM protein but also exhibit expansion in PCM size. Moreover, centrosome amplified cells have a greater MT density and more growing MT ends near centrosomes than unamplified cells. The semi-automated approach developed here enables facile, unbiased and quantitative measurements of centrosome aberrations. We show that these aberrations increase MT nucleation and promote changes to MT density and the spatial distribution of MTs around amplified centrosomes.
Neural evidence for recognition of naturalistic videos in monkey hippocampus
Authors: Sakon John J. , Suzuki Wendy A. 
Published: January 2020

AbstractThe role of the hippocampus in recognition memory has long been a source of debate. Tasks used to study recognition that typically require an explicit probe, where the participant must make a response to prove they remember, yield mixed results on hippocampal involvement. Here, we tasked monkeys to freely view naturalistic videos, and only tested their memory via looking times for two separate novel v. repeat video conditions on each trial. Notably, a large proportion of hippocampal neurons differentiated these videos via changes in firing rates time-locked to the duration of their presentation on screen, and not during the delay period between them as would be expected for working memory. Single neurons often contributed to both retrieval conditions, and did so across many trials with trial-unique video content, suggesting they detect familiarity. The majority of neurons contributing to the classifier showed an enhancement in firing rate on repeat compared to novel videos, a pattern which has not previously been shown in hippocampus. These results suggest the hippocampus contributes to recognition memory via familiarity during free-viewing.Significance StatementRecognition memory enables distinction of new from previously encountered stimuli. In the majority of recognition memory work, humans or animals are tasked to explicitly identify whether a stimulus is old or new. In some of these studies—but for unknown reasons not others—there is evidence of hippocampal involvement. Here, when we present trial-unique, naturalistic videos to monkeys, firing rates from many single hippocampal neurons surprisingly differentiate new from repeated videos. The ability of these hippocampal neurons to detect recently-viewed stimuli, despite the videos’ unfamiliar content, suggests they contribute to memory. These results are consistent with hippocampal involvement in the familiarity aspect of recognition memory during free-viewing.
Diagnosing uncertainty, producing neonatal abstinence syndrome
Authors: Chandler Amy , Whittaker Anne , Cunningham‐Burley Sarah , Elliott Lawrie , Midgley Paula , Cooper Sarah 
Published: January 2020

AbstractThe use of alcohol and other drugs during pregnancy is understood to be an important public health problem. One way in which this problem is expressed and responded to is via the identification and treatment of neonatal abstinence syndrome (NAS). In this article, we demonstrate how the processes of anticipating, identifying and responding to NAS are characterised by significant uncertainty among parents and health and social care practitioners. We draw on interviews with 16 parents who had recently had a baby at risk of NAS, and multidisciplinary focus groups with 27 health and social care professionals, held in Scotland, UK. NAS, and drug use in pregnancy, is a fraught and complex arena. Parents in the UK who use opioids risk losing custody of children, and must navigate a high degree of surveillance, governance and marginalisation. We suggest that considering NAS as a social diagnosis, further informed by Mol's political ontology of ‘multiple’ bodies/diseases, may help to produce clinical and social responses to uncertainty which avoid, rather than promote, further marginalisation of parents who use drugs. One such response is to develop a culture of relationship‐based care which empowers both service providers and service users to challenge existing practice and decision‐making.
Knockdown of long noncoding RNA TP73‐AS1 suppresses the malignant progression of breast cancer cells in vitro through targeting miRNA‐125a‐3p/metadherin axis
Authors: Liu Yuxiong , Wei Guangqing , Ma Qian , Han Yanyan 
Published: January 2020

BackgroundTP73 antisense RNA 1 (TP73‐AS1) is a long noncoding RNA which has been shown to be involved in the progression of multiple malignant tumors. Previous studies have demonstrated the oncogenic role of TP73‐AS1 in breast cancer. However, its molecular mechanism remains largely unknown in breast tumorigenesis.MethodsExpression of TP63‐AS1, miRNA‐125a‐3p (miR‐125a) and metadherin (MTDH) was detected by real‐time quantitative PCR and western blotting. The malignancy was evaluated by cell counting kit 8 (CCK‐8), transwell assays, flow cytometry and western blotting. The target binding was confirmed by dual luciferase reporter assay. Xenograft tumor model was performed to detect tumor growth in vivo.ResultsExpression of TP73‐AS1 was higher in breast cancer tissues and cell lines. Biologically, its knockdown could promote cell apoptosis rate, and inhibit proliferative capacity, migration and invasion ability in HCC‐70 and MB231 cells, accompanied with higher cleaved caspase 3 level and lower Ki67, N‐cadherin and Vimentin level. Moreover, TP73‐AS1 downregulation restrained the tumor growth of HCC‐70 cells in vivo. Mechanically, TP73‐AS1 functioned as a molecular “sponge” for miR‐125a to modulate MTDH, a downstream target of miR‐125a. Intriguingly, both miR‐125a overexpression and MTDH silencing exerted a tumor‐suppressive effect in the malignant progression of HCC‐70 and MB231 cells, which was counteracted by TP73‐AS1 upregulation and miR‐125a downregulation, respectively.ConclusionKnockdown of TP73‐AS1 inhibited cell proliferation, migration and invasion, but facilitated apoptosis in breast cancer cells in vitro through targeting miR‐125a and upregulating MTDH, suggesting a novel TP73‐AS1/miR‐125a/MTDH pathway in the malignant progression of breast cancer.
Automated tracheal intubation in an airway manikin using a robotic endoscope: a proof of concept study
Authors: Biro P. , Hofmann P. , Gage D. , Boehler Q. , Chautems C. , Braun J. , Spahn D. R. , Nelson B. J. 
Published: January 2020

SummaryRobotic endoscope‐automated via laryngeal imaging for tracheal intubation (REALITI) has been developed to enable automated tracheal intubation. This proof‐of‐concept study using a convenience sample of participants, comprised of trained anaesthetists and lay participants with no medical training, assessed the performance of a robotic device for the insertion of a tracheal tube into a manikin. A prototype robotic endoscope device was inserted into the trachea of an airway manikin by seven anaesthetists and seven participants with no medical training. Each individual performed six device insertions into the trachea in manual mode and six in automated mode. The anaesthetists succeeded with 40/42 (95%) manual insertions (median (IQR [range]) 17 (12–26 [4–132]) s) and 40/42 (95%) automated insertions (15 (13–18 [7–25]) s). The non‐trained participants succeeded in 41/42 (98%) manual insertions (median (IQR [range]) 18 (13–21 [8–133]) s) and 42/42 (100%) automated insertions (16 (13–23 [10–58])] s). The duration of insertion did not differ between groups. An effect of increasing experience was observed in both groups in manual mode. A Likert scale for ‘ease of use’ (0 = very difficult to 10 = very easy) showed similar results within the two groups; the mean (SD) was 5.9 (2.1) for the anaesthetists and 6.9 (1.3) for the non‐trained participants. We have successfully performed the first automated tracheal device insertion in a manikin with comparable results in a convenience sample of anaesthetists and lay participants with no medical training.
Transfusion rates after 800 Aquablation procedures using various haemostasis methods
Authors: Elterman Dean , Bach Thorsten , Rijo Enrique , Misrai Vincent , Anderson Paul , Zorn Kevin C. , Bhojani Naeem , El Hajj Albert , Chughtai Bilal , Desai Mihir 
Published: January 2020

ObjectiveTo determine if athermal methods are as effective in preventing blood transfusions as the use of cautery across various prostate volumes following prostate tissue resection for benign prostatic hyperplasia using Aquablation. Patients and methodsThe current commercial AQUABEAM robot that performs Aquablation therapy was first used in 2014. Since then numerous clinical studies have been conducted in various countries; Australia, Canada, Germany, India, Lebanon, Spain, New Zealand, United Kingdom, and the United States. All of the clinical trial data since 2014 were pooled with the early commercial procedures from France, Germany, and Spain to determine the effectiveness of haemostatic techniques in reducing the transfusion rate in patients after Aquablation.ResultsIn all, 801 patients were treated with Aquablation therapy from 2014 to early 2019. The mean (SD, range) prostate volume was 67 (33, 20–280) mL and 31 (3.9%) transfusions were reported. The largest contributing factor to transfusion risk was prostate size and method of traction. There was an increasing risk of transfusions in larger prostates when robust traction using a catheter‐tensioning device (CTD) without cautery was used, ranging from 0.8% to 7.8% in prostates ranging from 20 to 280 mL. However, when standard traction (taping the catheter to the leg, gauze knot synched up to the meatus, or no traction at all) was used and where the surgeon performed bladder neck cautery only when necessary, the risk of transfusion was 1.4–2.5% in prostates ranging from 20 to 280 mL.ConclusionsWhile the athermal subgroup with robust traction with a CTD had comparable transfusion rates for smaller prostates, the risk increased significantly as prostate volume increased. With standard traction methods and selective bladder neck cautery, the risk of transfusion was reduced to 1.9% across all prostate sizes.
How green is your packaging—A comparative international study of cues consumers use to recognize environmentally friendly packaging
Authors: Herbes Carsten , Beuthner Christoph , Ramme Iris 
Published: January 2020

AbstractConsumers have grown increasingly aware of the impact of packaging on the environment. Therefore, interest has grown in more environmentally friendly packaging, but we wondered how consumers recognize ‘green’ as distinct from ‘grey’ when evaluating packaging. We asked over 3,000 respondents from Germany, France and the United States how they recognize environmentally friendly packaging. To solicit responses that we may not have anticipated, we used an open‐ended format, which we then followed with a closed‐ended format so that we could compare the two sets of responses. Not surprisingly, in both sets of responses, we found labelling to be the attribute consumers rely upon most, as well as evidence of misleading labels. We also found consumers in Germany and the United States relied on information on the packaging and named searching for information as one of their preferred ways to decide whether packaging is environmentally friendly. French consumers seemed less trusting of published information and more trusting of the look and feel, especially the material, of the package. Our results point to the importance of cultural influences in the acquisition of perceptual cues by the consumer.
Legionella pneumophila occurrence in drinking water supplied by private wells
Authors: Mapili K. , Pieper K. J. , Dai D. , Pruden A. , Edwards M. A. , Tang M. , Rhoads W. J. 
Published: January 2020

Abstract
Unregulated private wells are understudied potential sources of community-acquired Legionnaires’ disease. Here we conducted a comprehensive survey of 44 homes supplied by private wells in Wake County, North Carolina, quantifying Legionella spp. DNA, Legionella pneumophila DNA, and total bacterial 16S rRNA genes via real-time polymerase chain reaction in hot and cold drinking water samples, along with culturable L. pneumophila via IDEXX Legiolert in cold drinking water samples. Legionella spp. DNA, L. pneumophila DNA and culturable L. pneumophila were detected in 100, 65·5 and 15·9% of the 44 homes, respectively, and culturable levels were comparable to some municipal surveys applying the same methods. Total coliforms and Escherichia coli were monitored as representative faecal indicators and were found in 20·4 and 0·0% of homes. Within certain sample types, Legionella spp. and L. pneumophila gene copy numbers were positively associated with total bacteria (i.e. total 16S rRNA genes) and water softener use, but were not associated with faecal indicator bacteria, inorganic water parameters or other well characteristics. These findings confirm that occurrence of Legionella and L. pneumophila is highly variable in private wells.

Significance and Impact of the Study
Legionella is the leading identified cause of waterborne disease outbreaks associated with US municipal water systems. While Legionella is known to occur naturally in groundwater, prior efforts to characterize its occurrence in unregulated private wells are limited to sampling at the wellhead and not in the home plumbing where Legionella can thrive. This work documents much higher levels of Legionella in home plumbing versus water directly from private wells and examines factors associated with higher Legionella occurrence.
Survival advantage of initiating dialysis in elderly and non‐elderly incident end‐stage kidney disease patients
Authors: Ch'ng Chin C. , Ong Loke M. , Beh Kelvin K. M. , Md Yusuf Wan S. , Chew Thian F. , Lee Ming L. , Hooi Lai S. , Wong Hin‐Seng , Shah Firdaus Khan Shahnaz , Ahmad Ghazali 
Published: January 2020

AbstractAimMany patients, especially the elderly, who require renal replacement therapies (RRT) have delayed or rejected dialysis for various reasons. Current dialysis guidelines may not be relevant for the elderly or frail patients. We aim to determine survival advantage of initiating dialysis in patients deemed to require RRT.MethodsThis was an observational cohort on incident end‐stage kidney disease (ESKD) patients from January 1, 2007 to December 31, 2008. The primary outcome was all‐cause mortality. Patients contributed person‐time from the date of ESKD diagnosis until death, transplant or end of study on December 31, 2014, whichever occurred first. An extended Cox regression model with time‐varying exposure to dialysis was used to account for immortal time bias.ResultsOf 3990 incident ESKD patients included, 70.2% patients initiated dialysis; 78.8% with haemodialysis (HD) while the remaining 21.2% with peritoneal dialysis (PD). Dialysis reduced hazard of death in both elderly and non‐elderly patients even after controlling for comorbidities (hazard ratio [HR] 0.58, 95% confidence interval [CI] 0.50, 0.68 and HR 0.76, 95% CI 0.69, 0.85, respectively). HD was protective in both the elderly and non‐elderly (HR 0.53, 95% CI 0.45, 0.63 and HR 0.71, 95% CI 0.64, 0.80, respectively). PD significantly reduced risk of death compared to no dialysis in the elderly but not in the non‐elderly.ConclusionDialysis improved survival in all incident ESKD patients. The findings suggested a larger protection offered by HD. Although improvement in survival from initiating dialysis was large, its true benefit should take overall quality of life into account.SUMMARY AT A GLANCEThis observational study showed that initiation of dialysis improves the survival of end‐stage kidney disease (ESKD) patients of all age groups, but the quality of life is an important aspect that has not been explored.
The plasma‐membrane polyamine transporter PUT3 is regulated by the Na+/H+ antiporter SOS1 and protein kinase SOS2
Authors: Chai Haoxi , Guo Jianfei , Zhong Yingli , Hsu Chuan‐Chih , Zou Changsong , Wang Pengcheng , Zhu Jian‐Kang , Shi Huazhong 
Published: January 2020

Summary

In Arabidopsis, the plasma membrane transporter PUT3 is important to maintain the cellular homeostasis of polyamines and plays a role in stabilizing mRNAs of some heat‐inducible genes. The plasma membrane Na+/H+ transporter SOS1 and the protein kinase SOS2 are two salt‐tolerance determinants crucial for maintaining intracellular Na+ and K+ homeostasis.
Here, we report that PUT3 genetically and physically interacts with SOS1 and SOS2, and these interactions modulate PUT3 transport activity.
Overexpression of PUT3 (PUT3OE) results in hypersensitivity of the transgenic plants to polyamine and paraquat. The hypersensitivity of PUT3OE is inhibited by the sos1 and sos2 mutations, which indicates that SOS1 and SOS2 are required for PUT3 transport activity. A protein interaction assay revealed that PUT3 physically interacts with SOS1 and SOS2 in yeast and plant cells. SOS2 phosphorylates PUT3 both in vitro and in vivo. SOS1 and SOS2 synergistically activate the polyamine transport activity of PUT3, and PUT3 also modulates SOS1 activity by activating SOS2 in yeast cells.
Overall, our findings suggest that both plasma‐membrane proteins PUT3 and SOS1 could form a complex with the protein kinase SOS2 in response to stress conditions and modulate the transport activity of each other through protein interactions and phosphorylation.
Apparent Complete Response of a Treatment Refractory and Recurrent Squamous Cell Carcinoma Lesion to Photochemical Internalization: A Clinical Case Study
Authors: Jerjes Waseem , Hamdoon Zaid , Berg Kristian , Høgset Anders , Hopper Colin 
Published: January 2020

AbstractPhotochemical internalization (PCI) depends on the delivery of sublethal photodynamic reaction to facilitate the work of a chemotherapeutic agent. We discuss our experience in managing a patient with extensive squamous cell carcinoma of the right face and scalp under the TPCS2a‐based bleomycin PCI treatment protocol. In this case, an 84‐year‐old Caucasian received 0.25 mg kg−1 of TPCS2a (Amphinex®, PCI Biotech AS, Oslo, Norway). Surface illumination photochemical internalization was carried out after 4 days, which was preceded by the chemotherapeutic agent infusion (Bleomycin). After one week from the illumination time, tissue necrosis was evident and tumor shrinkage was most noticeable at day 14 postillumination. Follow‐up at 6 weeks continued to show tissue healing and regeneration with no clinical evidence of recurrence. Multiple surgical biopsies were taken at 1 and 3 months postillumination and found to be tumor free. PCI’s depth of effect has been very significant with negligible damage to the collateral tissues. This technology has a role in interventional oncology especially when managing challenging cases.