bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photoreceptor Diversification Accompanies the Evolution of Anthozoa
Authors: Gornik Sebastian G , Bergheim Bruno Gideon , Morel Benoit , Stamatakis Alexandros , Foulkes Nicholas S , Guse Annika 
Published: November 2020

Abstract
Anthozoan corals are an ecologically important group of cnidarians, which power the productivity of reef ecosystems. They are sessile, inhabit shallow, tropical oceans and are highly dependent on sun- and moonlight to regulate sexual reproduction, phototaxis, and photosymbiosis. However, their exposure to high levels of sunlight also imposes an increased risk of UV-induced DNA damage. How have these challenging photic environments influenced photoreceptor evolution and function in these animals? To address this question, we initially screened the cnidarian photoreceptor repertoire for Anthozoa-specific signatures by a broad-scale evolutionary analysis. We compared transcriptomic data of more than 36 cnidarian species and revealed a more diverse photoreceptor repertoire in the anthozoan subphylum than in the subphylum Medusozoa. We classified the three principle opsin classes into distinct subtypes and showed that Anthozoa retained all three classes, which diversified into at least six subtypes. In contrast, in Medusozoa, only one class with a single subtype persists. Similarly, in Anthozoa, we documented three photolyase classes and two cryptochrome (CRY) classes, whereas CRYs are entirely absent in Medusozoa. Interestingly, we also identified one anthozoan CRY class, which exhibited unique tandem duplications of the core functional domains. We next explored the functionality of anthozoan photoreceptors in the model species Exaiptasia diaphana (Aiptasia), which recapitulates key photo-behaviors of corals. We show that the diverse opsin genes are differentially expressed in important life stages common to reef-building corals and Aiptasia and that CRY expression is light regulated. We thereby provide important clues linking coral evolution with photoreceptor diversification.
Design of experimental food patches to measure foraging intensity for octopus: a case study with the giant Pacific octopusEnteroctopus dofleini
Authors: Chancellor Stephanie , Scheel David , Brown Joel S 
Published: November 2020

ABSTRACTIn a study of the foraging behaviour of the giant Pacific octopus Enteroctopus dofleini, we designed two types of experimental food patches to measure habitat preferences and perceptions of predation risk. The first patch successfully measured giving-up densities (GUDs), confirmed by octopus prey presence and higher foraging at sites with historically greater octopus presence. However, nontarget foragers also foraged on these experimental food patches. Our second floating patch design successfully excluded nontarget species from subtidal patches, and from intertidal patches at high tide, but allowed for foraging by E. dofleini. The second design successfully measured GUDs and suggested that octopus preferred foraging in a subtidal habitat compared to an intertidal habitat. We ascribe the higher GUD in the intertidal habitat to its higher predation risk relative to the subtidal habitat. The second patch design seems well suited for E. dofleini and, in conjunction with a camera system, could be used to provide behavioural indicators of the octopus's abundance, perceptions of habitat quality and predation risk.
VEZF1–guanine quadruplex DNA interaction regulates alternative polyadenylation and detyrosinase activity of VASH1
Authors: Li Lin , Williams Preston , Gao Zi , Wang Yinsheng 
Published: November 2020

Abstract
Vascular endothelial zinc finger 1 (VEZF1) plays important roles in endothelial lineage definition and angiogenesis. Vasohibins 1 and 2 (VASH1 and VASH2) can form heterodimers with small vasohibin-binding protein (SVBP) and were recently shown to regulate angiogenesis by acting as tubulin detyrosinases. Here, we showed that VEZF1 binds directly with DNA guanine quadruplex (G quadruplex, G4) structures in vitro and in cells, which modulates the levels of the two isoforms of VASH1 mRNA. Disruption of this interaction, through genetic depletion of VEZF1 or treatment of cells with G4-stabilizing small molecules, led to increased production of the long over short isoform of VASH1 (i.e. VASH1A and VASH1B, respectively) mRNA and elevated tubulin detyrosinase activity in cells. Moreover, disruption of VEZF1-G4 interactions in human umbilical vein endothelial cells resulted in diminished angiogenesis. These results suggest that the interaction between VEZF1 and G4 structures assumes a crucial role in angiogenesis, which occurs through regulating the relative levels of the two isoforms of VASH1 mRNA and the detyrosinase activity of the VASH1-SVBP complex. Together, our work revealed VEZF1 as a G4-binding protein, identified a novel regulatory mechanism for tubulin detyrosinase, and illustrated that the VEZF1- and VASH1-mediated angiogenesis pathways are functionally connected.
NGS-based identification and tracing of microsatellite instability from minute amounts DNA using inter-Alu-PCR
Authors: Yu Fangyan , Leong Ka Wai , Makrigiorgos Alexander , Adalsteinsson Viktor A , Ladas Ioannis , Ng Kimmie , Mamon Harvey , Makrigiorgos G Mike 
Published: November 2020

AbstractSensitive detection of microsatellite instability (MSI) in tissue or liquid biopsies using next generation sequencing (NGS) has growing prognostic and predictive applications in cancer. However, the complexities of NGS make it cumbersome as compared to established multiplex-PCR detection of MSI. We present a new approach to detect MSI using inter-Alu-PCR followed by targeted NGS, that combines the practical advantages of multiplexed-PCR with the breadth of information provided by NGS. Inter-Alu-PCR employs poly-adenine repeats of variable length present in every Alu element and provides a massively-parallel, rapid approach to capture poly-A-rich genomic fractions within short 80–150bp amplicons generated from adjacent Alu-sequences. A custom-made software analysis tool, MSI-tracer, enables Alu-associated MSI detection from tissue biopsies or MSI-tracing at low-levels in circulating-DNA. MSI-associated indels at somatic-indel frequencies of 0.05–1.5% can be detected depending on the availability of matching normal tissue and the extent of instability. Due to the high Alu copy-number in human genomes, a single inter-Alu-PCR retrieves enough information for identification of MSI-associated-indels from ∼100 pg circulating-DNA, reducing current limits by ∼2-orders of magnitude and equivalent to circulating-DNA obtained from finger-sticks. The combined practical and informational advantages of inter-Alu-PCR make it a powerful tool for identifying tissue-MSI-status or tracing MSI-associated-indels in liquid biopsies.
Ribosome profiling reveals ribosome stalling on tryptophan codons and ribosome queuing upon oxidative stress in fission yeast
Authors: Rubio Angela , Ghosh Sanjay , Mülleder Michael , Ralser Markus , Mata Juan 
Published: November 2020

Abstract
Translational control is essential in response to stress. We investigated the translational programmes launched by the fission yeast Schizosaccharomyces pombe upon five environmental stresses. We also explored the contribution of defence pathways to these programmes: The Integrated Stress Response (ISR), which regulates translation initiation, and the stress-response MAPK pathway. We performed ribosome profiling of cells subjected to each stress, in wild type cells and in cells with the defence pathways inactivated. The transcription factor Fil1, a functional homologue of the yeast Gcn4 and the mammalian Atf4 proteins, was translationally upregulated and required for the response to most stresses. Moreover, many mRNAs encoding proteins required for ribosome biogenesis were translationally downregulated. Thus, several stresses trigger a universal translational response, including reduced ribosome production and a Fil1-mediated transcriptional programme. Surprisingly, ribosomes stalled on tryptophan codons upon oxidative stress, likely due to a decrease in charged tRNA-Tryptophan. Stalling caused ribosome accumulation upstream of tryptophan codons (ribosome queuing/collisions), demonstrating that stalled ribosomes affect translation elongation by other ribosomes. Consistently, tryptophan codon stalling led to reduced translation elongation and contributed to the ISR-mediated inhibition of initiation. We show that different stresses elicit common and specific translational responses, revealing a novel role in Tryptophan-tRNA availability.
Nucleotide resolution profiling of m3C RNA modification by HAC-seq
Authors: Cui Jia , Liu Qi , Sendinc Erdem , Shi Yang , Gregory Richard I 
Published: November 2020

Abstract
Cellular RNAs are subject to a myriad of different chemical modifications that play important roles in controlling RNA expression and function. Dysregulation of certain RNA modifications, the so-called ‘epitranscriptome’, contributes to human disease. One limitation in studying the functional, physiological, and pathological roles of the epitranscriptome is the availability of methods for the precise mapping of individual RNA modifications throughout the transcriptome. 3-Methylcytidine (m3C) modification of certain tRNAs is well established and was also recently detected in mRNA. However, methods for the specific mapping of m3C throughout the transcriptome are lacking. Here, we developed a m3C-specific technique, Hydrazine-Aniline Cleavage sequencing (HAC-seq), to profile the m3C methylome at single-nucleotide resolution. We applied HAC-seq to analyze ribosomal RNA (rRNA)-depleted total RNAs in human cells. We found that tRNAs are the predominant m3C-modified RNA species, with 17 m3C modification sites on 11 cytoplasmic and 2 mitochondrial tRNA isoacceptors in MCF7 cells. We found no evidence for m3C-modification of mRNA or other non-coding RNAs at comparable levels to tRNAs in these cells. HAC-seq provides a novel method for the unbiased, transcriptome-wide identification of m3C RNA modification at single-nucleotide resolution, and could be widely applied to reveal the m3C methylome in different cells and tissues.
Ultrafiltration rate and incident atrial fibrillation among older individuals initiating hemodialysis
Authors: Flythe Jennifer E , Liu Sai , Montez-Rath Maria E , Winkelmayer Wolfgang C , Chang Tara I 
Published: November 2020

Abstract

Background
Higher ultrafiltration (UF) rates are associated with numerous adverse cardiovascular outcomes among individuals receiving maintenance hemodialysis. We undertook this study to investigate the association of UF rate and incident atrial fibrillation in a large, nationally representative US cohort of incident, older hemodialysis patients.

Methods
We used the US Renal Data System linked to the records of a large dialysis provider to identify individuals ≥67 years of age initiating hemodialysis between January 2006 and December 2011. We applied an extended Cox model as a function of a time-varying exposure to compute adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) for the association of delivered UF rate and incident atrial fibrillation.

Results
Among the 15 414 individuals included in the study, 3177 developed atrial fibrillation. In fully adjusted models, a UF rate &gt;13 mL/h/kg (versus ≤13 mL/h/kg) was associated with a higher hazard of incident atrial fibrillation [adjusted HR 1.19 (95% CI 1.07–1.30)]. Analyses using lower UF rate thresholds (≤10 versus &gt;10 mL/h/kg and ≤8 versus &gt;8 mL/h/kg, separately) yielded similar results. Analyses specifying the UF rate as a cubic spline (per 1 mL/h/kg) confirmed an approximately linear dose–response relationship between the UF rate and the risk of incident atrial fibrillation: risk began at UF rates of ~6 mL/h/kg and the magnitude of this risk flattened, but remained elevated, at rates ≥9 mL/h/kg.

Conclusion
In this observational study of older individuals initiating hemodialysis, higher UF rates were associated with higher incidences of atrial fibrillation.
The effect of admission and pre-admission serum creatinine as baseline to assess incidence and outcomes of acute kidney injury in acute medical admissions
Authors: Pickup Luke , Loutradis Charalampos , Law Jonathan P , Arnold Julia J , Dasgupta Indranil , Sarafidis Pantelis , Townend Jonathan N , Cockwell Paul , Ferro Charles J 
Published: November 2020

Abstract

Background
Acute kidney injury (AKI) in hospital-admitted patients is a common complication associated with increased mortality. The diagnosis of AKI relies on the ascertainment of peak increase in serum creatinine (SCr). This study evaluated the incidence of AKI using the increase from mean 7–365 days pre-admission (AKIpre) and admission (AKIadm) SCr levels, and examined the associations of AKI and changes in SCr levels with all-cause mortality.

Methods
A total of 2436 patients admitted to a tertiary hospital were recruited and followed-up for a median of 47.70 (interquartile range 18.20) months. AKI incidence and severity were defined according to the Kidney Disease: Improving Global Outcomes-AKI Guidelines. Follow-up data were collected from the Hospital Episode Statistics and Office of National Statistics. Mortality was evaluated during a short- (30 days), mid- (1 year) and long-term (4 years) period.

Results
No difference in the AKI rates using AKIpre and AKIadm (12.5% versus 12.2%; P = 0.695) or in the AKI severity (P = 0.261) was evident. Agreement between the two definitions was modest (Kappa-statistic = 0.596, P &lt; 0.001). Patients with AKIpre or AKIadm had increased all-cause mortality compared with those without AKI during all follow-up periods. In fully adjusted regression analysis, AKIpre [hazard ratio (HR) = 2.226, 95% confidence interval (CI) 1.140–4.347; P = 0.027] and AKIadm (HR = 2.105, 95% CI 1.090–4.064; P = 0.027) remained associated with 30-day mortality. Results for the 1- and 4-year periods were similar. Increases of &gt;4.00 μmol/L and &gt;6.06% from pre-admission or &gt;6.00 μmol/L and &gt;17.24% from admission SCr levels presented increased mortality risk during follow-up.

Conclusions
Use of admission or pre-admission SCr provides similar incidence rates, but they diagnose different sets of patients. Even minor increases in SCr, below those required for the classification of AKI, were associated with increased mortality. These findings can help the clinicians to identify patients at higher risk for adverse outcomes.
Prospective, Multicenter Clinical Study of Microvascular Decompression for Hemifacial Spasm
Authors: Mizobuchi Yoshifumi , Nagahiro Shinji , Kondo Akinori , Arita Kazunori , Date Isao , Fujii Yukihiko , Fujimaki Takamitsu , Hanaya Ryosuke , Hasegawa Mitsuhiro , Hatayama Toru , Hongo Kazuhiro , Inoue Tooru , Kasuya Hidetoshi , Kobayashi Masahito , Kohmura Eiji , Matsushima Toshio , Masuoka Jun , Morita Akio , Munemoto Shigeru , Nishizawa Shigeru , Okayama Yoshihiro , Sato Kimitoshi , Shigeno Taku , Shimano Hiroshi , Takeshima Hideo , Tanabe Hideki , Yamakami Iwao 
Published: November 2020

Abstract

BACKGROUND
Microvascular decompression (MVD) is the most effective procedure for hemifacial spasm (HFS). MVD results from nonspecialized or low-volume institutes are not always reliable. Most studies on MVD for HFS are retrospective and single centered; to the best of our knowledge, no prospective, multicenter studies exist.

OBJECTIVE
To evaluate short- and long-term outcomes and complications in patients who underwent MVD for HFS in specialized Japanese institutions, in this multicenter, prospective, cohort study.

METHODS
Included patients had undergone MVD for HFS in study centers between April 2012 and March 2015. Patients’ postoperative grade of involuntary movements and complications were recorded postoperatively at 7 d (short-term) and at 1 (mid-term) and 3 (long-term) yr.

RESULTS
A total of 486 patients (150 men, 336 women; mean age 53.9 yr with 181 patients over 60 yr) were enrolled during the study period. Neuromonitoring was used in 96.3% of the cases. The complete cure rate of symptom relief, mortality rate, and complication rate at short-term follow-up were 70.6%, 0%, and 15%, respectively. The long-term follow-up was completed by 463 patients (95.3%); the complete cure rate of symptom relief and complication rate were 87.1% and 3.0%, respectively.

CONCLUSION
Our study revealed that under expert guidance and intraoperative neuromonitoring, the long-term curative effect rate of MVD for HFS is high, while complications are uncommon and usually transient. Our results indicate that MVD is an effective and safe treatment for patients with HFS, including elderly patients.
Interferon-related gene expression in response to TNF inhibitor treatment in ankylosing spondylitis patients: a pilot study
Authors: Harrison Stephanie R , Burska Agata N , Emery Paul , Marzo-Ortega Helena , Ponchel Frederique 
Published: November 2020

Abstract

Objective
Ankylosing spondylitis (AS) is a chronic inflammatory arthritis primarily affecting the spine and sacroiliac joints. TNF inhibitor (TNFi) drugs are recommended for patients not responding to NSAIDs; however, there is a significant need for biomarkers of response. IFN-regulated genes (IRGs) and other cytokines/chemokines are linked to autoimmune diseases and have been associated with treatment response. Our objective was to explore whether IRGs and cytokines/chemokines can be associated with response to TNFiagents in AS.

Methods
Peripheral blood mononuclear cells were obtained from 26 AS patients who were to receive a TNFi (I, n = 15) or placebo (P, n = 11) at week 0 and week 22. Response (R)/non-response (NR) was defined as reduction in ASDAS ≥ 1.2 points or reduction in sacroiliac/vertebral MRI lesions. The expression of 96 genes was quantified using TaqMan assays. Finally, ELISA was used to measure IL-6 in serum samples from another 38 AS patients.

Results
Analysis of gene expression in 26 baseline samples segregated patients into four groups defined by a signature of 15 genes (mainly IRGs). ASDAS response was associated with one group independently of treatment received. We then analysed response to the TNFi (n = 15) and identified a 12-gene signature associated with MRI response. A third IRG signature was also associated with a reduction in IRGs expression post-TNFi samples (n = 10 pairs). Finally, decreased circulating IL-6 was associated with BASDAI-R.

Conclusion
This pilot study suggests an association between IRG expression and response to TNFi in AS. These findings require validation in a larger cohort in order to construct predictive algorithms for patient stratification.
The influence of prior intention on joint action: an fNIRS-based hyperscanning study
Authors: Chen Yixin , Zhang Qihan , Yuan Sheng , Zhao Bingjie , Zhang Peng , Bai Xuejun 
Published: November 2020

Abstract
Motor performances of the same action are affected by prior intentions to move unintentionally, cooperatively or competitively. Here, a back-and-forth movement task combined with a motion capture system and functional near-infrared spectroscopy (fNIRS)-based hyperscanning technology was utilized to record both the behavioral and neural data of 18 dyads of participants acting in pairs [joint conditions: no-intention, cooperative (Coop) and competitive (Comp)] or alone (single conditions: self-paced and fast-speed). The results revealed that Coop or Comp intentions in the joint conditions significantly sped up motor performance compared with similar single conditions, e.g. shorter movement times (MTs) in the Coop/Comp condition than the self-paced/fast-speed condition. Hemodynamic response analysis demonstrated that stronger activities for all joint conditions than the single conditions in the premotor and the supplementary motor cortex (Brodmann area 6) were independent of variations of MTs, indicating that they might reflect more complex aspects of action planning rather than simple execution-based processes. The comparisons of joint conditions across distinct prior intentions before acting yielded significant results for both behavioral and neural measures, with the highest activation of the temporo-parietal junction (TPJ) and the shortest MTs in the Comp condition considered to be implications for the top-down influence of prior intentions on joint performance.
Effective science and technology assessment advice for congress: comparing options
Authors: Blair Peter D 
Published: November 2020

Abstract
Effective science and technology (S&T) assessment capabilities providing advice for Congress must be both credible and suitable to congressional needs. To be credible, from the perspective of those who will use the advice, its provision must be (1) authoritative, (2) objective, and (3) independent. To be suitable, the advice must be (4) relevant, (5) useful, and (6) timely. For S&T advice today, Congress draws on many sources but four traditional options stand out as having been used most frequently: (1) The National Research Council, the operating arm of the National Academies of Sciences, Engineering and Medicine, (2) The Congressional Research Service, (3) the former Office of Technology Assessment, and (4) the Government Accountability Office. This article chronicles the evolution of these four organizations and evaluates their relative strengths and weaknesses in terms of the six defined key characteristics for providing effective S&T advice for Congress, drawing conclusions for organizational improvements.
BMAA and MCLR Interact to Modulate Behavior and Exacerbate Molecular Changes Related to Neurodegeneration in Larval Zebrafish
Authors: Martin Rubia M , Bereman Michael S , Marsden Kurt C 
Published: November 2020

AbstractExposure to toxins produced by cyanobacteria (ie, cyanotoxins) is an emerging health concern due to their increasing prevalence and previous associations with neurodegenerative diseases including amyotrophic lateral sclerosis. The objective of this study was to evaluate the neurotoxic effects of a mixture of two co-occurring cyanotoxins, β-methylamino-l-alanine (BMAA) and microcystin leucine and arginine (MCLR), using the larval zebrafish model. We combined high-throughput behavior-based toxicity assays with discovery proteomic techniques to identify behavioral and molecular changes following 6 days of exposure. Although neither toxin caused mortality, morphological defects, nor altered general locomotor behavior in zebrafish larvae, both toxins increased acoustic startle sensitivity in a dose-dependent manner by at least 40% (p &lt; .0001). Furthermore, startle sensitivity was enhanced by an additional 40% in larvae exposed to the BMAA/MCLR mixture relative to those exposed to the individual toxins. Supporting these behavioral results, our proteomic analysis revealed a 4-fold increase in the number of differentially expressed proteins in the mixture-exposed group. Additionally, prediction analysis reveals activation and/or inhibition of 8 enriched canonical pathways (enrichment p-value &lt; .01; z-score≥|2|), including ILK, Rho Family GTPase, RhoGDI, and calcium signaling pathways, which have been implicated in neurodegeneration. We also found that expression of TDP-43, of which cytoplasmic aggregates are a hallmark of amyotrophic lateral sclerosis pathology, was significantly upregulated by 5.7-fold following BMAA/MCLR mixture exposure. Together, our results emphasize the importance of including mixtures of cyanotoxins when investigating the link between environmental cyanotoxins and neurodegeneration as we reveal that BMAA and MCLR interact in vivo to enhance neurotoxicity.