Miracle-dz/UniFAR-FTUs huggingface dataset:
iPhosH-PseAAC: Identify Phosphohistidine Sites in Proteins by Blending Statistical Moments and Position Relative Features According to the Chou's 5-Step Rule and General Pseudo Amino Acid Composition

Protein phosphorylation is one of the key mechanism in prokaryotes and eukaryotes and is responsible for various biological functions such as protein degradation, intracellular localization, the multitude of cellular processes, molecular association, cytoskeletal dynamics, and enzymatic inhibition/activation. Phosphohistidine (PhosH) has a key role in a number of biological processes, including central metabolism to signalling in eukaryotes and bacteria. Thus, identification of phosphohistidine sites in a protein sequence is crucial, and experimental identification can be expensive, time-taking, and laborious. To address this problem, here, we propose a novel computational model namely iPhosH-PseAAC for prediction of phosphohistidine sites in a given protein sequence using pseudo amino acid composition (PseAAC), statistical moments, and position relative features. The results of the proposed predictor are validated through self-consistency testing, 10-fold cross-validation, and jackknife testing. The self-consistency validation gave the 100 percent accuracy, whereas, for cross-validation, the accuracy achieved is 94.26 percent. Moreover, jackknife testing gave 97.07 percent accuracy for the proposed model. Thus, the proposed model iPhosH-PseAAC for prediction of iPhosH site has the great ability to predict the PhosH sites in given proteins.
Removal of Linear and Branched Alkylphenols with the Combined Use of Polyphenol Oxidase and Chitosan

Removal of linear and branched alkylphenols with different alkyl chain lengths or different branchings (normal, secondary, and tertiary), some of which are suspected as endocrine disrupting chemicals, from an aqueous medium were investigated through quinone oxidation by polyphenol oxidase (PPO) and subsequent quinone adsorption on chitosan beads or powders at pH 7.0 and 40 °C. PPO-catalyzed quinone oxidation increased with an increase in alkyl chain length of the alkylphenols used. Although a higher PPO dose was required for quinone oxidation of branched alkylphenols, they were completely or mostly removed by quinone adsorption on chitosan beads or powders. The apparent activity of PPO increased by a decrease in quinone concentration. On the other hand, in the homogeneous systems with solutions of chitosan and PPO at pH 6.0, longer reaction times were required to generate insoluble aggregates, and a small amount of quinone derivatives were left in the solution even under optimum conditions. These results support that the two-step reaction, that is, PPO-catalyzed quinone oxidation and subsequent quinone adsorption on chitosan beads or powders, in the heterogeneous system is a good procedure for removing linear and branched alkylphenols from aqueous medium.
An iterative cross-subject negative-unlabeled learning algorithm for quantifying passive fatigue

Objective. This paper proposes an iterative negative-unlabeled (NU) learning algorithm for cross-subject detection of passive fatigue from labelled alert (negative) and unlabeled driving EEG data. Approach. Unlike other studies which used manual labeling of the fatigue state, the proposed algorithm (PA) first iteratively uses 29 subjects’ alert data and unlabeled driving data to identify the most fatigued block of EEG data in each subject in a cross-subject manner. Subsequently, the PA computes subjects’ driving fatigue score. Repeated measures correlations of the score to EEG band powers are then performed. Main results. The PA yields an averaged accuracy of 93.77% ± 8.15% across subjects in detecting fatigue, which is significantly better than the various baselines. The fatigue scores obtained are also significantly positively correlated with theta band power and negatively correlated with beta band power that are known to respectively increase and decrease in presence of passive fatigue. There is a strong negative correlation with alpha band power as well. Significance. The proposed iterative NU learning algorithm is capable of labelling and quantifying the most fatigued block in a cross-subject manner despite the lack of ground truth in the fatigue levels of unlabeled driving EEG data. Together with the significant correlations with theta, alpha and beta band power, the results show promise in the application of the proposed algorithm to detect fatigue from EEG.
Sleep problems and associations with psychopathology and cognition in young people with 22q11.2 deletion syndrome (22q11.2DS)

Abstract Background Young people with 22q11.2 deletion syndrome (22q11.2DS) are at high risk for neurodevelopmental disorders. Sleep problems may play a role in this risk but their prevalence, nature and links to psychopathology and cognitive function remain undescribed in this population. Method Sleep problems, psychopathology, developmental coordination and cognitive function were assessed in 140 young people with 22q11.2DS (mean age = 10.1, s.d. = 2.46) and 65 unaffected sibling controls (mean age = 10.8, s.d.SD = 2.26). Primary carers completed questionnaires screening for the children's developmental coordination and autism spectrum disorder. Results Sleep problems were identified in 60% of young people with 22q11.2DS compared to 23% of sibling controls (OR 5.00, p < 0.001). Two patterns best-described sleep problems in 22q11.2DS: restless sleep and insomnia. Restless sleep was linked to increased ADHD symptoms (OR 1.16, p < 0.001) and impaired executive function (OR 0.975, p = 0.013). Both patterns were associated with elevated symptoms of anxiety disorder (restless sleep: OR 1.10, p = 0.006 and insomnia: OR 1.07, p = 0.045) and developmental coordination disorder (OR 0.968, p = 0.0023, and OR 0.955, p = 0.009). The insomnia pattern was also linked to elevated conduct disorder symptoms (OR 1.53, p = 0.020). Conclusions Clinicians and carers should be aware that sleep problems are common in 22q11.2DS and index psychiatric risk, cognitive deficits and motor coordination problems. Future studies should explore the physiology of sleep and the links with the neurodevelopment in these young people.
Retrieval practice benefits memory precision

ABSTRACT Although previous research on retrieval practice (RP) has predominantly featured stimuli with discrete right-or-wrong answers, continuous measures offer potentially greater sensitivity in assessing the effects of RP on memory precision. The present study used a colour gradient (125 points ranging from magenta to yellow) as a continuous response variable. The colours of different images were learned through either RP or restudy and either one or three cycles of practice after initial study. On a delayed final test, participants’ memory was assessed for each item’s colour. Participants also created per-item intervals representing the region where they believed the correct colour most likely to have been. We found that repeated rounds of RP enhanced the correspondence between responses and the correct colour. In addition, RP led to participants creating more accurate (correct answers were more likely to be within the participant-specified intervals) and more precise (narrower) intervals relative to restudy, suggesting that RP enhances the precision of memories.
Dramatic Enhancement of Optoelectronic Properties in Electrophoretically Deposited C60-Graphene Hybrids.

Fullerene (C60) and multi-layer graphene hybrid devices were fabricated using electrophoretic deposition, where the C60 clusters are electrically charged upon the application of an external bias in a polar solvent, acetonitrile, mixed with toluene, which facilitates their deposition on the graphene membranes. Raman spectroscopy unveiled the unique vibrational fingerprints associated with the A2g mode of the C60 molecules at ~ 1453 cm-1, while a blue-shift of ~ 6 cm-1 and ~ 17 cm-1 was also attributed to the G- and 2D-bands of the hybrids relative to bare graphene, suggestive of p-doped graphene. The intensity ratio of the G- and the 2D-bands I2D/IG (hybrid) dropped to ~ 0.18 from ~ 0.3 (bare graphene), and this reduction in I2D/IG is also a signature of hole-doped graphene, consistent with the relatively strong electron accepting nature of C60. The electronic conductance of the two-terminal hybrid devices increased relative to bare graphene at room temperature which was attributed to the increased carrier density, and temperature-dependent electronic transport measurements were also conducted from ambient down to ~ 5.8 K. Additionally, a low energy shift in the Fermi level EF ~ 140 meV was calculated for the hybrids. When the hybrid devices were irradiated with a broadband white light source and a tunable laser source (with wavelength λ ranging from ~ 400-1100 nm), a strong photoresponse was evident, in contrast to the bare graphene devices which appeared unresponsive. The responsivity ℛ of the hybrids was measured to be ~ 109 A/W at λ ~ 400 nm and ~ 298 K, while the detectivity and external quantum efficiency were also exceptional, ~ 1015 Jones and ~ 109 %, respectively at ~ 1 V and light power density of ~ 3 mW/cm2. The ℛ values are ∼ 10 times higher compared to other hybrid devices derived from graphene reported previously, such as quantum dot-graphene and few-layer MoS2-graphene heterostructures. The strong photo-response of the C60-graphene hybrids reported here is attributed to the doping enhancement arising in the graphene upon the adsorption of C60. This work demonstrates the exceptional potential of such hybrid nanocarbon-based structures for optoelectronics.
Anti-vascular endothelial growth factor treatment for retinal conditions: a systematic review and meta-analysis

Objectives To evaluate the comparative effectiveness and safety of intravitreal bevacizumab, ranibizumab and aflibercept for patients with choroidal neovascular age-related macular degeneration (cn-AMD), diabetic macular oedema (DMO), macular oedema due to retinal vein occlusion (RVO-MO) and myopic choroidal neovascularisation (m-CNV). Design Systematic review and random-effects meta-analysis. Methods Multiple databases were searched from inception to 17 August 2017. Eligible head-to-head randomised controlled trials (RCTs) comparing the (anti-VEGF) drugs in adult patients aged ≥18 years with the retinal conditions of interest. Two reviewers independently screened studies, extracted data and assessed risk of bias. Results 19 RCTs involving 7459 patients with cn-AMD (n=12), DMO (n=3), RVO-MO (n=2) and m-CNV (n=2) were included. Vision gain was not significantly different in patients with cn-AMD, DMO, RVO-MO and m-CNV treated with bevacizumab versus ranibizumab. Similarly, vision gain was not significantly different between cn-AMD patients treated with aflibercept versus ranibizumab. Patients with DMO treated with aflibercept experienced significantly higher vision gain at 12 months than patients receiving ranibizumab or bevacizumab; however, this difference was not significant at 24 months. Rates of systemic serious harms were similar across anti-VEGF agents. Posthoc analyses revealed that an as-needed treatment regimen (6–9 injections per year) was associated with a mortality increase of 1.8% (risk ratio: 2.0 [1.2 to 3.5], 2 RCTs, 1795 patients) compared with monthly treatment in cn-AMD patients. Conclusions Intravitreal bevacizumab was a reasonable alternative to ranibizumab and aflibercept in patients with cn-AMD, DMO, RVO-MO and m-CNV. The only exception was for patients with DME and low visual acuity (<69 early treatment diabetic retinopathy study [ETDRS] letters), where treatment with aflibercept was associated with significantly higher vision gain (≥15 ETDRS letters) than bevacizumab or ranibizumab at 12 months; but the significant effects were not maintained at 24 months. The choice of anti-VEGF drugs may depend on the specific retinal condition, baseline visual acuity and treatment regimen. PROSPERO registration number CRD42015022041.
Effects of Site Thermal Variation and Physiography on Flight Synchrony and Phenology of the North American Spruce Beetle (Coleoptera: Curculionidae, Scolytinae) and Associated Species in Colorado

Abstract Spruce beetle, Dendroctonus rufipennis Kirby, is associated with forest mortality in Colorado and across western North America, yet it is not well understood how thermal variability affects basic population processes such as flight phenology. However, phenology–temperature relationships are important for understanding patterns of ecosystem disturbance, especially under projected climate warming. Here, we use a multiyear trapping study to test the hypothesis that spruce beetle flight synchrony, timing, and fitness traits (body size) are affected by variation in regional temperature and physiography. Large quantities of co-colonizing scolytines (Polygraphus convexifrons) (Coleoptera: Curculionidae, Scolytinae) and predatory beetles (Thanasimus undulatus) (Coleoptera: Cleridae) that may affect D. rufipennis populations also responded to spruce beetle synthetic pheromone lures. Relationships between flight patterns and environmental conditions were also analyzed for these species. The winter of 2018 was warmer and drier than winter 2017 and was associated with earlier flight for both scolytine species across most sites. The most important environmental factor driving D. rufipennis flight phenology was accumulated growing degree-days, with delayed flight cessation under warmer conditions and larger beetles following a warm winter. Flight was consistently more synchronous under colder growing season conditions for all species, but synchrony was not associated with winter temperatures. Warmer-than-average years promoted earlier flight of D. rufipennis and associated species, and less synchronous, prolonged flight across the region. Consequently, climate warming may be associated with earlier and potentially extended biotic pressure for spruce trees in the Rocky Mountain region, and flight phenology of multiple scolytines is plastic in response to thermal conditions.
Top K Hypotheses Selection on a Knowledge Graph

A Knowledge Graph (KG), popularly used in both industry and academia, is an effective representation of knowledge. It consists of a collection of knowledge elements, each of which in turn is extracted from the web or other sources. Information extractors that use natural language processing techniques or other complex algorithms are usually noisy. That is, the vast number of knowledge elements extracted from the web may not only be associated with different conﬁdence values but may also be inconsistent with each other. Many applications such as question answering systems that are built on top of large-scale KGs are required to reason efﬁciently about these conﬁdence values and inconsistencies. In addition, they are required to incorporate ontological constraints in their reasoning. One way to do this is to extract a subgraph of a KG that is consistent with the ontological constraints and is of maximum total conﬁdence value. Such a subgraph is referred to as the top hypothesis and is combinatorially hard to ﬁnd. In this paper, we introduce an algorithmic framework for ef-ﬁciently addressing the combinatorial hardness and selecting the top K hypotheses. Our approach is based on powerful algorithmic techniques recently invented in the context of the Weighted Constraint Satisfaction Problem (WCSP).
In vivo Exon Replacement in Mouse Atp7b Gene by CRISPR/Cas9 System.

The application of CRISPR/Cas9 has opened a new era in gene therapy, making it possible to correct mutated genomes in vivo. Exon replacement can correct many mutations and has potential clinical value. In this study, we used a lentivirus-delivered transgene to obtain transgenic mice in which Cas9 and GFP were driven by the hTBG promoter and were specifically expressed in the liver. In Cas9-positive mice, only approximately 11.6% of hepatocytes were GFP positive. The newborn Cas9-positive F1 mice were injected via the temporal vein with rAAV carrying a modified homologous replacement sequence for exon 8 of Atp7b and a pair of sgRNAs targeting the introns surrounding exon 8. When the Cas9-positive hepatocytes were sorted and analysed by PCR and next generation deep sequencing (NGS) with different labels, approximately16.34±4.02% to 19.37±6.50% of the analysed copies of exon8 were replaced by the donor template in the genome of GFP-positive hepatocytes, i.e.,1.81±0.29% to 2.09±0.54% replacement occurred in all liver genomes. However, when rAAV carrying a modified homologous replacement sequence was injected into the adult spCas9 mice, a double-cut deletion ratio of up to 99%, only about 1.10% to 1.13% of the E8 replacement rate was detected in Cas9-positive hepatocytes. This study is the first to achieve exon replacement via CRISPR/Cas9, which will benefit research on CRISPR/Cas9 technology for gene therapy.
Motor imagery and error related potential induced position control of a robotic arm

The paper introduces an electroencephalography U+0028 EEG U+0029 driven online position control scheme for a robot arm by utilizing motor imagery to activate and error related potential U+0028 ErrP U+0029 to stop the movement of the individual links, following a fixed U+0028 pre-defined U+0029 order of link selection. The right U+0028 left U+0029 hand motor imagery is used to turn a link clockwise U+0028 counterclockwise U+0029 and foot imagery is used to move a link forward. The occurrence of ErrP here indicates that the link under motion crosses the visually fixed target position, which usually is a plane U+002F line U+002F point depending on the desired transition of the link across 3D planes U+002F around 2D lines U+002F along 2D lines respectively. The imagined task about individual link U+00BC s movement is decoded by a classifier into three possible class labels: clockwise, counterclockwise and no movement in case of rotational movements and forward, backward and no movement in case of translational movements. One additional classifier is required to detect the occurrence of the ErrP signal, elicited due to visually inspired positional link error with reference to a geometrically selected target position. Wavelet coefficients and adaptive autoregressive parameters are extracted as features for motor imagery and ErrP signals respectively. Support vector machine classifiers are used to decode motor imagination and ErrP with high classification accuracy above 80 U+0025. The average time taken by the proposed scheme to decode and execute control intentions for the complete movement of three links of a robot is approximately 33 seconds. The steady-state error and peak overshoot of the proposed controller are experimentally obtained as 1.1 U+0025 and 4.6 U+0025 respectively.
Interaction of phages, bacteria, and the human immune system: Evolutionary changes in phage therapy

Phages and bacteria are known to undergo dynamic and co‐evolutionary arms race interactions in order to survive. Recent advances from in vitro and in vivo studies have improved our understanding of the complex interactions between phages, bacteria, and the human immune system. This insight is essential for the development of phage therapy to battle the growing problems of antibiotic resistance. It is also pivotal to prevent the development of phage‐resistance during the implementation of phage therapy in the clinic. In this review, we discuss recent progress of the interactions between phages, bacteria, and the human immune system and its clinical application for phage therapy. Proper phage therapy design will ideally produce large burst sizes, short latent periods, broad host ranges, and a low tendency to select resistance.
Effects of outdoor air pollutants on platelet activation in people with type 2 diabetes

Exposure to air pollution is associated with increased morbidity and mortality from cardiovascular disease. We hypothesized that increases in exposure to ambient air pollution are associated with platelet activation and formation of circulating tissue factor-expressing microparticles. We studied 19 subjects with type 2 diabetes, without clinical evidence of cardiovascular disease, who had previously participated in a human clinical study of exposure to ultrafine particles (UFP). Blood was obtained for measurements of platelet activation following an overnight stay in the Clinical Research Center, prior to each of their two pre-exposure visits. Air pollution and meteorological data, including UFP counts, were analyzed for the 5 days prior to the subjects’ arrival at the Clinical Research Center. Contrary to expectations, increases in UFP were associated with decreases in surface expression of platelet activation markers. The number of platelet-leukocyte conjugates decreased by −80 (95% confidence interval (CI) −123 to −37, p = 0.001) on the first lag day (20–44 h prior to the blood draw) and by −85 (CI −139 to −31, p = 0.005) on combined lag days 1 to 5, per interquartile range (IQR) increase in UFP particle number (2482). However, levels of soluble CD40L increased 104 (CI 3 to 205, p = 0.04) pg/ml per IQR increase in UFP on lag day 1, a finding consistent with prior platelet activation. We speculate that, in people with diabetes, exposure to UFP activates circulating platelets within hours of exposure, followed by an increase in soluble CD40L and a rebound reduction in circulating platelet surface markers.
Eye tracking support for visual analytics systems: foundations, current applications, and research challenges

Visual analytics (VA) research provides helpful solutions for interactive visual data analysis when exploring large and complex datasets. Due to recent advances in eye tracking technology, promising opportunities arise to extend these traditional VA approaches. Therefore, we discuss foundations for eye tracking support in VA systems. We first review and discuss the structure and range of typical VA systems. Based on a widely used VA model, we present five comprehensive examples that cover a wide range of usage scenarios. Then, we demonstrate that the VA model can be used to systematically explore how concrete VA systems could be extended with eye tracking, to create supportive and adaptive analytics systems. This allows us to identify general research and application opportunities, and classify them into research themes. In a call for action, we map the road for future research to broaden the use of eye tracking and advance visual analytics.
Ultrasound-guided lumbar selective nerve root block plus T12 paravertebral and sacral plexus block for hip and knee arthroplasty

Abstract Rationale: For hip or knee arthroplasty, it is essential to develop a satisfied peripheral nerve block method that will benefit elderly patients or patients who are contraindicated to neuraxial anesthesia. Patients concerns: Patient in Case 1 suffered from the right intertrochanteric fracture, combined with chronic obstructive pulmonary disease; Patient in Case 2 suffered from hip osteoarthritis; combined with ankylosing spondylitis; Patient in Case 3 suffered from rheumatoid arthritis, combined with ischemic encephalopathy. Diagnosis: Case 1: Right intertrochanteric fracture, chronic obstructive pulmonary disease. Case 2: hip osteoarthritis. Case 3: rheumatoid arthritis. Interventions: Ultrasound-guided lumbar selective nerve root block (SNRB) plus T12 paravertebral and sacral plexus block were performed in 2 patients who received hip arthroplasty and 1 patient who received knee arthroplasty. Outcomes: All patients successfully received surgeries with this peripheral nerve block method and no postoperative complication was reported. Lessons: Ultrasound-guided lumbar SNRB plus T12 paravertebral and sacral plexus block not only satisfied the analgesia requirement of surgery, but also reduced the consumption of local anesthetic.