Miracle-dz/UniFAR-FTUs huggingface dataset:
LARP4A recognizes polyA RNA via a novel binding mechanism mediated by disordered regions and involving the PAM2w motif, revealing interplay between PABP, LARP4A and mRNA

Abstract LARP4A belongs to the ancient RNA-binding protein superfamily of La-related proteins (LARPs). In humans, it acts mainly by stabilizing mRNAs, enhancing translation and controlling polyA lengths of heterologous mRNAs. These activities are known to implicate its association with mRNA, protein partners and translating ribosomes, albeit molecular details are missing. Here, we characterize the direct interaction between LARP4A, oligoA RNA and the MLLE domain of the PolyA-binding protein (PABP). Our study shows that LARP4A–oligoA association entails novel RNA recognition features involving the N-terminal region of the protein that exists in a semi-disordered state and lacks any recognizable RNA-binding motif. Against expectations, we show that the La module, the conserved RNA-binding unit across LARPs, is not the principal determinant for oligoA interaction, only contributing to binding to a limited degree. Furthermore, the variant PABP-interacting motif 2 (PAM2w) featured in the N-terminal region of LARP4A was found to be important for both RNA and PABP recognition, revealing a new role for this protein–protein binding motif. Our analysis demonstrates the mutual exclusive nature of the PAM2w-mediated interactions, thereby unveiling a tantalizing interplay between LARP4A, polyA and PABP.
Underreporting of Research Biopsies from Clinical Trials in Oncology

Purpose: Research biopsies are frequently incorporated within clinical trials in oncology and are often a mandatory requirement for trial enrollment. However, limited information is available regarding the extent and completeness of research biopsy reporting. Experimental Design: We identified a cohort of therapeutic clinical trials where research biopsies were performed between January 2005 and October 2010 from an IR database at our institution. Clinical trial protocols were compared with the highest level of corresponding publication as a manuscript or registry report. Results: A total of 866 research biopsies were performed across 46 clinical trials, with a median of 8 patients biopsied/trial and 19 biopsies collected/trial. After a median follow-up time of 4.3 years from trial completion, 36 of 46 trials (78%) reported trial results: published manuscripts (n = 35), or registry report (n = 1). A total of 635 conducted biopsies were reported in 18 of the 46 trials (39%). Six (33%) of these 18 trials underreported the number of biopsies performed. Of 33 trials with mandatory research biopsies, 13 (39%) trials reported on these biopsies. Biopsy complications occurred in 8 trials [n = 39 patients, 6 grade 3/4 adverse events (AE)] but only 1 trial reported these. Factors associated with biopsy reporting included a larger number of biopsies (P ≤ 0.001) and serial biopsies (P < 0.001). Twelve of 16 (75%) trials with >12 biopsies performed reported on these biopsies compared with only 20% (6/30) that performed ≤12 biopsies. Conclusions: Despite ethical obligations to report research biopsies, the majority (61%) of trials do not report results from research biopsies. Complications are rarely reported in these studies. Improved reporting of results and AEs from research biopsies is needed. Clin Cancer Res; 23(21); 6450–7. ©2017 AACR.
Social relationships, neighbourhood poverty and cumulative biological risk: findings from a multi-racial US urban community

Abstract Prior research has established associations between neighbourhood poverty and cumulative biological risk (CBR). CBR is conceptualized as indicative of the effects of stress on biological functioning, and is linked with increased morbidity and mortality. Studies suggest that supportive social relationships may be health protective, and may erode under conditions of poverty. This study examines whether social relationships are inversely associated with CBR and whether associations between neighbourhood poverty and CBR are mediated through social relationships. Data were from a stratified probability sample community survey (n=919) of residents of Detroit, Michigan, USA (2002–2003) and from the 2000 US Census. The outcome variable, CBR, included anthropometric and clinical measures. Independent variables included four indicators of social relationships: social support, neighbourhood satisfaction, social cohesion and neighbourhood participation. Multilevel models were used to test both research questions, with neighbourhood poverty and social relationships included at the block group level, and social relationships also included at the individual level, to disentangle individual from neighbourhood effects. Findings suggest some associations between social relationships and CBR after accounting for neighbourhood poverty and individual characteristics. In models that accounted for all indicators of social relationships, individual-level social support was associated with greater CBR (β=0.12, p=0.04), while neighbourhood-level social support was marginally significantly protective of CBR (within-neighbourhood: β=−0.36, p=0.06; between-neighbourhood: β=−0.24, p=0.06). In contrast, individual-level neighbourhood satisfaction was protective of CBR (β=−0.10, p=0.02), with no within-neighbourhood (β=0.06, p=0.54) or between-neighbourhood association (β=−0.04, p=0.38). Results indicate no significant association between either social cohesion or neighbourhood participation and CBR. Associations between neighbourhood poverty and CBR were not mediated by social relationships. These findings suggest that neighbourhood-level social support and individual-level neighbourhood satisfaction may be health protective and that neighbourhood poverty, social support and neighbourhood satisfaction are associated with CBR through independent pathways.
Utility of multicolor optic disc photography in evaluation of glaucomatous optic disc in myopic eyes: A novel approach

Interpretation of optic disc cupping and neuroretinal rim is challenging in myopic eyes because of large, shallow, and tilted disc, myopic crescent, and macular degeneration. Color and red-free optic disc photographs do not reveal the cup/disc ratio often in myopic eyes. We report characteristics of multicolor optic disc photography in three myopic eyes. All eyes underwent multicolor imaging Spectralis SDOCT system (Heidelberg Engineering, Germany). Owing to use of three laser lights in a confocal design, multicolor optic disc photography was able to delineate the neuroretinal rim and optic cup more clearly than color and red-free optic disc photographs.
Estimation of respiratory variables from thoracoabdominal breathing distance: a review of different techniques and calibration methods

The precise measurement of respiratory variables, such as tidal volume, minute ventilation, and respiratory rate, is necessary to monitor respiratory status, overcome several diseases, improve patient health conditions and reduce health care costs. This measurement has conventionally been performed by breathing into a mouthpiece connected to a flow rate measuring device. However, a mouthpiece can be uncomfortable for the subject and is difficult to use for long-term monitoring. Other noninvasive systems and devices have been developed that do not require a mouthpiece to quantitatively measure respiratory variables. These techniques are based on measuring size changes of the rib cage (RC) and abdomen (ABD), as lung volume is known to be a function of these variables. Among these systems, we distinguish respiratory inductive plethysmography (RIP), respiratory magnetometer plethysmography (RMP), and optoelectronic plethysmography devices. However, these devices should be previously calibrated for the correct evaluation of respiratory variables. The most popular calibration methods are isovolume manoeuvre calibration (ISOCAL), qualitative diagnostic calibration (QDC), multiple linear regression (MLR) and artificial neural networks (ANNs). The aim of this review is first to present how thoracoabdominal breathing distances can be used to estimate respiratory variables and second to present the different techniques and calibration methods used for this purpose.
Offline and online myoelectric pattern recognition analysis and real-time control of a robotic hand after spinal cord injury

Objective. The objective of this study was to investigate the feasibility of applying myoelectric pattern recognition for controlling a robotic hand in individuals with spinal cord injury (SCI). Approach. Surface electromyogram (sEMG) signals of six hand motion patterns were recorded from 12 subjects with SCI. Online and offline classification performance of two classifiers (Gaussian Naive Bayes classifier, GNB, and support vector machine, SVM) were investigated. An exoskeleton hand was then controlled in real-time using the classification results. The control accuracy and its correlation with function assessments were investigated. Main results. Average offline classification accuracy of all tested SCI subjects was (73.6 ± 14.0)% for GNB and (77.6 ± 11.6)% for SVM, respectively. Average online classification accuracy was significantly lower, (64.3 ± 15.0)% for GNB and (70.2 ± 13.2)% for SVM. Average control accuracy of (81.0 ± 16.3)% was achieved in real-time control of the robotic hand using myoelectric pattern recognition. Correlation between control accuracy and grip/pinch force was observed. Significance. The results show that it is feasible to extract hand motion intent from individuals with SCI and control a robotic hand device using myoelectric pattern recognition. The performance of real-time control can be predicted based on functional assessments.
Design of a Dual-Technology Fusion Sensor Chip with a Ring Electrode for Biosensing Application

Quartz crystal microbalance (QCM) is still a new high-precision surface detection technique. However, the adsorption quality detected by the QCM currently contains a solvent-coupling quality and cannot separate the actual biomolecular mass. Local surface plasmon resonance (LSPR) can detect the mass of biomolecules, but requires a certain contrast between the solvent of the surrounding medium and the refractive index of the adsorbed layer. The sensor chip, combining two compatible technologies, can realize the simultaneous detection of biomolecules and improve the refractive index sensitivity. The structure of our chip is to prepare the ring-shaped gold electrode on the upper surface of the quartz crystal, the circular gold electrode on the bottom surface, and the spherical gold nanoparticles arrays in the center region of the ring electrode to form a QCM/LSPR dual-technology chip. Through simulation, we finally get the size of the best energy trap by the two electrodes on the upper surface and the lower surface: the ring-top electrode with a thickness of 100 nm, an inner diameter of 4 mm, and an outer diameter of 8 mm; and the bottom electrode with a thickness of 100 nm and a radius of 6 mm. By comparing the refractive index sensitivity, we chose a spherical gold nanoparticle with a radius of 30 nm and a refractive sensitivity of 61.34 nm/RIU to design the LSPR sensor chip.
Effects of Shot Peening on Fretting Fatigue Crack Initiation Behavior

This study analyzes the effects of shot peening on the crack initiation behavior under fretting loading by using a numerical method. The residual stress relaxation and the contact stress evolution are both considered. The crack initiation life is predicted by the critical plane Smith–Watson–Topper (SWT) model. Considering that the fretting contact region has a high stress gradient along the depth direction, the process volume approach is adopted to calculate the SWT parameters. The results show that the remaining residual stress after relaxation strongly affects crack initiation life. The remaining residual stress decreases with the increase of fatigue loading, and the effect of shot peening on the improvement of crack initiation life is more obvious under smaller fatigue loading. Furthermore, under smaller fatigue loading, the crack initiation life of specimens with high shot peening intensity is longer than that of specimens with low shot peening intensity. However, the opposite phenomenon appears when the fatigue loading is large enough.
Catalyzing Cancer Prevention Research CaPR: A New Year/New Opportunities

Dear Colleagues: From all of us at Cancer Prevention Research (CaPR), we wish you, our esteemed readers and contributors, a Happy New Year! As always,CaPRwill strive topublish high-impact papers of central relevance to our readers. Inspired by the Special Report in this issue (1), here is a glimpse of just a few of our 2016 offerings: Following our recently completed Immunoprevention series, we will publish reviews on this and the related topics of inflammation and infection:
Electrical Property of Graphene and Its Application to Electrochemical Biosensing

Graphene, a single atom thick layer of two-dimensional closely packed honeycomb carbon lattice, and its derivatives have attracted much attention in the field of biomedical, due to its unique physicochemical properties. The valuable physicochemical properties, such as high surface area, excellent electrical conductivity, remarkable biocompatibility and ease of surface functionalization have shown great potentials in the applications of graphene-based bioelectronics devices, including electrochemical biosensors for biomarker analysis. In this review, we will provide a selective overview of recent advances on synthesis methods of graphene and its derivatives, as well as its application to electrochemical biosensor development. We believe the topics discussed here are useful, and able to provide a guideline in the development of novel graphene and on graphene-like 2-dimensional (2D) materials based biosensors in the future.
Fluoroquinolone resistance in carbapenem-resistant Elizabethkingia anophelis: phenotypic and genotypic characteristics of clinical isolates with topoisomerase mutations and comparative genomic analysis.

BACKGROUND MDR Elizabethkingia anophelis strains are implicated in an increasing number of healthcare-associated infections worldwide, including a recent cluster of E. anophelis infections in the Midwestern USA associated with significant morbidity and mortality. However, there is minimal information on the antimicrobial susceptibilities of E. anophelis strains or their antimicrobial resistance to carbapenems and fluoroquinolones. OBJECTIVES Our aim was to examine the susceptibilities and genetic profiles of clinical isolates of E. anophelis from our hospital, characterize their carbapenemase genes and production of MBLs, and determine the mechanism of fluoroquinolone resistance. METHODS A total of 115 non-duplicated isolates of E. anophelis were examined. MICs of antimicrobial agents were determined using the Sensititre 96-well broth microdilution panel method. QRDR mutations and MBL genes were identified using PCR. MBL production was screened for using a combined disc test. RESULTS All E. anophelis isolates harboured the blaGOB and blaB genes with resistance to carbapenems. Antibiotic susceptibility testing indicated different resistance patterns to ciprofloxacin and levofloxacin in most isolates. Sequencing analysis confirmed that a concurrent GyrA amino acid substitution (Ser83Ile or Ser83Arg) in the hotspots of respective QRDRs was primarily responsible for high-level ciprofloxacin/levofloxacin resistance. Only one isolate had no mutation but a high fluoroquinolone MIC. CONCLUSIONS Our study identified a strong correlation between antibiotic susceptibility profiles and mechanisms of fluoroquinolone resistance among carbapenem-resistant E. anophelis isolates, providing an important foundation for continued surveillance and epidemiological analyses of emerging E. anophelis opportunistic infections. Minocycline or ciprofloxacin has the potential for treatment of severe E. anophelis infections.
The biomechanics of concussion for ice hockey head impact events

Abstract The purpose of this research was to conduct reconstructions of concussive and non-concussive impacts in ice hockey to determine the biomechanics and thresholds of concussive injury in ice hockey. Videos of concussive and non-concussive impacts in an elite professional ice hockey league in North America were reconstructed using physical and finite element model methods. Eighty concussive and 45 non-concussive events were studied. Logistic regressions indicate significant thresholds for concussion for linear/rotational acceleration and CSDM10%. Impacts in ice hockey were mostly long duration events, longer than 15 ms. These results have significant implications for helmet standards and development to prevent concussion.
lncRNA MIAT suppression alleviates corneal angiogenesis through regulating miR-1246/ACE

ABSTRACT Corneal neovascularization (CRNV) is a prevalence eye disorder that affects the transparency and refraction properties of eyes. To explore the correlation between the level of Angiotensin II (Ang II) and corneal angiogenesis, the rat model of CRNV was established using alkali-burn, while the human umbilical vein endothelial cells (HUVECs) were stimulated using VEGF to induce the CRNV cells in vitro. RNA immunoprecipitation (RIP) and RNA pull-down were performed to validate the relationship between MIAT and miR-1246. The expression of MIAT and Ang II was increased, while miR-1246 was decreased in CRNV rat model. VEGF stimulation significantly promoted cell proliferation and migration of HUVECs, knockdown of MIAT dramatically reversed the effects of VEGF, while cells co-transfected with miR-1246 inhibitor obviously abolished the effect of VEGF+si-MIAT, however, enalaprilat abolished the effects of VEGF+si-MIAT+miR-1246 inhibitor. MIAT directly regulated the expression of miR-1246. In conclusion, VEGF stimulation promoted cell proliferation and migration of HUVECs mainly through regulating MIAT/miR-1246/ACE.
Validating camera trap distance sampling for chimpanzees

The extension of distance sampling methods to accommodate observations from camera traps has recently enhanced the potential to remotely monitor multiple species without the need of additional data collection (sign production and decay rates) or individual identification. However, the method requires that the proportion of time is quantifiable when animals can be detected by the cameras. This can be problematic, for instance, when animals spend time above the ground, which is the case for most primates. In this study, we aimed to validate camera trap distance sampling (CTDS) for the semiarboreal western chimpanzee (Pan troglodytes verus) in Taï National Park, Côte d'Ivoire by estimating abundance of a population of known size and comparing estimates to those from other commonly applied methods. We estimated chimpanzee abundance using CTDS and accounted for limited availability for detection (semiarboreal). We evaluated bias and precision of estimates, as well as costs and efforts required to obtain them, and compared them to those from spatially explicit capture‐recapture (SECR) and line transect nest surveys. Abundance estimates obtained by CTDS and SECR produced a similar negligible bias, but CTDS yielded a larger coefficient of variation (CV = 39.70% for CTDS vs. 1%/19% for SECR). Line transects generated the most biased abundance estimates but yielded a better coefficient of variation (27.40–27.85%) than CTDS. Camera trap surveys were twice more costly than line transects because of the initial cost of cameras, while line transects surveys required more than twice as much time in the field. This study demonstrates the potential to obtain unbiased estimates of the abundance of semiarboreal species like chimpanzees by CTDS.
The consensus of integrative diagnosis and treatment of acute pancreatitis‐2017

Acute pancreatitis (AP) is one of the most common acute abdominal diseases. The digestive disease committee, Chinese Association of Integrative Medicine, released Integrated traditional Chinese and Western medicine for diagnosis and treatment of acute pancreatitis in 2010.1 Since then, further studies and great progress have been made by domestic and foreign counterparts from the perspective of both Chinese and Western medicine in AP, including the classification, fluid resuscitation, organ function maintenance, surgery intervention, enteral nutrition (EN), and syndrome differentiation and treatment. It is necessary to update the consensus on diagnosis and treatment of integrated Chinese and Western medicine to meet clinical needs. Therefore, the 2012 Revision of the Atlanta Classification Standard (RAC) by the International AP Consensus,2 the 2013 the Management of Acute Pancreatitis by the American College of Gastroenterology,3, 4 the 2014 Guidelines for diagnosis and treatment of the acute pancreatitis guide (2014) by the Chinese medical association branch,5 the 2014 Guidelines on Integrative Medicine for Severe Acute Pancreatitis by the General Surgery Committee of the Chinese Society of Integrated Traditional Chinese and Western Medicine,6 and Traditional Chinese Medicine Consensus on the Diagnosis and Treatment for Acute Pancreatitis by the Spleen and Stomach committee of China Association of Traditional Chinese Medicine7, 8 were taken into account for the revision of the consensus published in 2010. The digestive specialists in Chinese and Western medicine had a discussion on traditional Chinese medicine (TCM) types, syndrome differentiation, the main points of integrative medicine, and so on. According to the Delphi method, Consensus of Integrative Diagnosis and Treatment of Acute Pancreatitis (the 2017 revision) has been passed after three rounds votes. (The voting options are as follows: (a) totally agree; (b) agree, but with some reservations; (c) agree, but with larger reservations; (d) disagree, but reserved; and (e) absolutely disagree. If more than two out of three choose (a), or over 85% choose (a) + (b), the consensus will be passed. ) The final validation was carried out by the core expert group in Taizhou, Jiangsu on June 9, 2017. The full text is as follows.
New Amylase Inhibitor Present in Corn Seeds Active In Vitro Against Amylase from Fusarium verticillioides.

A screening for specific amylase inhibitor levels against amylase from Fusarium verticillioides (Fusarium moniliforme), the most relevant mycotoxigenic fungus in corn, was conducted on 37 corn hybrids. The amylase inhibitor levels in these hybrids ranged from 5.5 to 16.0 amylase inhibitor units per gram of corn (AIU/g) in the MASTER and AG5011 hybrids, respectively. The hybrid with the maximum content of inhibitor was used as the source of this new protein. The inhibitor was partially purified using fractional precipitation, gel filtration on Sephadex G-75 column, high performance liquid chromatography (HPLC) Superose HR 10/30 column, and HPLC anion exchange chromatography, obtaining a 20.7-fold purification. Electrophoresis after denaturing and heating under reductive conditions showed an apparent 23.8 kDa molecular mass and an acidic isoelectric point of 5.4, which differs from previous molecular masses reported for other inhibitors present in corn seeds (14 and 22 kDa). This inhibitor showed activity against amylases from human saliva and pancreas, from the fungi F. verticillioides and Aspergillus flavus, and from the insects Acanthoscelides obtectus, Zabrotes subfasciatus, Tribolium castaneum, and Sitotroga cerealella. The mycoflora found in the corn grain indicated Fusarium sp. as the most prevalent fungi (81.1% of the samples), with a count ranging from 1.5 × 102 to 2.4 × 106 CFU/g of corn. The presence of fumonisins was detected in 21 out of the 37 hybrids studied, ranging from 0.05 to 2.67 μg of FB per gram of corn. No correlation could be established between this amylase inhibitor level in the corn seeds and the presence of Fusarium sp. or with the fumonisin content under the experimental conditions of the test.