Miracle-dz/UniFAR-FTUs huggingface dataset:
Broadly-reactive IgG responses to heterologous H5 prime-boost influenza vaccination are shaped by antigenic relatedness to priming strains

Prime-boost vaccinations of humans with different H5 strains have generated broadly protective antibody levels. However, the effect of an individual’s H5 exposure history on antibody responses to subsequent H5 vaccination is poorly understood. To investigate this, we analyzed the IgG response to H5 A/Indonesia/5/2005 (Ind05) vaccination in three cohorts: (1) a double primed group that received two H5 vaccinations: A/Vietnam/203/2004 (Vie04) 5 years ago and A/Hong Kong/156/1997 (HK97) 11 years ago, (2) a single primed group that received Vie04 5 years ago, and (3) an H5-naïve group that received two doses of the Ind05 vaccine 28 days apart. Hemagglutinin (HA)-reactive IgG levels were estimated by multiplex assay against an HA panel that included 21 H5 strains and 9 other strains representing H1, H3, H7, and H9 subtypes. Relative HA antibody landscapes were generated to quantitatively analyze the magnitude and breadth of antibody binding after vaccination. We found that short-interval prime-boosting with the Ind05 in the naïve group generated a low anti-H5 response. Both primed groups generated robust antibody responses reactive to a broad range of H5 strains after boosting with Ind05; IgG antibody levels persisted longer in subjects who had been double primed years ago. Notably, the IgG responses were strongest against the first priming H5 strain, that reflecting influenza virus immune imprinting. Finally, the broad anti-H5 IgG response was stronger against strains having a small antigenic distance to the initial priming strain. IMPORTANCE The antigenic shift and draft of hemagglutinin (HA) in influenza viruses is accepted as one of the major reasons for immune evasion. The analysis of B cell immune responses to influenza infection and vaccination is complicated by the impact of exposure history and antibody cross-reaction between antigenically similar influenza strains. To assist in such analyses, the influenza “antibody landscape” method has been used to analyze and visualize the relationship of antibody mediated immunity to the antigenic distance between influenza strains. In this study, we describe a “relative antibody landscape” method, calculating the antigenic distance between the vaccine influenza strain and other H5 strains, and using this relative antigenic distance to plot with the anti-H5 IgG levels post-vaccination. This new method quantitatively estimates and visualizes the correlation between the humoral response to a particular influenza strain, and the antigenic distance to other strains. Our findings demonstrate the effect of H5 exposure history on H5 vaccine responses quantified by the relative antibody landscape method.
Vitamin C—Protective Role in Oxidative Stress Conditions Induced in Human Normal Colon Cells by Label-Free Raman Spectroscopy and Imaging

Colorectal cancer is the second most frequently diagnosed cancer worldwide. Conventional diagnostics methods of colorectal cancer, can detect it in advanced stage. Spectroscopic methods, including Raman spectroscopy and imaging, are becoming more and more popular in medical applications, and allow fast, precise and unambiguous differentiation of healthy and cancerous samples. the most important advantage of Raman spectroscopy is ability to identify biomarkers that help in differentiation of healthy and cancerous cells based on biochemistry of sample and spectra typical for: lipids, proteins, DNA. The aim of the study was to evaluate the biochemical and structural features of human colon cell lines based on Raman spectroscopy and imaging: normal cells CCD-18 Co, normal cells CCD-18 Co under oxidative stress conditions, normal cells CCD-18 Co at first treated by using tert-Butyl hydroperoxide and then supplemented by vitamin C in high concentration to show the protective role of vitamin C in micromolar concentrations against ROS by spectroscopic methods. Raman data obtained for normal cells injured by ROS were compared with spectra typical for cancerous cells. Statistically assisted analysis has shown that normal, ROS injured and cancerous human colon cells can be distinguished based on their unique vibrational properties. The research carried out proves that label-free Raman spectroscopy may play an important role in clinical diagnostics differentiation of normal and cancerous colon cells and may be a source of intraoperative information supporting histopathological analysis.
Temporal specificity of abnormal neural oscillations during phonatory events in laryngeal dystonia

Laryngeal Dystonia is a debilitating disorder of voicing in which the laryngeal muscles are intermittently in spasm resulting in involuntary interruptions during speech. The central pathophysiology of laryngeal dystonia, underlying computational impairments in vocal motor control, remains poorly understood. Although prior imaging studies have found aberrant activity in the central nervous system during phonation in patients with laryngeal dystonia, it is not known at what timepoints during phonation these abnormalities emerge and what function may be impaired. To investigate this question, we recruited 22 adductor laryngeal dystonia patients (15 female, age range = 28.83-72.46 years) and 18 controls (8 female, age range = 27.40-71.34 years). We leveraged the fine temporal resolution of magnetoencephalography to monitor neural activity around glottal movement onset, subsequent voice onset and after the onset of pitch feedback perturbations. We examined event-related beta-band (12-30 Hz) and high-gamma band (65-150 Hz) neural oscillations. Prior to glottal movement onset, we observed abnormal frontoparietal motor preparatory activity. After glottal movement onset, we observed abnormal activity in somatosensory cortex persisting through voice onset. Prior to voice onset and continuing after, we also observed abnormal activity in the auditory cortex and the cerebellum. After pitch feedback perturbation onset, we observed no differences between controls and patients in their behavioural responses to the perturbation. But in patients, we did find abnormal activity in brain regions thought to be involved in the auditory feedback control of vocal pitch (premotor, motor, somatosensory and auditory cortices). Our study results confirm the abnormal processing of somatosensory feedback that has been seen in other studies. However, there were several remarkable findings in our study. First, patients have impaired vocal motor activity even before glottal movement onset, suggesting abnormal movement preparation. These results are significant because: (i) they occur before movement onset, abnormalities in patients cannot be ascribed to deficits in vocal performance, and (ii) they show that neural abnormalities in laryngeal dystonia are more than just abnormal responses to sensory feedback during phonation as has been hypothesised in some previous studies. Second, abnormal auditory cortical activity in patients begins even before voice onset, suggesting abnormalities in setting up auditory predictions before the arrival of auditory feedback at voice onset. Generally, activation abnormalities identified in key brain regions within the speech motor network around various phonation events not only provide temporal specificity to neuroimaging phenotypes in laryngeal dystonia but also may serve as potential therapeutic targets for neuromodulation.
Abundance-Occupancy Relationships Along Taxonomic Ranks Reveal a Consistency of Niche Differentiation in Marine Bacterioplankton With Distinct Lifestyles

Abundance-occupancy relationships (AORs) are an important determinant of biotic community dynamics and habitat suitability. However, little is known about their role in complex bacterial communities, either within a phylogenetic framework or as a function of niche breadth. Based on data obtained in a field study in the St. Lawrence Estuary, we used 16S rRNA gene sequencing to examine the vertical patterns, strength, and character of AORs for particle-attached and free-living bacterial assemblages. Free-living communities were phylogenetically more diverse than particle-attached communities. The dominant taxa were consistent in terms of their presence/absence but population abundances differed in surface water vs. the cold intermediate layer. Significant, positive AORs characterized all of the surveyed communities across all taxonomic ranks of bacteria, thus demonstrating an ecologically conserved trend for both free-living and particle-attached bacteria. The strength of the AORs was low at the species level but higher at the genus and phylum levels. These results demonstrate that an assessment of the distributions and population densities of finely resolved taxa does not necessarily improve determinations of apparent niche differences in marine bacterioplankton communities at regional scales compared with the information inferred from a broad taxonomic classification. Subject Category microbial population and community ecology
Online Closed-Loop Real-Time tES-fMRI for Brain Modulation: Feasibility, Noise/Safety and Pilot Study

Recent studies suggest that transcranial electrical stimulation (tES) can be performed during functional magnetic resonance imaging (fMRI). The novel approach of using concurrent tES-fMRI to modulate and measure targeted brain activity/connectivity may provide unique insights into the causal interactions between the brain neural responses and psychiatric/neurologic signs and symptoms, and importantly, guide the development of new treatments. However, tES stimulation parameters to optimally influence the underlying brain activity in health and disorder may vary with respect to phase, frequency, intensity and electrode’s montage. Here, we delineate how a closed-loop tES-fMRI study of frontoparietal network modulation can be designed and performed. We also discuss the challenges of running a concurrent tES-fMRI, describing how we can distinguish clinically meaningful physiological changes caused by tES from tES-related artifacts. There is a large methodological parameter space including electrode types, electrolytes, electrode montages, concurrent tES-fMRI hardware, online fMRI processing pipelines and closed-loop optimization algorithms that should be carefully selected for closed-loop tES-fMRI brain modulation. We also provide technical details on how safety and quality of tES-fMRI settings can be tested, and how these settings can be monitored during the study to ensure they do not exceed safety standards. The initial results of feasibility and applicability of closed-loop tES-fMRI are reported and potential hypotheses for the outcomes are discussed. Highlight points Methodological details of a closed-loop tES-fMRI study protocol are provided. The protocol is performed successfully on a frontoparietal network without side-effects. The temperature of electrodes in concurrent tES-fMRI remains in the safe range. Properly setup concurrent tES does not introduce MRI artifacts and noise. Simplex optimizer could be used to find an optimal tES stimulation parameter.
Understanding the genetic pathology of Stargardt disease: a review of current findings and challenges

ABSTRACT Introduction: Stargardt macular dystrophy (STGD1), an autosomal recessive disorder, is caused by genetic mutations affecting ATP-Binding Cassette, subfamily A, member 4 (ABCA4). The genetic pathology of STGD1 is complex. Over 1200 disease-causing ABCA4 mutations have been identified which vary in disease severity and geographic/ethnic frequency. Areas Covered: This article provides an introduction to STGD1 and its pathophysiology, including a summary of the normal visual cycle and a description of the ABCA4 protein. The current understanding of the genetic pathology of STGD1 is reviewed, including the relationship between STGD1 and similar diseases, genotype-phenotype correlations of ABCA4-associated retinopathy, types of disease-causing genetic variations, geographic/ethnic considerations, and gene therapy. Expert Opinion: In STGD1, ABCA4 gene mutations and gene variation combinations in individuals can be used to predict phenotype, and can be categorized by severity. However, some cases of STGD1 remain unsolved, and disease severity for many variants remains unknown. Increasing our understanding of the genetic pathology of Stargardt disease will drive the development of future therapies.
Face dissimilarity judgements are predicted by representational distance in deep neural networks and principal-component face space

Despite the importance of face perception in human and computer vision, no quantitative model of perceived face dissimilarity exists. 1 We designed an efﬁcient behavioural task to collect dissimilarity and same/different identity judgements for 232 pairs of realistic faces 2 that densely sampled geometric relationships in a face space derived from principal components of 3D shape and texture (Basel Face 3 Model, BFM). In a comparison of 15 models, we found that representational distances in deep neural networks (DNNs) and Euclidean 4 distances within BFM space predicted human judgements best. A face-trained DNN explained unique variance over simpler models 5 and was statistically indistinguishable from the noise ceiling. Sigmoidal transformation of distances improved performance for all 6 models. Identity judgements were better predicted by Euclidean than angular or radial distances in BFM space. DNNs provide 7 the best available image-computable models of perceived face dissimilarity. The success of BFM space suggests that human face 8 perception is attuned to the natural distribution of faces. 9
Improved data sets and evaluation methods for the automatic prediction of DNA-binding proteins

Motivation Accurate automatic annotation of protein function relies on both innovative models and robust datasets. Due to their importance in biological processes, the identification of DNA-binding proteins directly from protein sequence has been the focus of many studies. However, the data sets used to train and evaluate these methods have suffered from substantial flaws. We describe some of the weaknesses of the data sets used in previous DNA-binding protein literature and provide several new data sets addressing these problems. We suggest new evaluative benchmark tasks that more realistically assess real-world performance for protein annotation models. We propose a simple new model for the prediction of DNA-binding proteins and compare its performance on the improved data sets to two previously published models. Additionally, we provide extensive tests showing how the best models predict across taxonomies. Results Our new gradient boosting model, which uses features derived from a published protein language model, outperforms the earlier models. Perhaps surprisingly, so does a baseline nearest neighbor model using BLAST percent identity. We evaluate the sensitivity of these models to perturbations of DNA-binding regions and control regions of protein sequences. The successful data-driven models learn to focus on DNA-binding regions. When predicting across taxonomies, the best models are highly accurate across species in the same kingdom and can provide some information when predicting across kingdoms. Code and Data Availability All the code and data for this paper can be found at https://github.com/AZaitzeff/tools_for_dna_binding_proteins. Contact alexander.zaitzeff@twosixtech.com
Development of Perceptual Inhibition in Adolescents - A Critical Period?

Recent studies suggest that the developmental curves in adolescence, related to the development of executive functions, could be fitted to a non-linear trajectory of development with progressions and retrogressions. Therefore, the present study proposes to analyze the pattern of development in Perceptual Inhibition (PI), considering all stages of adolescence (early, middle, and late) in intervals of one year. To this aim, we worked with a sample of 275 participants between 10 and 25 years, who performed a joint visual and search task (to measure PI). We have fitted ex-Gaussian functions to the probability distributions of the mean response time across the sample and performed a covariance analysis (ANCOVA). The results showed that the 10- to 13-year-old groups performed similarly in the task and differ from the 14- to 19-year-old participants. We found significant differences between the older group and all the rest of the groups. We discuss the important changes that can be observed in relation to the nonlinear trajectory of development that would show the PI during adolescence.
Assessing Determinants of Continuance Intention towards Personal Cloud Services: Extending UTAUT2 with Technology Readiness

In addition to the rapid development of global information and communications technology (ICT) and the Internet, recent rapid growth in cloud computing technology represents another important trend. Individual continuance intention towards information technology is a critical area in which information systems research can be performed. This study aims to develop an integrated model designed to explain and predict an individual’s continuance intention towards personal cloud services based on the concepts of technology readiness (TR) and the unified theory of acceptance and use of technology 2 (UTAUT2), moderated by gender, age, and experience of personal cloud services. The key results of the partial least square test largely support the proposed model’s validity and the significant impact of effort expectancy, social influence, hedonic motivation, price value, habit, and technology readiness on continuance intention towards personal cloud services. In addition to providing symmetric theoretical support with the proposed model and transforming the individual characteristics of TR into UTAUT2, this study could be used to enhance and analyze users’ adoption of personal cloud services and also increase the symmetry of the model’s explanation and prediction. The findings from this research contribute to providing practical implications and academic resources as well as improving our understanding of personal cloud service applications.
Impact of Managerial Responses on Product Sales: Examining the Moderating Role of Competitive Intensity and Market Position

Online review platforms have become very popular in recent years, generating massive numbers of online reviews and thus enticing numerous enterprises to respond to reviews. Although the economic impact (e.g., sales impact) of managerial responses is well recognized, it is unclear whether such an impact is moderated by competitive intensity and market position. This study examines the moderating effects of competitive intensity and market position in the relationship between managerial responses and sales. Using a panel dataset from one of the largest restaurant review platforms in China, this research found that the influence of the volume of managerial responses to positive word-of-mouth (WOM) on sales declined with increasing competitive intensity and decreasing market position. Moreover, we found the volume and degree of personalization of managerial responses to negative WOM to be more important for enterprises with a low market position versus those with a high market position. Our results provide insights into the effectiveness of managerial responses in different environments. We also offer managerial implications to service providers on response strategies.
Determination of Critical Limit for Copper in Soil-Plant and Grain for Predicting Response of Rice to Copper Application in Soil

ABSTRACT In order to identify critical limit of copper (Cu) in soil, grain, and straw of rice plant, soil samples were collected from twenty; 12, 5, and 3 soil locations of low, medium, and high Cu status from Madurai district, Tamil Nadu, India for pot culture experiment. Based on the results of pot culture experiment, the critical limits of Cu established for straw and grain of rice both by graphical and statistical methods were 8.07 and 5.22 mg kg−1 respectively. Similarly, critical limits of soil available Cu as per the graphical and statistical methods was found to be 0.98 and 0.97 mg kg−1 respectively. Rice plants were highly responded to Cu application in soils below this critical limit whereas soils with Cu greater than 0.98 mg kg−1 did not respond. The grain and straw yield of rice increased with increasing levels of Cu and application of 1 mg kg−1 Cu or 8 kg ha−1 as copper sulfate was sufficient to alleviate the Cu deficiency and also to attain higher yield of rice in the district.
The Effects of Isoflurane Anesthesia on Hematologic and Plasma Biochemical Values of American Kestrels

The effect of repeat blood sampling and anesthesia on hematologic and plasma bio- chemical values of American kestrels (Falco sparverius) was investigated. In a validation study, blood samples from six awake kestrels were collected twice, 10 minutes apart, and results of hematologic testing and plasma biochemical analysis were compared. Of the analytes measured, only the pack cell volume (PCV) value significantly changed (decreased) in the second sample. A weight-normalized model was used to correct for the dilutional effect of the first blood collection on the second sample values. However, with correction, the decrease in the PCV value remained, suggesting that this decrease was not likely to be caused solely by sampling-induced hemodilution. In a second study of 29 kestrels, hematologic and plasma biochemical values were compared before and after 10 minutes of isoflurane anesthesia. In this comparison, significant differences were ob- served in the basophil count and in the values of albumin, alanine aminotransferase, alkaline phos- phatase, blood urea nitrogen, cholesterol, creatinine, globulin, PCV, plasma protein, potassium, total protein, and uric acid. However, after correcting for the effects of sampling dilution, only the changes in uric acid and potassium values could be attributed to the effects of anesthesia. Age, sex, and weight-related effects were also observed for selected values. Thus, the combined effect of isoflurane anesthesia and repeat blood sampling causes more dramatic changes in analyte values than repeat sampling alone. Therefore, both the method and frequency of blood sample collection in kestrels must be considered when interpreting blood values.
High hydrostatic pressure applications on liquid whole egg

SUMMARY High hydrostatic pressure (HHP) treatment at the pressure and temperature range of 300–450 MPa and 0–50°C for up to 30 min can be used successfully to inactivate several bacteria in liquid whole egg (LWE). On the other hand, to avoid egg protein coagulation, pressure levels ≤ 300 MPa and temperature levels ≤ 20°C should be selected and holding times ≤ 5 min are desirable for commercial HHP application. However, these conditions are not suitable for pasteurising LWE. Therefore, antimicrobial agents such as nisin, in combination with HHP or successive use of HHP with heat or other non-thermal methods such as pulsed electric field or ultrasound have been tried for maximum microbial inactivation with minimum changes in physical, chemical and functional properties of LWE. This review compiles the studies on HHP and LWE. While microbial inactivation by HHP and inactivation kinetics is the main focus, the impact of HHP on functional properties of LWE is also discussed.