Miracle-dz/UniFAR-FTUs huggingface dataset:
Current and Investigational Agents Targeting the Phosphoinositide 3‐Kinase Pathway

Prevalent molecular alterations of the phosphoinositide 3‐kinase (PI3K) pathway are found on solid tumors and are expressed in leukocytes, making it a desirable target in both solid and hematologic malignancies. In recent years, two agents targeting this pathway have been approved by the United States Food and Drug Administration, idelalisib and copanlisib, with many others under investigation. Due to the off‐target effects seen with these agents, those under development have varying isoform specificity that mitigates toxicity. In this review, we attempt to illustrate the varying differences among these agents, both mechanistically as well as highlight differences in their respective adverse effect profiles.
Central Compensation in Auditory Brainstem after Damaging Noise Exposure

Abstract Noise exposure is one of the most common causes of hearing loss and peripheral damage to the auditory system. A growing literature suggests that the auditory system can compensate for peripheral loss through increased central neural activity. The current study sought to investigate the link between noise exposure, increases in central gain, synaptic reorganization, and auditory function. All axons of the auditory nerve project to the cochlear nucleus, making it a requisite nucleus for sound detection. As the first synapse in the central auditory system, the cochlear nucleus is well positioned to respond plastically to loss of peripheral input. To investigate noise-induced compensation in the central auditory system, we measured auditory brainstem responses (ABRs) and auditory perception and collected tissue from mice exposed to broadband noise. Noise-exposed mice showed elevated ABR thresholds, reduced ABR wave 1 amplitudes, and spiral ganglion neuron loss. Despite peripheral damage, noise-exposed mice were hyperreactive to loud sounds and showed nearly normal behavioral sound detection thresholds. Ratios of late ABR peaks (2–4) relative to the first ABR peak indicated that brainstem pathways were hyperactive in noise-exposed mice, while anatomical analysis indicated there was an imbalance between expression of excitatory and inhibitory proteins in the ventral cochlear nucleus. The results of the current study suggest that a reorganization of excitation and inhibition in the ventral cochlear nucleus may drive hyperactivity in the central auditory system. This increase in central gain can compensate for peripheral loss to restore some aspects of auditory function.
Seeking information from government resources: A comparative analysis of two communities' Web searching of municipal government Web sites

The published Web search literature lacks the analysis of large amounts of unobtrusively collected data such as those found in Web logs to determine the types of information sought through municipal government Web sites and how these data might differ or be similar when comparing two municipal government Web sites. This study analyzes a large purposive sample of three years’ worth of query data that resulted from hundreds of thousands of Web searches submitted by information seekers through two urban municipal government Web sites; one for London, Ontario (www.london.ca) and the other for Kitchener, Ontario (www.kitchener.ca).
Profiles of Risk for Suicidal Behavior in Past and Current United States Military Personnel: Latent Profile Analysis of Current Risk Factors

Person-centered approaches are underutilized to identify people with shared risk profiles. In this study, an at-risk sample of 773 past/current military personnel (Mage = 31.3 years, SD = 6.8) with current ideation (90.6%) and/or a prior suicide attempt (43.9%) were assessed using latent profile analysis. Variables included prior suicide attempts, suicidal ideation, alcohol/drug use, insomnia, depression, belongingness, burdensomeness, and post-traumatic stress disorder symptoms. Three classes emerged: Low Symptoms (N = 502), Elevated Suicidality (N = 176), and Elevated Substance Use (N = 95). At 1-month follow-up, the Elevated Suicidality and Elevated Substance Use classes had the highest odds of suicidal behavior. The finding concerning the Elevated Substance Use class suggests it may represent a distinct short-term risk group in military personnel.
Staging Uveal Melanoma with Whole-Body Positron-Emission Tomography/Computed Tomography and Abdominal Ultrasound: Low Incidence of Metastatic Disease, High Incidence of Second Primary Cancers

PURPOSE: The purpose of this study was to report the results of staging primary uveal melanoma with whole-body (18) fluorodeoxyglucose (FDG) positron-emission tomography/computed tomography (PET/CT) and abdominal ultrasound. MATERIALS AND METHODS: From January 2012, patients with uveal melanoma over 4 mm in thickness were staged with FDG PET/CT and abdominal ultrasound. RESULTS: Over 2 years, 108 patients with medium-to-large melanoma underwent dual imaging. According to the tumor, node, and metastasis classification, there were 75% T3, 11% T2, and 14% T1 uveal melanomas. Only, three of 108 patients (2.8%) were found to have metastatic uveal melanoma. All three had liver metastases confirmed following biopsy; one of three had additional extrahepatic widespread metastases. In these three patients, liver findings using both imaging techniques were consistent in one patient. In the second case, abdominal ultrasound missed the diagnosis of metastatic disease; however, FDG PET/CT revealed intense metabolic activity of the liver. In the third case, PET/CT missed the liver metastases; however, this was identified on abdominal ultrasound. PET/CT identified incidental second primary malignancies in 10 patients (9%). Second malignancies were found in the lung, breast, colon, thyroid, and adrenal gland. Abdominal ultrasound detected benign hepatic abnormalities in 20 patients (18%). CONCLUSIONS: Whole-body PET/CT and abdominal ultrasound complement each other in the staging of uveal melanoma. Benign hepatic abnormalities found using ultrasound is common. Of importance, a second asymptomatic primary malignancy associated with uveal melanoma was detected almost one in 10 patients.
Assessment of surgeon experience with femtosecond laser-assisted cataract surgery

Purpose To evaluate the collective user experience with an image-guided femtosecond laser (FSL) for cataract surgery in a high-volume, multi-surgeon, ambulatory surgical center. Subjects and methods A detailed online survey was distributed to all surgeons in a single ambulatory surgical center who had performed cataract surgery using a FSL since its acquisition in December 2012. Information collected included the number of cases performed, typical surgical techniques and parameters, satisfaction with individual features of the laser (rated on a scale from 1=completely unsatisfied to 10=extremely satisfied) and commentary on ease of use and suggested improvements. Results Seventeen of 30 surgeons (56.7%) completed the survey, representing a case volume of 1,967 eyes. Fourteen surgeons (82.4%) felt they required ≤10 cases with the FSL to operate with the same safety and control as in standard phacoemulsification surgery. Satisfaction was highest for capsulotomies, lens fragmentation, lens softening, arcuate incisions and the graphic user interface (mean scores 9.4, 8.7, 8.7, 7.2 and 8.9, respectively). Preferred capsulotomy diameter was 4.8–5.2 mm (64.7% of respondents). About half (52.9%) of respondents centered the capsulotomy on the pupil and the other 47.1% centered the capsulotomy using optical coherence tomography. Most respondents (81.3%) preferred transepithelial arcuate incisions compared to intrastromal incisions. Satisfaction was lowest with FSL-created, main, clear corneal incisions and paracenteses (mean scores 4.4 and 4.2, respectively). Conclusion Laser-assisted cataract surgery has a short learning curve and a high rate of user satisfaction. Further software and hardware development is warranted to improve user satisfaction with peripheral and clear corneal incisions.
Antimicrobial quaternary ammonium organosilane cross-linked nanofibrous collagen scaffolds for tissue engineering

Introduction In search for cross-linkers with multifunctional characteristics, the present work investigated the utility of quaternary ammonium organosilane (QOS) as a potential cross-linker for electrospun collagen nanofibers. We hypothesized that the quaternary ammonium ions improve the electrospinnability by reducing the surface tension and confer antimicrobial properties, while the formation of siloxane after alkaline hydrolysis could cross-link collagen and stimulate cell proliferation. Materials and methods QOS collagen nanofibers were electrospun by incorporating various concentrations of QOS (0.1%–10% w/w) and were cross-linked in situ after exposure to ammonium carbonate. The QOS cross-linked scaffolds were characterized and their biological properties were evaluated in terms of their biocompatibility, cellular adhesion and metabolic activity for primary human dermal fibroblasts and human fetal osteoblasts. Results and discussion The study revealed that 1) QOS cross-linking increased the flexibility of otherwise rigid collagen nanofibers and improved the thermal stability; 2) QOS cross-linked mats displayed potent antibacterial activity and 3) the biocompatibility of the composite mats depended on the amount of QOS present in dope solution – at low QOS concentrations (0.1% w/w), the mats promoted mammalian cell proliferation and growth, whereas at higher QOS concentrations, cytotoxic effect was observed. Conclusion This study demonstrates that QOS cross-linked mats possess anti-infective properties and confer niches for cellular growth and proliferation, thus offering a useful approach, which is important for hard and soft tissue engineering and regenerative medicine.
Diurnal periodicity of conidia of aquatic hyphomycetes in water and entrapment on latex-coated slides in two South Indian streams

ABSTRACT Aquatic hyphomycete conidial trapping efficiency by the banyan (F. benghalensis L.) latex-coated glass slides was tested diurnally (3 h intervals) in the Western Ghats (Sampaje) and west coast (Konaje) streams in relation to abiotic factors (humidity, air temperature and water temperature). The conidial trapping efficiency of latex-coated slides was compared with plain glass slides and drift conidia in water. Three methods of assessment showed higher species richness, conidial richness and diversity in Sampaje than in Konaje stream. In both streams, species richness, conidial richness and diversity in latex-coated slides were the highest followed by conidia in water and plain slides. Three-way ANOVA revealed significant differences in overall species and conidial richness between the streams, sampling methods and time of sampling (p < 0.001). Multiple comparisons by Holm–Sidak test revealed significant differences in overall species and conidial richness between Sampaje and Konaje (p < 0.001); latex-coated slides and plain slides (p < 0.001); latex-coated slides and water filtration (p < 0.001); plain slides and water filtration (p < 0.001). Total species, total conidia and diversity assessed by the three methods peaked during 12 am–3 am in Sampaje stream, while during 3 am–6 am in Konaje stream. Cooler conditions due to relatively low water temperature favoured higher diversity of aquatic hyphomycetes in Sampaje than in Konaje stream. The three methods employed in the present study were not biased towards scolecoid or stauroid conidia. The top five species in both streams was composed of both types of conidia corroborating earlier annual or biannual studies in Konaje and Sampaje streams. Thus, assessment of population of aquatic hyphomycetes using banyan latex-coated slides will be advantageous over plain slides and drift conidia in streams.
An explicit structure‐preserving numerical scheme for EPDiff

We present a new structure‐preserving numerical scheme for solving the Euler‐Poincaré Differential (EPDiff) equation on arbitrary triangle meshes. Unlike existing techniques, our method solves the difficult non‐linear EPDiff equation by constructing energy preserving, yet fully explicit, update rules. Our approach uses standard differential operators on triangle meshes, allowing for a simple and efficient implementation. Key to the structure‐preserving features that our method exhibits is a novel numerical splitting scheme. Namely, we break the integration into three steps which rely on linear solves with a fixed sparse matrix that is independent of the simulation and thus can be pre‐factored. We test our method in the context of simulating concentrated reconnecting wavefronts on flat and curved domains. In particular, EPDiff is known to generate geometrical fronts which exhibit wave‐like behavior when they interact with each other. In addition, we also show that at a small additional cost, we can produce globally‐supported periodic waves by using our simulated fronts with wavefronts tracking techniques. We provide quantitative graphs showing that our method exactly preserves the energy in practice. In addition, we demonstrate various interesting results including annihilation and recreation of a circular front, a wave splitting and merging when hitting an obstacle and two separate fronts propagating and bending due to the curvature of the domain.
Personalized Visual-Interactive Music Classification

We present an interactive visual music classification tool that will allow users to automatically structure music collections in a personalized way. With our approach, users play an active role in an iterative process of building classification models, using different interactive interfaces for labeling songs. The interactive tool conflates interfaces for the detailed analysis at different granularities, i.e., audio features, music songs, as well as classification results at a glance. Interactive labeling is provided with three complementary interfaces, combining model-centered and human-centered labeling-support principles. A clean visual design of the individual interfaces depicts complex model characteristics for experts, and indicates our work-in-progress towards the abilities of non-experts. The result of a preliminary usage scenario shows that, with our system, hardly any knowledge about machine learning is needed to create classification models of high accuracy with less than 50 labels.
Comparison of Three Junctional Tourniquets Using a Randomized Trial Design

Abstract Background: Hemorrhage remains a leading cause of death in both civilian and military settings. Of preventable deaths from hemorrhage, a significant portion occurs from junctional wounds that are not amenable to traditional extremity tourniquets. Junctional tourniquets (JTQs) can potentially provide hemorrhage control by compressing the arteries at the junction of the trunk and extremities. The FDA has cleared 3 JTQ products: The Combat Ready Clamp (CRoC®), the Junctional Emergency Treatment Tool (JETT™), and the SAM® Junctional Tourniquet (SJT). However, little is known regarding which of these JTQs is superior in application time, effectiveness in pulse elimination, effectiveness during transport, and user preference. Methods: Active duty corpsmen (N = 49) were given standardized instruction and hands-on training with the CRoC®, JETT™, and SJT, then sequentially applied each JTQ unilaterally to a fellow study participant in a randomized order. Pulse elimination was determined by Doppler ultrasound at the dorsalis pedis immediately then reevaluated after a short transport. User preference data were collected following testing. Data were analyzed using repeated measures ANOVA and non-parametric statistics at p < 0.05. Results: The CRoC® was significantly slower in application time than the JETT™ and SJT. Effectiveness was similar for CRoC®, JETT™, and SJT. Effectiveness during transport was significantly higher for SJT than for the JETT™, but no JTQ performed well during transport (24–48% effectiveness). SJT ranked first in perceived ease of use, stability, and reliability, and in user trust and overall preference. Participants provided cogent suggestions for product improvement. Conclusions: All JTQ devices performed poorly during transport. Combined, present findings highlight the potential of JTQ products for saving lives threatened by junctional wounds, but also highlight the need for specific product improvements towards fostering JTQ performance in patient transport.
Active Students Are Healthier and Happier Than Their Inactive Peers: The Results of a Large Representative Cross-Sectional Study of University Students in Ireland.

BACKGROUND Time spent in university represents a period of transition and may be an appropriate time to promote physical activity among young adults. The aim of this study was to assess participation of university students in sport and physical activity in Ireland and to explore the association between physical activity and perceptions of overall health, mental health, and happiness. METHODS The Student Activity and Sport Study Ireland was a cross-sectional online survey among a representative sample (n = 8122) of university students in Ireland. Binary logistic regressions were performed to examine associations between self-reported physical activity and gender (predictor variables) and individual perceptions of overall health, mental health, and happiness (binary outcomes). RESULTS Only 64.3% of respondents met the recommended level of 150 minutes of moderate to vigorous physical activity per week with males significantly more active than females (72.1% vs 57.8% meeting guidelines). Those meeting physical activity guidelines were more likely to report greater overall health and higher mental health and happiness scores compared with their inactive peers. CONCLUSIONS Active students enjoy better health (overall and mental) and are happier than their inactive peers. This provides a clear rationale for providing students with opportunities to be active at university. The data provide a baseline to monitor changes in physical activity patterns.
Isolation and characterization of the bioactive metabolites from the soil derived fungus Trichoderma viride

ABSTRACT The aim of the present study was to evaluate different biological activities of Trichoderma viride fungus (Family Hypocreaceae). Trichoderma viride isolated for the first time from the cucumber soil (rhizosphere). It was tested as antimicrobial, antioxidant and anticancer agent. Trichoderma viride from the cucumber soil (rhizosphere) caused inhibition of the mycelial growth of Fusarium solani, Rhizoctonia solani and Sclerotium rolfsii. Also, the alcoholic extract of the fungal mycelia proved a potent antibacterial activity against Bacillus subtilis, Escherichia coli and Pseudomonas fluorescens. In addition, it exhibited a significant antifungal activity against Candida albicans, Fusarium solani, Fusarium oxysporium, Rhizoctonia solani and Pythium ultimum at 100 µg/disc. Study of the antimicrobial and antioxidant activities of the volatile constituents had been done. The in vitro antioxidant, anticancer and antiviral activities of the isolated proteins, and carbohydrates were determined. Furthermore, the volatile constituents were isolated from fresh mycelia of Trichoderma viride and subjected to GC/MS analysis. Total protein (10%), carbohydrate (19.57%), steroidal (13.95%) and triterpenoidal content (38.34%) were determined in the alcoholic extract of Trichoderma viride mycelia. In conclusion, this fungus showed antioxidant, anticancer, antiviral and antibacterial effects. Further studies must be done to identify the molecules responsible for its effect and to consider its application in the pharmacological and medicinal purposes.
Real Time Implementation of Overcome Frequency Jammer

----Mobile phones play an important role in our day to day life. Inspite of various limitations, it is a part and partial of human life. Hence we can’t avoid the usage of mobile phones, thus we have to eliminate its drawbacks to make it more efficient. This paper also deals with the most common drawback of using mobile phones, it is nothing but usage of mobile phones in prohibited areas. A common board or a watch keeper insists the people who get inside the mobile phone prohibited areas like Temples, Conference halls, Hospitals etc., to switch off their mobile phones. It is prohibited in those areas in order to avoid noise pollution, mainly. Though it is insisted some people won’t do it and some won’t notice it. This is all about this project, to automatically disable the mobile phones in these prohibited
A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates

Until recently, most phylogenetic and population genetics studies of nonhuman primates have relied on mitochondrial DNA and/or a small number of nuclear DNA markers, which can limit our understanding of primate evolutionary and population history. Here, we describe a cost-effective reduced representation method (ddRAD-seq) for identifying and genotyping large numbers of SNP loci for taxa from across the New World monkeys, a diverse radiation of primates that shared a common ancestor ~20–26 mya. We also estimate, for the first time, the phylogenetic relationships among 15 of the 22 currently-recognized genera of New World monkeys using ddRAD-seq SNP data using both maximum likelihood and quartet-based coalescent methods. Our phylogenetic analyses robustly reconstructed three monophyletic clades corresponding to the three families of extant platyrrhines (Atelidae, Pitheciidae and Cebidae), with Pitheciidae as basal within the radiation. At the genus level, our results conformed well with previous phylogenetic studies and provide additional information relevant to the problematic position of the owl monkey (Aotus) within the family Cebidae, suggesting a need for further exploration of incomplete lineage sorting and other explanations for phylogenetic discordance, including introgression. Our study additionally provides one of the first applications of next-generation sequencing methods to the inference of phylogenetic history across an old, diverse radiation of mammals and highlights the broad promise and utility of ddRAD-seq data for molecular primatology.
Harnessing the MinION: An example of how to establish long‐read sequencing in a laboratory using challenging plant tissue from Eucalyptus pauciflora

Long‐read sequencing technologies are transforming our ability to assemble highly complex genomes. Realizing their full potential is critically reliant on extracting high‐quality, high‐molecular‐weight (HMW) DNA from the organisms of interest. This is especially the case for the portable MinION sequencer which enables all laboratories to undertake their own genome sequencing projects, due to its low entry cost and minimal spatial footprint. One challenge of the MinION is that each group has to independently establish effective protocols for using the instrument, which can be time‐consuming and costly. Here, we present a workflow and protocols that enabled us to establish MinION sequencing in our own laboratories, based on optimizing DNA extraction from a challenging plant tissue as a case study. Following the workflow illustrated, we were able to reliably and repeatedly obtain >6.5 Gb of long‐read sequencing data with a mean read length of 13 kb and an N50 of 26 kb. Our protocols are open source and can be performed in any laboratory without special equipment. We also illustrate some more elaborate workflows which can increase mean and average read lengths if this is desired. We envision that our workflow for establishing MinION sequencing, including the illustration of potential pitfalls and suggestions of how to adapt it to other tissue types, will be useful to others who plan to establish long‐read sequencing in their own laboratories.