bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of gross genome rearrangements in Deinococcus radiodurans recA mutants
Authors: Repar Jelena , Zahradka Davor , Sović Ivan , Zahradka Ksenija
Published: May 2021

Genome stability in radioresistant bacterium Deinococcus radiodurans depends on RecA, the main bacterial recombinase. Without RecA, gross genome rearrangements occur during repair of DNA double-strand breaks. Long repeated (insertion) sequences have been identified as hot spots for ectopic recombination leading to genome rearrangements, and single-strand annealing (SSA) postulated to be the most likely mechanism involved in this process. Here, we have sequenced five isolates of D. radiodurans recA mutant carrying gross genome rearrangements to precisely characterize the rearrangements and to elucidate the underlying repair mechanism. The detected rearrangements consisted of large deletions in chromosome II in all the sequenced recA isolates. The mechanism behind these deletions clearly differs from the classical SSA; it utilized short (4–11 bp) repeats as opposed to insertion sequences or other long repeats. Moreover, it worked over larger linear DNA distances from those previously tested. Our data are most compatible with alternative end-joining, a recombination mechanism that operates in eukaryotes, but is also found in Escherichia coli. Additionally, despite the recA isolates being preselected for different rearrangement patterns, all identified deletions were found to overlap in a 35 kb genomic region. We weigh the evidence for mechanistic vs. adaptive reasons for this phenomenon.
Beauvericin potentiates the activity of pesticides by neutralizing the ATP-binding cassette transporters in arthropods
Authors: Al Khoury Charbel , Nemer Nabil , Nemer Georges
Published: May 2021

Multi-drug resistance is posing major challenges in suppressing the population of pests. Many herbivores develop resistance, causing a prolonged survival after exposure to a previously effective pesticide. Consequently, resistant pests reduce the yield of agricultural production, causing significant economic losses and reducing food security. Therefore, overpowering resistance acquisition of crop pests is a must. The ATP binding cassette transporters (ABC transporters) are considered as the main participants to the pesticide efflux and their neutralization will greatly contribute to potentiate failed treatments. Real-Time PCR analysis of 19 ABC transporter genes belonging to the ABCB, ABCC, ABCG, and ABCH revealed that a broad range of efflux pumps is activated in response to the exposure to pesticides. In this study, we used beauvericin (BEA), a known ABC transporters modulator, to resensitize different strains of Tetranychus urticae after artificial selection for resistance to cyflumetofen, bifenazate, and abamectin. Our results showed that the combinatorial treatment of pesticide (manufacturer’s recommended doses) + BEA (sublethal doses: 0.15 mg/L) significantly suppressed the resistant populations of T. urticae when compared to single-drug treatments. Moreover, after selective pressure for 40 generations, the LC50 values were significantly reduced from 36.5, 44.7, and 94.5 (pesticide) to 8.3, 12.5, and 23.4 (pesticide + BEA) for cyflumetofen, bifenazate, and abamectin, respectively. While the downstream targets for BEA are still elusive, we demonstrated hereby that it synergizes with sub-lethal doses of different pesticides and increases their effect by inhibiting ABC transporters. This is the first report to document such combinatorial activity of BEA against higher invertebrates paving the way for its usage in treating refractory cases of resistance to pesticides. Moreover, we demonstrated, for the first time, using in silico techniques, the higher affinity of BEA to ABC transformers subfamilies when compared to xenobiotics; thus, elucidating the pathway of the mycotoxin.
Biological autoluminescence for assessing oxidative processes in yeast cell cultures
Authors: Vahalová Petra , Červinková Kateřina , Cifra Michal
Published: May 2021

Nowadays, modern medicine is looking for new, more gentle, and more efficient diagnostic methods. A pathological state of an organism is often closely connected with increased amount of reactive oxygen species. They can react with biomolecules and subsequent reactions can lead to very low endogenous light emission (biological autoluminescence—BAL). This phenomenon can be potentially used as a non-invasive and low-operational-cost tool for monitoring oxidative stress during diseases. To contribute to the understanding of the parameters affecting BAL, we analyzed the BAL from yeast Saccharomyces cerevisiae as a representative eukaryotic organism. The relationship between the BAL intensity and the amount of reactive oxygen species that originates as a result of the Fenton reaction as well as correlation between spontaneous BAL and selected physical and chemical parameters (pH, oxygen partial pressure, and cell concentration) during cell growth were established. Our results contribute to real-time non-invasive methodologies for monitoring oxidative processes in biomedicine and biotechnology.
Preverbal infants expect agents exhibiting counterintuitive capacities to gain access to contested resources
Authors: Meng Xianwei , Nakawake Yo , Hashiya Kazuhide , Burdett Emily , Jong Jonathan , Whitehouse Harvey
Published: May 2021

Claims to supernatural power have been used as a basis for authority in a wide range of societies, but little is known about developmental origins of the link between supernatural power and worldly authority. Here, we show that 12- to 16-month-old infants expect agents exhibiting counterintuitive capacities to win out in a two-way standoff over a contested resource. Infants watched two agents gain a reward using either physically intuitive or physically counterintuitive methods, the latter involving simple forms of levitation or teleportation. Infants looked longer, indicating surprise, when the physically intuitive agent subsequently outcompeted a physically counterintuitive agent in securing a reward. Control experiments indicated that infants’ expectations were not simply motived by the efficiency of agents in pursuing their goals, but specifically the deployment of counterintuitive capacities. This suggests that the link between supernatural power and worldly authority has early origins in development.
Variable coastal hypoxia exposure and drivers across the southern California Current
Authors: Low Natalie H. N. , Micheli Fiorenza , Aguilar Juan Domingo , Arce Daniel Romero , Boch Charles A. , Bonilla Juan Carlos , Bracamontes Miguel Ángel , De Leo Giulio , Diaz Eduardo , Enríquez Eduardo , Hernandez Arturo , Martinez Ramón , Mendoza Ramon , Miranda Claudia , Monismith Stephen , Ramade Mario , Rogers-Bennett Laura , Romero Alfonso , Salinas Carmina , Smith Alexandra E. , Torre Jorge , Villavicencio Gustavo , Woodson C. Brock
Published: May 2021

Declining oxygen is one of the most drastic changes in the ocean, and this trend is expected to worsen under future climate change scenarios. Spatial variability in dissolved oxygen dynamics and hypoxia exposures can drive differences in vulnerabilities of coastal ecosystems and resources, but documentation of variability at regional scales is rare in open-coast systems. Using a regional collaborative network of dissolved oxygen and temperature sensors maintained by scientists and fishing cooperatives from California, USA, and Baja California, Mexico, we characterize spatial and temporal variability in dissolved oxygen and seawater temperature dynamics in kelp forest ecosystems across 13° of latitude in the productive California Current upwelling system. We find distinct latitudinal patterns of hypoxia exposure and evidence for upwelling and respiration as regional drivers of oxygen dynamics, as well as more localized effects. This regional and small-scale spatial variability in dissolved oxygen dynamics supports the use of adaptive management at local scales, and highlights the value of collaborative, large-scale coastal monitoring networks for informing effective adaptation strategies for coastal communities and fisheries in a changing climate.
Effects of occipital-atlas stabilization in the upper cervical spine kinematics: an in vitro study
Authors: Hidalgo-García César , Lorente Ana I. , López-de-Celis Carlos , Lucha-López Orosia , Malo-Urriés Miguel , Rodríguez-Sanz Jacobo , Maza-Frechín Mario , Tricás-Moreno José Miguel , Krauss John , Pérez-Bellmunt Albert
Published: May 2021

This study compares upper cervical spine range of motion (ROM) in the three cardinal planes before and after occiput-atlas (C0–C1) stabilization. After the dissection of the superficial structures to the alar ligament and the fixation of C2, ten cryopreserved upper cervical columns were manually mobilized in the three cardinal planes of movement without and with a screw stabilization of C0–C1. Upper cervical ROM and mobilization force were measured using the Vicon motion capture system and a load cell respectively. The ROM without C0–C1 stabilization was 19.8° ± 5.2° in flexion and 14.3° ± 7.7° in extension. With stabilization, the ROM was 11.5° ± 4.3° and 6.6° ± 3.5°, respectively. The ROM without C0–C1 stabilization was 4.7° ± 2.3° in right lateral flexion and 5.6° ± 3.2° in left lateral flexion. With stabilization, the ROM was 2.3° ± 1.4° and 2.3° ± 1.2°, respectively. The ROM without C0–C1 stabilization was 33.9° ± 6.7° in right rotation and 28.0° ± 6.9° in left rotation. With stabilization, the ROM was 28.5° ± 7.0° and 23.7° ± 8.5° respectively. Stabilization of C0–C1 reduced the upper cervical ROM by 46.9% in the sagittal plane, 55.3% in the frontal plane, and 15.6% in the transverse plane. Also, the resistance to movement during upper cervical mobilization increased following C0–C1 stabilization.
Recommendation for management of patients with their first episode of primary spontaneous pneumothorax, using video-assisted thoracoscopic surgery or conservative treatment
Authors: Chiu Hsin-Yi , Ho Yi-Chia , Yang Pei-Chen , Chiang Chi-Ming , Chung Cheng-Chin , Wu Wei-Ciao , Lin Yu-Cih , Chen Chien-Yu , Wu Yu-Chung
Published: May 2021

International guidelines do not recommend surgery for the first episode of primary spontaneous pneumothorax (PSP), except in cases of persistent air leak, hemopneumothorax, bilateral pneumothorax, or occupations at risk. However, these recommendations have been challenged because of a significant reduction in the recurrence rate in emerging studies. We evaluated the rationale of recommendations by systematically reviewing RCTs and observational studies by using the Grading of Recommendations, Assessment, Development, and Evaluations (GRADE) system. We searched articles in PubMed, EMBASE, and Cochrane databases up to August 15, 2020. The primary outcomes were the recurrence rate and complication rate. The secondary outcomes were hospital stay and drainage duration. Nine eligible studies with 1121 patients were retrieved and analyzed. The recurrence rate was lower in the VATS than in conservative treatment with moderate evidence (OR 0.13, 95% CI 0.09 to 0.19, P < 0.001, I2 = 0%). We did not find significant differences in complication rate (Peto OR 1.17, 95% CI 0.33 to 4.12, P = 0.80), hospital stay duration (MD − 0.48 days, 95% CI − 2.84 to 1.87, P = 0.69, very low evidence), and in drainage duration (MD − 3.99 days, 95% CI − 9.06 to 1.08, P = 0.12, very low evidence) between the two groups. Our results would suggest VATS treatment as a weak recommendation for patients with the first episode of PSP, based on our systematic review of the current evidence by using the GRADE system, indicating that different treatments will be appropriate for different patients and that patients’ values and preferences should be incorporated through shared decision making.

Trial REGISTRY: PROSPERO; No.: CRD42020162267.
Modeling cometabolism of hexavalent chromium by iron reducing bacteria in tertiary substrate system
Authors: Upadhyay Shivangi , Sinha Alok
Published: May 2021

In this study, a bacterial strain Serratia sp. was employed for the reduction of synthetically prepared different concentration of Cr(VI) solution (10, 25, 40, 50 and 100 mg/L). Cometabolism study have been carried out in the binary substrate system as well as in the tertiary substrate system. The results revealed that when glucose was added as a co-substrate, at low Cr(VI) concentration, complete reduction was achieved followed by increased biomass growth, but when Cr(VI) concentration was increased to 100 mg/L, the reduction decline to 93%. But in presence of high carbon iron filings (HCIF) as co-substrate even at higher Cr(VI) concentration i.e. 100 mg/L, 100% reduction was achieved and the cell growth continued till 124 h. The study was illustrated via Monod growth kinetic model for tertiary substrate system and the kinetic parameters revealed that the HCIF and glucose combination showed least inhibition to hexavalent chromium reduction by Serratia sp.
Changing friction at the base of an Alpine glacier
Authors: Gräff Dominik , Walter Fabian
Published: May 2021

Repeating earthquakes are a global phenomenon of tectonic faults. Multiple ruptures on the same fault asperities lead to nearly identical waveforms characteristic for these seismic events. We identify their microseismic counterparts beneath an Alpine glacier, where basal sliding accounts for a significant amount of ice flow. In contrast to tectonic faults, Alpine glacier beds are subject to large variations in sliding velocity and effective normal stresses. This leads to inter- and sub-seasonal variations in released seismic moment from stick–slip asperities, which we explain with the rate-and-state friction formalism. During summer, numerically modelled effective normal stresses at asperities are three times higher than in winter, which increases the local shear resistance by the same factor. Stronger summer asperities therefore tend to form in bed regions well connected to the efficient subglacial drainage system. Moreover, asperities organise themselves into a state of subcriticality, transferring stresses between each other. We argue that this seismic stick–slip behavior has potentially far-reaching consequences for glacier sliding and in particular for catastrophic failure of unstable ice masses.
Establishment of open-source semi-automated behavioral analysis system and quantification of the difference of sexual motivation between laboratory and wild strains
Authors: Tomihara Soma , Oka Yoshitaka , Kanda Shinji
Published: May 2021

Behavioral analysis plays an important role in wide variety of biological studies, but behavioral recordings often tend to be laborious and are associated with inevitable human-errors. It also takes much time to perform manual behavioral analyses while replaying the videos. On the other hand, presently available automated recording/analysis systems are often specialized for certain types of behavior of specific animals. Here, we established an open-source behavioral recording system using Raspberry Pi, which automatically performs video-recording and systematic file-sorting, and the behavioral recording can be performed more efficiently, without unintentional human operational errors. We also developed an Excel macro that enables us to easily perform behavioral annotation with simple manipulation. Thus, we succeeded in developing an analysis suite that mitigates human tasks and thus reduces human errors. By using this suite, we analyzed the sexual behavior of a laboratory and a wild medaka strain and found a difference in sexual motivation presumably resulting from domestication.
A case–control study investigating food addiction in Parkinson patients
Authors: de Chazeron Ingrid , Durif F. , Lambert C. , Chereau-Boudet I. , Fantini M. L. , Marques A. , Derost P. , Debilly B. , Brousse G. , Boirie Y. , Llorca P. M.
Published: May 2021

Eating disorders (EDs) in patients with Parkinson’s disease (PD) are mainly described through impulse control disorders but represent one end of the spectrum of food addiction (FA). Although not formally recognized by DSM-5, FA is well described in the literature on animal models and humans, but data on prevalence and risk factors compared with healthy controls (HCs) are lacking. We conducted a cross-sectional study including 200 patients with PD and 200 age- and gender-matched HCs. Characteristics including clinical data (features of PD/current medication) were collected. FA was rated using DSM-5 criteria and the Questionnaire on Eating and Weight Patterns-Revised (QEWP-R). Patients with PD had more EDs compared to HCs (27.0% vs. 13.0%, respectively, p < 0.001). They mainly had FA (24.5% vs. 12.0%, p = 0.001) and night eating syndrome (7.0% vs. 2.5% p = 0.03). In PD patients, FA was associated with female gender (p = 0.04) and impulsivity (higher attentional non-planning factor) but not with the dose or class of dopaminergic therapy. Vigilance is necessary, especially for PD women and in patients with specific impulsive personality traits. Counterintuitively, agonist dopaminergic treatment should not be used as an indication for screening FA in patients with PD.
A reliable set of reference genes to normalize oxygen-dependent cytoglobin gene expression levels in melanoma
Authors: De Backer Joey , Maric Darko , Bosman Matthias , Dewilde Sylvia , Hoogewijs David
Published: May 2021

Cytoglobin (CYGB) is a ubiquitously expressed protein with a protective role against oxidative stress, fibrosis and tumor growth, shown to be transcriptionally regulated under hypoxic conditions. Hypoxia-inducible CYGB expression is observed in several cancer cell lines and particularly in various melanoma-derived cell lines. However, reliable detection of hypoxia-inducible mRNA levels by qPCR depends on the critical choice of suitable reference genes for accurate normalization. Limited evidence exists to support selection of the commonly used reference genes in hypoxic models of melanoma. This study aimed to select the optimal reference genes to study CYGB expression levels in melanoma cell lines exposed to hypoxic conditions (0.2% O2) and to the HIF prolyl hydroxylase inhibitor roxadustat (FG-4592). The expression levels of candidate genes were assessed by qPCR and the stability of genes was evaluated using the geNorm and NormFinder algorithms. Our results display that B2M and YWHAZ represent the most optimal reference genes to reliably quantify hypoxia-inducible CYGB expression in melanoma cell lines. We further validate hypoxia-inducible CYGB expression on protein level and by using CYGB promoter-driven luciferase reporter assays in melanoma cell lines.
Positive Epstein–Barr virus detection in coronavirus disease 2019 (COVID-19) patients
Authors: Chen Ting , Song Jiayi , Liu Hongli , Zheng Hongmei , Chen Changzheng
Published: May 2021

The objective of this study was to detect the Epstein–Barr virus (EBV) coinfection in coronavirus disease 2019 (COVID-19). In this retrospective single-center study, we included 67 COVID-19 patients with onset time within 2 weeks in Renmin Hospital of Wuhan University from January 9 to February 29, 2020. Patients were divided into EBV/SARS-CoV-2 coinfection group and SARS-CoV-2 infection alone group according to the serological results of EBV, and the characteristics differences between the two groups were compared. The median age was 37 years, with 35 (52.2%) females. Among these COVID-19 patients, thirty-seven (55.2%) patients were seropositive for EBV viral capsid antigen (VCA) IgM antibody. EBV/SARS-CoV-2 coinfection patients had a 3.09-fold risk of having a fever symptom than SARS-CoV-2 infection alone patients (95% CI 1.11–8.56; P = 0.03). C-reactive protein (CRP) (P = 0.02) and the aspartate aminotransferase (AST) (P = 0.04) in EBV/SARS-CoV-2 coinfection patients were higher than that in SARS-CoV-2 infection alone patients. EBV/SARS-CoV-2 coinfection patients had a higher portion of corticosteroid use than the SARS-CoV-2 infection alone patients (P = 0.03). We find a high incidence of EBV coinfection in COVID-19 patients. EBV/SARS-CoV-2 coinfection was associated with fever and increased inflammation. EBV reactivation may associated with the severity of COVID-19.
The association between hepatitis C virus infection and renal cell cancer, prostate cancer, and bladder cancer: a systematic review and meta-analysis
Authors: Ma Yucheng , Huang Zhongli , Jian Zhongyu , Wei Xin
Published: May 2021

To update the current evidence on whether hepatitis C virus (HCV) infection represents a possible risk factor for renal cell cancer (RCC), prostate cancer (PCa), and bladder cancer (BC). We searched the literature on Pubmed, Web of Science, and Embases before April 2021. A systematic review and meta-analysis were performed. Finally, we extracted 12 studies based on the eligible criteria. Across 11 studies for HCV and RCC, the incorporated RR was 1.28 (95% CI 1.05–1.55), which meant that participants with HCV infection were associated with higher RCC risk. The pooled RR in hazard ratio (HR) subgroup (HR 1.59, 95% CI 1.22–2.08), cohort studies subgroup (RR 1.47, 95% CI 1.18–1.82), and North America subgroup (RR 1.71, 95% CI 1.40–2.09) detected a stronger association between HCV and RCC risk. Although an inverse association was seen for PCa (RR 0.75, 95% CI 0.54–1.03) across seven studies, it was not statistically significant (P = 0.075). There was no significant association between HCV and BC with an incorporated RR of 0.92 (95% CI, 0.82–1.03) across five studies. Our study demonstrated that HCV infection was significantly associated with increased RCC risk. There appeared to be an inverse association for HCV in PCa risk but not statistically significant. No significant association was found between HCV and BC risk. Prospective, large-scale, and well-designed cohort studies are required to validate the association between HCV and RCC, and to investigate the role of HCV on PCa.
The dynamics of evolutionary rescue from a novel pathogen threat in a host metapopulation
Authors: Jiao Jing , Fefferman Nina
Published: May 2021

When a novel disease strikes a naïve host population, there is evidence that the most immediate response can involve host evolution while the pathogen remains relatively unchanged. When hosts also live in metapopulations, there may be critical differences in the dynamics that emerge from the synergy among evolutionary, ecological, and epidemiological factors. Here we used a Susceptible-Infected-Recovery model to explore how spatial and temporal ecological factors may drive the epidemiological and rapid-evolutionary dynamics of host metapopulations. For simplicity, we assumed two host genotypes: wild type, which has a positive intrinsic growth rate in the absence of disease, and robust type, which is less likely to catch the infection given exposure but has a lower intrinsic growth rate in the absence of infection. We found that the robust-type host would be strongly selected for in the presence of disease when transmission differences between the two types is large. The growth rate of the wild type had dual but opposite effects on host composition: a smaller increase in wild-type growth increased wild-type competition and lead to periodical disease outbreaks over the first generations after pathogen introduction, while larger growth increased disease by providing more susceptibles, which increased robust host density but decreased periodical outbreaks. Increased migration had a similar impact as the increased differential susceptibility, both of which led to an increase in robust hosts and a decrease in periodical outbreaks. Our study provided a comprehensive understanding of the combined effects among migration, disease epidemiology, and host demography on host evolution with an unchanging pathogen. The findings have important implications for wildlife conservation and zoonotic disease control.
Extracting neuronal activity signals from microscopy recordings of contractile tissue using B-spline Explicit Active Surfaces (BEAS) cell tracking
Authors: Kazwiny Youcef , Pedrosa João , Zhang Zhiqing , Boesmans Werend , D’hooge Jan , Vanden Berghe Pieter
Published: May 2021

Ca2+ imaging is a widely used microscopy technique to simultaneously study cellular activity in multiple cells. The desired information consists of cell-specific time series of pixel intensity values, in which the fluorescence intensity represents cellular activity. For static scenes, cellular signal extraction is straightforward, however multiple analysis challenges are present in recordings of contractile tissues, like those of the enteric nervous system (ENS). This layer of critical neurons, embedded within the muscle layers of the gut wall, shows optical overlap between neighboring neurons, intensity changes due to cell activity, and constant movement. These challenges reduce the applicability of classical segmentation techniques and traditional stack alignment and regions-of-interest (ROIs) selection workflows. Therefore, a signal extraction method capable of dealing with moving cells and is insensitive to large intensity changes in consecutive frames is needed. Here we propose a b-spline active contour method to delineate and track neuronal cell bodies based on local and global energy terms. We develop both a single as well as a double-contour approach. The latter takes advantage of the appearance of GCaMP expressing cells, and tracks the nucleus’ boundaries together with the cytoplasmic contour, providing a stable delineation of neighboring, overlapping cells despite movement and intensity changes. The tracked contours can also serve as landmarks to relocate additional and manually-selected ROIs. This improves the total yield of efficacious cell tracking and allows signal extraction from other cell compartments like neuronal processes. Compared to manual delineation and other segmentation methods, the proposed method can track cells during large tissue deformations and high-intensity changes such as during neuronal firing events, while preserving the shape of the extracted Ca2+ signal. The analysis package represents a significant improvement to available Ca2+ imaging analysis workflows for ENS recordings and other systems where movement challenges traditional Ca2+ signal extraction workflows.
Single channel properties of mitochondrial large conductance potassium channel formed by BK-VEDEC splice variant
Authors: Gałecka Shur , Kulawiak Bogusz , Bednarczyk Piotr , Singh Harpreet , Szewczyk Adam
Published: May 2021

The activation of mitochondrial large conductance calcium-activated potassium (mitoBKCa) channels increases cell survival during ischemia/reperfusion injury of cardiac cells. The basic biophysical and pharmacological properties of mitoBKCacorrespond to the properties of the BKCachannels from the plasma membrane. It has been suggested that the VEDEC splice variant of theKCNMA1gene product encoding plasma membrane BKCais targeted toward mitochondria. However there has been no direct evidence that this protein forms a functional channel in mitochondria. In our study, we used HEK293T cells to express the VEDEC splice variant and observed channel activity in mitochondria using the mitoplast patch-clamp technique. For the first time, we found that transient expression with the VEDEC isoform resulted in channel activity with the conductance of 290 ± 3 pS. The channel was voltage-dependent and activated by calcium ions. Moreover, the activity of the channel was stimulated by the potassium channel opener NS11021 and inhibited by hemin and paxilline, which are known BKCachannel blockers. Immunofluorescence experiments confirmed the partial colocalization of the channel within the mitochondria. From these results, we conclude that the VEDEC isoform of the BKCachannel forms a functional channel in the inner mitochondrial membrane. Additionally, our data show that HEK293T cells are a promising experimental model for expression and electrophysiological studies of mitochondrial potassium channels.
IMP3 protein is an independent prognostic factor of clinical stage II rectal cancer
Authors: Bevanda Glibo Daniela , Bevanda Danijel , Vukojević Katarina , Tomić Snježana
Published: May 2021

Immunohistochemical level of IMP3-protein in patients with rectal cancer in clinical stage II (141), were correlated with sociodemographic, pathohistological and clinical indicators and duration of overall-survival and progression-free-survival. Vascular invasion was associated with IMP3-positive immunostaining (p < 0.001). Vascular invasion ratio in the group of poorly-differentiated-tumors was 21 times higher than in the group of well-differentiated-tumors. IMP3-positive patients lived 2.2 times shorter than negative (p < 0.001). Patients with well-differentiated-tumors lived 1.7 times longer than the subjects with poorly-differentiated-tumors (p < 0.001). Patients without vascular invasion lived 2.7 times longer than the subjects with vascular invasion (p < 0.001). The risk of mortality was 2.3 times higher for IMP3 positive patients (p = 0.027) and 10.4 higher for the patients with vascular invasion (p < 0.001). IMP3-negative participants had 2.3 times longer free interval without disease (p < 0.001). The free interval without disease was 3.6 times longer in the group without vascular invasion (p < 0.001). The risk of disease relapse in the IMP3 positive group was 5.3 times higher (p < 0.001) and with vascular invasion was 8 times longer (p < 0.001). The risk of disease relapse was 6.8 times higher in the group with vascular invasion (p < 0.001). Patients with rectal cancer and high IMP3-protein level will have a shorter overall survival relative to patients without or with low levels of IMP3. The analysis of IMP3 expression by immunohistochemistry pointed IMP3 as an independent prognostic factor of clinical stage II rectal cancer.
Multi Locus View: an extensible web-based tool for the analysis of genomic data.
Authors: Sergeant Martin J. , Hughes Jim R. , Hentges Lance , Lunter Gerton , Downes Damien J. , Taylor Stephen
Published: May 2021

Tracking and understanding data quality, analysis and reproducibility are critical concerns in the biological sciences. This is especially true in genomics where next generation sequencing (NGS) based technologies such as ChIP-seq, RNA-seq and ATAC-seq are generating a flood of genome-scale data. However, such data are usually processed with automated tools and pipelines, generating tabular outputs and static visualisations. Interpretation is normally made at a high level without the ability to visualise the underlying data in detail. Conventional genome browsers are limited to browsing single locations and do not allow for interactions with the dataset as a whole. Multi Locus View (MLV), a web-based tool, has been developed to allow users to fluidly interact with genomics datasets at multiple scales. The user is able to browse the raw data, cluster, and combine the data with other analysis and annotate the data. User datasets can then be shared with other users or made public for quick assessment from the academic community. MLV is publically available athttps://mlv.molbiol.ox.ac.uk.
A combined approach for single-cell mRNA and intracellular protein expression analysis
Authors: Reimegård Johan , Tarbier Marcel , Danielsson Marcus , Schuster Jens , Baskaran Sathishkumar , Panagiotou Styliani , Dahl Niklas , Friedländer Marc R. , Gallant Caroline J.
Published: May 2021

Combined measurements of mRNA and protein expression in single cells enable in-depth analysis of cellular states. We present SPARC, an approach that combines single-cell RNA-sequencing with proximity extension essays to simultaneously measure global mRNA and 89 intracellular proteins in individual cells. We show that mRNA expression fails to accurately reflect protein abundance at the time of measurement, although the direction of changes is in agreement during neuronal differentiation. Moreover, protein levels of transcription factors better predict their downstream effects than do their corresponding transcripts. Finally, we highlight that protein expression variation is overall lower than mRNA variation, but relative protein variation does not reflect the mRNA level. Our results demonstrate that mRNA and protein measurements in single cells provide different and complementary information regarding cell states. SPARC presents a state-of-the-art co-profiling method that overcomes current limitations in throughput and protein localization, including removing the need for cell fixation.
Microscale tracking of coral-vibrio interactions
Authors: Gavish Assaf R , Shapiro Orr H , Kramarsky-Winter Esti , Vardi Assaf
Published: May 2021

To improve our understanding of coral infection and disease, it is important to study host-pathogen interactions at relevant spatio-temporal scales. Here, we provide a dynamic microscopic view of the interaction between a coral pathogen, Vibrio coralliilyticus and its coral host Pocillopora damicornis. This was achieved using a microfluidics-based system facilitating control over flow, light and temperature conditions. Combined with time-resolved biochemical and microbial analyses of the system exudates, this approach provides novel insights into the early phases of a coral infection at unprecedented spatio-temporal resolution. We provide evidence that infection may occur through ingestion of the pathogen by the coral polyps, or following pathogen colonization of small tissue lesions on the coral surface. Pathogen ingestion invariably induced the release of pathogen-laden mucus from the gastrovascular cavity. Despite the high bacterial load used in our experiments, approximately one-third of coral fragments tested did not develop further symptoms. In the remaining two-thirds, mucus spewing was followed by the severing of calicoblastic connective tissues (coenosarc) and subsequently necrosis of most polyps. Despite extensive damage to symptomatic colonies, we frequently observed survival of individual polyps, often accompanied by polyp bail-out. Biochemical and microbial analyses of exudates over the course of symptomatic infections revealed that severing of the coenosarc was followed by an increase in matrix metaloprotease activity, and subsequent increase in both pathogen and total bacterial counts. Combined, these observations provide a detailed description of a coral infection, bringing us a step closer to elucidating the complex interactions underlying coral disease.
Development of a numerical simulation method for modelling column breakthrough from extraction chromatography resins
Authors: Burrell Frances M. , Warwick Phillip E. , Croudace Ian W. , Walters W. Stephen
Published: May 2021

A numerical simulation method was developed in LabVIEW using rate constants derived from batch experiments. The successful application to chromatographic breakthrough demonstrates potential for integration with automated radioanalytical systems.
Natural biomaterial sarcosine as an interfacial layer enables inverted organic solar cells to exhibit over 16.4% efficiency
Authors: Liu Mei , Xu Yujie , Gao Zhicheng , Zhang Chao , Yu Jing , Wang Jian , Ma Xiaoling , Hu Haixia , Yin Hang , Zhang Fujun , Man Baoyuan , Sun Qianqian
Published: May 2021

The natural biomaterial sarcosine from animal muscle as an electron transport layer (ETL) was successfully introduced into inverted organic solar cells (OSCs).
Can a field molecular diagnosis be accurate? A performance evaluation of colorimetric RT-LAMP for the detection of SARS-CoV-2 in a hospital setting
Authors: Silva Lívia do Carmo , dos Santos Carlos Abelardo , Mendes Geovana de Melo , Oliveira Kézia Gomes de , de Souza Júnior Marcio Neres , Estrela Paulo Felipe Neves , Costa Sérgio Henrique Nascente , Silveira-Lacerda Elisângela de Paula , Duarte Gabriela Rodrigues Mendes
Published: May 2021

We developed a molecular test for the detection of SARS-CoV-2 directly from swab samples. The test is based on colorimetric RT-LAMP, with results comparable to the gold standard method (RT -qPCR), performed in a hospital and laboratory environment.
Tuning the shape and crystal phase of TiO2 nanoparticles for catalysis
Authors: Zhao Wenning , Li Yong , Shen Wenjie
Published: May 2021

The shape and crystal phase of TiO2 alter the surface atomic arrangements and further mediate its interaction with metal species.
A modular olefination reaction between aldehydes and diborylsilylmethide lithium salts
Authors: Salvado Oriol , Fernández Elena
Published: May 2021

Preparation of densely functionalised 1,1-silylborylated trisubstituted alkenes, between LiC(Bpin)2(SiMe3) and aliphatic or aromatic aldehydes,viaa boron-Wittig reaction.
First-principles microkinetic simulations revealing the scaling relations and structure sensitivity of CO2hydrogenation to C1& C2oxygenates on Pd surfaces
Authors: Ke Jun , Wang Yang-Dong , Wang Chuan-Ming
Published: May 2021

CO2hydrogenation to alcohols and other oxygenates on Pd(211) and Pd(111) surfaces was studied by microkinetic modelling. Energy scaling relations on two surfaces were established. Activity plots as a function of reaction conditions were identified.
Tribological properties of a series of carbon dots modified by ionic liquids with various anion species: experimental findings and density functional theory calculations
Authors: Wang Baogang , Zhang Lilong , Wang Na , Duan Wenmeng , Tang Weiwei
Published: May 2021

The tribological performance of a series of carbon dots modified by ionic liquids with various anion species as lubricant additives of polyethylene glycol (PEG) was evaluated under the ball-on-plate reciprocating mode and steel/steel contact.
Activation and modification of carbon dioxide by redox-active low-valent gallium species
Authors: Dodonov Vladimir A. , Kushnerova Olga A. , Baranov Evgeny V. , Novikov Alexander S. , Fedushkin Igor L.
Published: May 2021

Gallium(i) species offer a facile way for the activation of carbon dioxide and its further modification with heterocumulenes.
Comprehensive evaluation of non-catalytic wet air oxidation as a pretreatment to remove pharmaceuticals from hospital effluents
Authors: Boucher Valérie , Beaudon Margot , Ramirez Pedro , Lemoine Pascal , Volk Kalyssa , Yargeau Viviane , Segura Pedro A.
Published: May 2021

Non-catalytic wet air oxidation removes pharmaceuticals efficiently from hospital wastewater in low chemical oxygen demand conditions.
The neuroprotective effects of isoquercitrin purified from apple pomace by high-speed countercurrent chromatography in the MPTP acute mouse model of Parkinson's disease
Authors: Liu Cong , Wang Wenjuan , Li Hao , Liu Jiangang , Zhang Peng , Cheng Yong , Qin Xiaoyan , Hu Yang , Wei Yun
Published: May 2021

Isoquercitrin was isolated from apple pomace by HSCCC and proved to have neuroprotective effects on Parkinson's mice induced by MPTP.
One-pot hydrodeoxygenation of bioderived furans into octane at low temperaturesviaan octanediol route
Authors: Li Song , Ma Qiaozhi , Zhong Wenxin , Zhao Xuelai , Wei Xiangqian , Zhang Xinghua , Liu Qiying , Wang Chenguang , Ma Longlong , Zhang Qi
Published: May 2021

A novel octanediol-route was developed to produce octane from bioderived furans at low temperatures.
Imaging of nanoparticle uptake and kinetics of intracellular trafficking in individual cells
Authors: Vtyurina Natalia , Åberg Christoffer , Salvati Anna
Published: May 2021

Fluorescence microscopy is used to quantify nanoparticle colocalization with the lysosomes and other organelles over time in live cells. From this, intracellular trafficking kinetics are determined and how they vary with nanoparticle size and in individual cells.
Ab initio nonadiabatic molecular dynamics of charge carriers in metal halide perovskites
Authors: Li Wei , She Yalan , Vasenko Andrey S. , Prezhdo Oleg V.
Published: May 2021

Atomistic details govern quantum dynamics of charge carriers in metal halide perovskites, which exhibit properties of solid state and molecular semiconductors, as revealed by time-domain density functional theory and nonadiabatic molecular dynamics.
Reductive cross-coupling to access C–N bonds from aryl halides and diazoesters under dual nickel/photoredox-catalyzed conditions
Authors: Wu Xiaoqiang , Zheng Purui , Li Wanfang , XU Tao
Published: May 2021

A reductive cross-coupling reaction to access C–N bondsviadual Ni/photoredox-catalyzed systems has been reported. This method tolerates a broad scope of functional groups and the products can be transformed into several heterocycles.
Enantioselective organocatalytic amination of 2-perfluoroalkyl-oxazol-5(2H)-ones towards the synthesis of chiral N,O-aminals with perfluoroalkyl and amino groups
Authors: Zhu Bo , Yang Tianxiao , Gu Yingxin , Zhu Shuping , Zhu Gongming , Chang Junbiao
Published: May 2021

The first highly enantioselective amination at the C-2 position of oxazol-5(2H)-ones has been presented. Two efficient relay asymmetric transformation processes were successfully utilized to synthesize chiral N,O-aminals with a quaternary center.
Ultrafast conversion of carcinogenic 4-nitrophenol into 4-aminophenol in the dark catalyzed by surface interaction on BiPO4/g-C3N4 nanostructures in the presence of NaBH4
Authors: Azzam Ahmed B. , Djellabi Ridha , Sheta Sheta M. , El-Sheikh S. M.
Published: May 2021

The heterogeneous catalytic conversion of pollutants into useful industrial compounds is a two-goals at once process, which is highly recommended from the environmental, economic, and industrial points of view.
Particle encapsulation in aqueous ferrofluid drops and sorting of particle-encapsulating drops from empty drops using a magnetic field
Authors: Banerjee U. , Jain S. K. , Sen A. K.
Published: May 2021

We report encapsulation of microparticles in aqueous ferrofluid droplets and sorting of particle-encapsulating droplets from empty droplets at the fluid–fluid interface using a magnetic field.
Pulsed electrocatalysis enables an efficient 2-electron oxygen reduction reaction for H2O2production
Authors: Ding Yani , Zhou Wei , Xie Liang , Chen Shuai , Gao Jihui , Sun Fei , Zhao Guangbo , Qin Yukun
Published: May 2021

The H2O2productionvia2eORR was increased by 138.12% by adjusting the pulse parameters, which was observed to be related to the non-Faraday process. A comprehensive mechanism of promoting effect of pulsed electrocatalysis was proposed.
Gelatin methacryloyl hydrogels functionalized with endothelin-1 for angiogenesis and full-thickness wound healing
Authors: Li Meng-Na , Yu Hong-Ping , Ke Qin-Fei , Zhang Chang-Qing , Gao You-Shui , Guo Ya-Ping
Published: May 2021

A therapeutic system was constructed first in which endothelin-1 (ET-1) as an endogenous vasoconstrictor peptide was embedded in a photo-crosslinking gelatin methacryloyl (GelMA) hydrogel for full-thickness wound healing.
Diversified amino acid-mediated allosteric regulation of phosphoglycerate dehydrogenase for serine biosynthesis in land plants
Authors: Okamura Eiji , Ohtaka Kinuka , Nishihama Ryuichi , Uchida Kai , Kuwahara Ayuko , Mochida Keiichi , Hirai Masami Yokota
Published: May 2021

The phosphorylated pathway of serine biosynthesis is initiated with 3-phosphoglycerate dehydrogenase (PGDH). The liverwort Marchantia polymorpha possesses an amino acid-sensitive MpPGDH which is inhibited by l-serine and activated by five proteinogenic amino acids, while the eudicot Arabidopsis thaliana has amino acid-sensitive AtPGDH1 and AtPGDH3 as well as amino acid-insensitive AtPGDH2. In this study, we analyzed PGDH isozymes of the representative land plants: the monocot Oryza sativa (OsPGDH1–3), basal angiosperm Amborella trichopoda (AmtriPGDH1–2), and moss Physcomitrium (Physcomitrella) patens (PpPGDH1–4). We demonstrated that OsPGDH1, AmtriPGDH1, PpPGDH1, and PpPGDH3 were amino acid-sensitive, whereas OsPGDH2, OsPGDH3, AmtriPGDH2, PpPGDH2, and PpPGDH4 were either sensitive to only some of the six effector amino acids or insensitive to all effectors. This indicates that PGDH sensitivity to effectors has been diversified among isozymes and that the land plant species examined, except for M. polymorpha, possess different isozyme types in terms of regulation. Phylogenetic analysis suggested that the different sensitivities convergently evolved in the bryophyte and angiosperm lineages. Site-directed mutagenesis of AtPGDH1 revealed that Asp538 and Asn556 residues in the ACT domain are involved in allosteric regulation by the effectors. These findings provide insight into the evolution of PGDH isozymes, highlighting the functional diversification of allosteric regulation in land plants.
Identification of the contact region responsible for the formation of the homomeric CYP1A2•CYP1A2 complex
Authors: Saha Aratrika , Connick J. Patrick , Reed James R. , Lott Charles S. , Backes Wayne L.
Published: May 2021

Previous studies showed that cytochrome P450 1A2 (CYP1A2) forms a homomeric complex that influences its metabolic characteristics. Specifically, CYP1A2 activity exhibits a sigmoidal response as a function of NADPH-cytochrome P450 reductase (POR) concentration and is consistent with an inhibitory CYP1A2•CYP1A2 complex that is disrupted by increasing [POR] (Reed et al. (2012) Biochem. J. 446, 489–497). The goal of this study was to identify the CYP1A2 contact regions involved in homomeric complex formation. Examination of X-ray structure of CYP1A2 implicated the proximal face in homomeric complex formation. Consequently, the involvement of residues L91–K106 (P1 region) located on the proximal face of CYP1A2 was investigated. This region was replaced with the homologous region of CYP2B4 (T81–S96) and the protein was expressed in HEK293T/17 cells. Complex formation and its disruption was observed using bioluminescence resonance energy transfer (BRET). The P1-CYP1A2 (CYP1A2 with the modified P1 region) exhibited a decreased BRET signal as compared with wild-type CYP1A2 (WT-CYP1A2). On further examination, P1-CYP1A2 was much less effective at disrupting the CYP1A2•CYP1A2 homomeric complex, when compared with WT-CYP1A2, thereby demonstrating impaired binding of P1-CYP1A2 to WT-CYP1A2 protein. In contrast, the P1 substitution did not affect its ability to form a heteromeric complex with CYP2B4. P1-CYP1A2 also showed decreased activity as compared with WT-CYP1A2, which was consistent with a decrease in the ability of P1-CYP1A2 to associate with WT-POR, again implicating the P1 region in POR binding. These results indicate that the contact region responsible for the CYP1A2•CYP1A2 homomeric complex resides in the proximal region of the protein.