Miracle-dz/UniFAR-FTUs huggingface dataset:
Intrinsic pKas of ionizable residues in proteins: An explicit solvent calculation for lysozyme

Molecular dynamics simulations of triclinic hen egg white lysozyme in aqueous solution were performed to calculate the intrinsic pKas of 14 ionizable residues. An all‐atom model was used for both solvent and solute, and a single 180 ps simulation in conjunction with a Gaussian fluctuation analysis method was used. An advantage of the Gaussian fluctuation method is that it only requires a single simulation of the system in a reference state to calculate all the pKas in the protein, in contrast to multiple simulations for the free energy perturbation method. pKint shifts with respect to reference titratable residues were evaluated and compared to results obtained using a finite difference Poisson‐Boltzmann (FDPB) method with a continuum solvent model; overall agreement with the direction of the shifts was generally observed, though the magnitude of the shifts was typically larger with the explicit solvent model. The contribution of the first solvation shell to the total charging free energies of the titratable groups was explicitly evaluated and found to be significant. Dielectric shielding between pairs of titratable groups was examined and found to be smaller than expected. The effect of the approximations used to treat the long‐range interactions on the pKint shifts is discussed. © 1994 Wiley‐Liss, Inc.
Evaluation of an Expanded Microarray for Detecting Antibiotic Resistance Genes in a Broad Range of Gram-Negative Bacterial Pathogens

ABSTRACT A microarray capable of detecting genes for resistance to 75 clinically relevant antibiotics encompassing 19 different antimicrobial classes was tested on 132 Gram-negative bacteria. Microarray-positive results correlated >91% with antimicrobial resistance phenotypes, assessed using British Society for Antimicrobial Chemotherapy clinical breakpoints; the overall test specificity was >83%. Microarray-positive results without a corresponding resistance phenotype matched 94% with PCR results, indicating accurate detection of genes present in the respective bacteria by microarray when expression was low or absent and, hence, undetectable by susceptibility testing. The low sensitivity and negative predictive values of the microarray results for identifying resistance to some antimicrobial resistance classes are likely due to the limited number of resistance genes present on the current microarray for those antimicrobial agents or to mutation-based resistance mechanisms. With regular updates, this microarray can be used for clinical diagnostics to help accurate therapeutic options to be taken following infection with multiple-antibiotic-resistant Gram-negative bacteria and prevent treatment failure.
Intercellular signaling and signal transduction in C. elegans.

Intercellular signaling and signal transduction underlie most aspects of development and behavior. To understand any specific case we must identify the ligands, receptors and transducers, as well as regulators that modulate the activity of the signaling pathway. To understand more general aspects of signaling, we have to address the questions: To what extent are there modular signaling pathways, i.e. pathways that act as coherent units? How many such pathways are there? What factors affect the action of a universal pathway in particular cases? How widely is a given component or pathway used? How are the effects of multiple signaling pathways integrated? Here I discuss the use of Caenorhabditis elegans molecular genetics to study problems of intercellular signaling and signal transduction.
Biomechanical analysis of knee and trunk in badminton players with and without knee pain during backhand diagonal lunges

Abstract The contribution of core neuromuscular control to the dynamic stability of badminton players with and without knee pain during backhand lunges has not been investigated. Accordingly, this study compared the kinematics of the lower extremity, the trunk movement, the muscle activation and the balance performance of knee-injured and knee-uninjured badminton players when performing backhand stroke diagonal lunges. Seventeen participants with chronic knee pain (injured group) and 17 healthy participants (control group) randomly performed two diagonal backhand lunges in the forward and backward directions, respectively. This study showed that the injured group had lower frontal and horizontal motions of the knee joint, a smaller hip–shoulder separation angle and a reduced trunk tilt angle. In addition, the injured group exhibited a greater left paraspinal muscle activity, while the control group demonstrated a greater activation of the vastus lateralis, vastus medialis and medial gastrocnemius muscle groups. Finally, the injured group showed a smaller distance between centre of mass (COM) and centre of pressure, and a lower peak COM velocity when performing the backhand backward lunge tasks. In conclusion, the injured group used reduced knee and trunk motions to complete the backhand lunge tasks. Furthermore, the paraspinal muscles contributed to the lunge performance of the individuals with knee pain, whereas the knee extensors and ankle plantar flexor played a greater role for those without knee pain.
Non-prescription medicine misuse, abuse and dependence: a cross-sectional survey of the UK general population.

Background Non-prescription medicines (NPMs) can be misused, abused or lead to dependence, but the prevalence of these problems within the UK general population was unknown. The aim of this study was to estimate the prevalence of self-reported misuse, abuse and dependence to NPMs. Methods A cross-sectional postal survey was sent to 1000 individuals aged � 18 randomly drawn from the UK Edited Electoral Register. Results A response rate of 43.4% was achieved. The lifetime prevalence of NPM misuse was 19.3%. Lifetime prevalence of abuse was 4.1%. Younger age, having a long-standing illness requiring regular NPM use and ever having used illicit drugs or legal highs were predictive of misuse/ abuse of NPMs. In terms of dependence, lifetime prevalence was 2% with 0.8% currently dependent and 1.3% dependent in the past. Dependence was reported with analgesics (with and without codeine), sleep aids and nicotine products. Conclusion Given the increasing emphasis on self-care and empowering the public to manage their health with NPMs, the findings highlight the need for improved pharmacovigilance of these medicines to maximize benefits with minimal risk. Healthcare providers need to be aware of the potential for misuse, abuse and dependence, particularly in patients with long-term illness.
Clostridium perfringens urease genes are plasmid borne

Although many bacteria are ureolytic, and in some cases urease acts as a virulence factor, the urease phenotype has not been analyzed in the anaerobic pathogen Clostridium perfringens. In this study, approximately 2% of C. perfringens strains, representing the principal biotypes, were found to harbor the urease structural genes, ureABC, and these were localized on large plasmids that often encode, in addition, the lethal epsilon or iota toxins or the enterotoxin. This represents the first report of a plasmid-encoded urease in a gram-positive bacterium. The C. perfringens enzyme was highly similar to the ureases of other bacteria and cross-reacted with antibodies raised against the urease purified from Helicobacter pylori. Urease production was inhibited by urea and induced under growth conditions where the availability of nitrogen sources was limiting. To date, this form of regulation has been observed only for chromosomal ureABC genes.
Classifiers combination for forms sorting

A method of combination applied to automatic forms identification is presented. This method separately makes use of two classifiers which are respectively based on a global and a structural approach of the document. Each of these classifiers is presented and combination methods are discussed. Then, some results of combination using Dempster-Shafer evidence theory are emphasized.
Color Doppler imaging of the ophthalmic artery in patients with chronic heart failure

Purpose: To evaluate the ophthalmic artery hemodynamics in patients with chronic heart failure. Methods: Doppler parameters of ophthalmic artery of 18 patients with chronic heart failure in different stages of the disease were compared with 21 healthy volunteers (control group). These parameters were also correlated with echocardiographic assessments and clinical cardiologic status. Results: Mean diastolic velocity was 5.14 ± 2.4 cm/s in the chronic heart failure group and 7.44 ± 3.5 cm/s in the control group (p=0.007). Mean resistance index of the ophthalmic artery was 0.76 ± 0.08 in the chronic heart failure group and 0.70 ± 0.08 in the control group (p=0.04). Mean systolic velocity of the ophthalmic artery was 22.03 ± 7.7 cm/s in the chronic heart failure group and 25.32 ± 9.2 cm/s in the control group (p=0.24). There was a negative correlation between the resistance index of the ophthalmic artery and systemic blood pressure of patients with chronic heart failure (r= -0.47, p=0.007). Diastolic velocity of the ophthalmic artery correlated positively with systemic blood pressure (r=0.44, p=0.02). Conclusion: Lower diastolic velocity and higher resistance index were observed in the ophthalmic artery of chronic heart failure patients when compared to the control group, which probably reflects the presence of orbital vasoconstriction in response to low cardiac output. Therefore, the influence of these findings on the structure and function of the optic nerve head deserves investigation.
Evolution of the caregiving experience in the initial 2 years following stroke.

Relationships between stroke survivor and family caregiver factors and the caregiver's health-related quality of life (HRQL) and overall quality of life (QoL) were examined in 97 dyads during the first and second years after stroke. Compared to age- and sex-matched population norms, caregivers scored significantly lower on the mental subscales of HRQL, and differences were greater for women than for men. Caregiver characteristics (older age, less burden, and fewer physical symptoms) were associated with better HRQL (mental summary scale) in the first year, with similar findings in the second year. Moderate stroke survivor physical impairment and caregiver characteristics (younger age and better HRQL) were associated with better QoL in the first year. During the second year poorer caregiver physical and mental health and caring for a stroke survivor with communication difficulties were associated with diminished QoL.
Geographical Variations in the Presentation of Ruptured Aneurysms of Sinuses of Valsalva: Evaluation of Surgical Repair

From 1981 to 1992, 13 male and 7 female patients underwent surgical correction for ruptured aneurysms of sinus of valsalva. A total surgical experience of 22 procedures including 2 reoperations is presented, accounting for 1.37% of open heart surgery for congenital heart disease at PGIMER Chandigarh. Ninty percent were in the 20‐to 40‐year age group. Forty‐five percent of patients had symptoms of > 1‐year duration (range 2 months to 20 years) and catastrophic onset of symptoms was noted in four (18%). All patients had localized aneurysms originating either in right coronary sinus (14 pts) or noncoronary sinus (8 pts). Sites of origin and rupture are detailed. Associated congenital abnormalities such as ventricular septal defect (VSD) (13 pts), aortic regurgitation (3 pts), and left superior vena cava and atrial septal defect (ASD) (1 pt each) were noted. The data pertaining to Oriental and Western groups of patients were analyzed, and the differences in age, mode of presentation, site of origin, rupture, and the spectrum of associated abnormalities were elucidated. The majority of the patients (86.4%) were operated by the Bicameral approach. Repair was tailored according to the extent and severity of the defect in the sinus of Valsalva and aortic valve annulus and also the presence and site of VSD.
Nanocore/CMOS hybrid system-on-package (SoP) architecture for autonomous error-tolerant (AET) cellular array network

In this paper, the nanocore/CMOS hybrid system-on-package (SoP) autonomous error-tolerant (AET) cellular network architecture, which integrates today's mature CMOS technology with emerging nanotechnology, is proposed. Within the cellular network, each AET cell contains a nanocore, CMOS cell peripherals and their interface circuits in a silicon platform. The overall network is homogeneous. These imply strict constraints for intercellular connection schemes and routing policies. Depending on the communication requirement between two nodes.
Development of algorithms and products for supporting the Italian hyperspectral PRISMA mission: The SAP4PRISMA project

The SAP4PRISMA is a four year research project which aims at developing algorithms and products for the future PRISMA mission. The project started on May 2010 and is now entering his full activities as the ”PRISMA like” data set has been defined and the test areas were selected. The paper describes the main project objectives and the activities realized in the first 9 months of the project.
Rapid spatial mapping of the acoustic pressure in high intensity focused ultrasound fields at clinical intensities using a novel planar Fabry-Pérot interferometer

Measurement of high acoustic pressures is necessary in order to fully characterise clinical high-intensity focused ultrasound (HIFU) fields, and for accurate validation of computational models of ultrasound propagation. However, many existing methods are unable to withstand the extreme pressures generated in these fields, and those that can often have high noise levels. Here, a robust sensor, based on a planar Fabry-Pérot interferometer with hard dielectric spacer and mirrors, was used to measure acoustic pressure in the field of a 3.3 MHz single element spherically focused bowl transducer. In preliminary measurements, peak positive pressures of 27 MPa, and peak negative pressures of 14 MPa were measured. The noise equivalent pressure scaled with the adjustable dynamic range of the system between 50 kPa for pressures up to 8 MPa and 235 kPa for measurements up to 70 MPa. This makes the system suitable for measuring low pressure regions of the field as well as the high focal pressures. The -3 dB bandwidth of the sensor was 600 MHz, and the effective element size was 25 μm, which makes the sensor well suited to the measurement of the highly nonlinear and localised high-pressure focal regions generated in HIFU fields. Waveforms were acquired at a rate of 200 Hz, several orders of magnitude faster than can be achieved with a hydrophone scanning system. This sensor represents a critical improvement in measurement capability for HIFU fields in terms of dynamic range, bandwidth, noise equivalent pressure, and acquisition speed.
Incremental hierarchical discriminating regression for indoor visual navigation

In this paper, we investigate vision-based navigation using the incremental hierarchical discriminating regression (IHDR) algorithm. Based on the learned experience, the system gradually improves its performance through online interaction with environment. The learning process is interactive and on-line. The hierarchical structure of the IHDR algorithm allows each associative recall to be completed in O(log n) time, where it is the number of cases learned. This makes real time performance possible. The IHDR learns incrementally: each learning sample is learned or rejected based on the real time response. The proposed scheme has been successfully applied to indoor navigation.
Sexual Assault Victimization, Fear of Sexual Assault, and Self-Protective Behaviors: A Test of General Strain Theory

ABSTRACT According to Agnew’s General Strain Theory, many individuals who experience strain are more likely to engage in crime or become delinquent. To date, past research has examined the relationship between victimization and fear of crime, as well as the corresponding relationship between fear of crime and self-protective behaviors. Yet, the mediating role fear of sexual assault may have in accounting for the association between prior sexual assault victimization and self-protective behaviors has not been evaluated. The current study addresses this gap in the literature using data collected from a random sample of college students from 12 universities in the United States. The results indicated that the relationship between prior sexual assault victimization and self-protective behavior is partially mediated by fear of sexual assault. The study concludes with a discussion of implications and limitations, as well as directions for future research.
Muvee: An Alternative Approach to Mobile Video Trimming

Video content creation on mobile devices has rapidly increased during the last years, whereas the on-site mobile post-production capability has not yet followed this trend. On-the-fly video editing is not a common approach among amateur or professional content producers. This paper presents a proof-of-concept mobile application for video trimming that is practicable and efficient. The implementation is evaluated through a user study involving a task-based exercise, a questionnaire and an open interview. The study indicates that even complex applications can offer positive user experience when the particular design is carefully thought through to overcome the limitations of mobile devices.
The role of psychological factors in fatigue among end-stage kidney disease patients: a critical review

Fatigue is a common and debilitating symptom, affecting 42–89% of end-stage kidney disease patients, persisting even in pre–dialysis care and stable kidney transplantation, with huge repercussions on functioning, quality of life and patient outcomes. This paper presents a critical review of current evidence for the role of psychological factors in renal fatigue. To date, research has concentrated primarily on the contribution of depression, anxiety and subjective sleep quality to the experience of fatigue. These factors display consistent and strong associations with fatigue, above and beyond the role of demographic and clinical factors. Considerably less research is available on other psychological factors, such as social support, stress, self-efficacy, illness and fatigue-specific beliefs and behaviours, and among transplant recipients and patients in pre-dialysis care. Promising evidence is available on the contribution of illness beliefs and behaviours to the experience of fatigue and there is some indication that these factors may vary according to treatment modality, reflecting the differential burdens and coping necessities associated with each treatment modality. However, the use of generic fatigue scales casts doubt on what specifically is being measured among dialysis patients, illness-related fatigue or post-dialysis-specific fatigue. Therefore, it is important to corroborate the available evidence and further explore, qualitatively and quantitatively, the differences in fatigues and fatigue-specific beliefs and behaviours according to renal replacement therapy, to ensure that any model and subsequent intervention is relevant and grounded in the experiences of patients.
The Water Channel Aquaporin 1 Is a Novel Molecular Target of Polychlorinated Biphenyls for in Utero Anomalies*

Despite serious health risks in humans and wild life, the underlying mechanisms that explain the gene-environment effects of chemical toxicants are largely unknown. Polychlorinated biphenyls (PCBs) are one of the most ubiquitous environmental toxicants worldwide, with reported epidemiological evidence for reproductive and neurocognitive anomalies in humans. Here, we show that Aroclor 1254, a mixture of structurally distinct PCBs, causes preterm birth in interleukin (IL)-10-/- mice at a dose that does not show any adverse effects in wild type mice, highlighting the significance of IL-10 as an anti-toxicant cytokine. Aroclor 1254-treated IL-10-/- mice demonstrated increased amniotic fluid, intrauterine growth restriction, and reduced litter size with postnatal neuromotor defects. Further, our results identify aquaporin 1 (AQP1), a potent effector of fluid volume regulation and angiogenic activity, as a novel placental target of PCBs. In vivo or in vitro exposure to Aroclor 1254 coupled with IL-10 deficiency significantly reduced the protein content of AQP1. Reduced uterine AQP1 levels were associated with defective spiral artery transformation. Importantly, recombinant IL-10 reversed PCB-induced in vivo and in vitro effects. These data demonstrate for the first time that the IL-10-AQP1 axis is a novel regulator of PCB-induced in utero effects.
Individual ability-based system configuration cognitive profiling with Bayesian Networks

In this paper, we present a new method to model individual cognitive abilities, which were originally described by structural equation models and which can be used to reduce the possibility of human error when interacting with complex technical system. Our proposed model is based on hierarchical Bayesian networks and deals therefore with uncertain and noisy data. The validity of the method is demonstrated on the basis of simulations of real-life data. The inference from the Bayesian network demonstrates that estimating the user's cognitive abilities is possible in a reliable manner in real-time. Structural and data dependency analyses further show that less evidence data are necessary to provide cognitive profile classification. This especially highlights the advantage of our new method in comparison to the - in psychology - traditionally used structural equation models. Such cognitive profiling will allow adapting a system's demand character to the cognitive ability level of an individual user, which will make operating that system less error-prone, as many human errors result out of systems requesting more cognitive abilities than the operator has available.
The role of core and accessory type IV pilus genes in natural transformation and twitching motility in the bacterium Acinetobacter baylyi

Here we present an examination of type IV pilus genes associated with competence and twitching in the bacterium Acinetobacter baylyi (strain ADP1, BD413). We used bioinformatics to identify potential competence and twitching genes and their operons. We measured the competence and twitching phenotypes of the bioinformatically-identified genes. These results demonstrate that competence and twitching in A. baylyi both rely upon a core of the same type IV pilus proteins. The core includes the inner membrane assembly platform (PilC), a periplasmic assemblage connecting the inner membrane assembly platform to the secretin (ComM), a secretin (ComQ) and its associated pilotin (PilF) that assists with secretin assembly and localization, both cytoplasmic pilus retraction ATPases (PilU, PilT), and pilins (ComP, ComB, PilX). Proteins not needed for both competence and twitching are instead found to specialize in either of the two traits. The pilins are varied in their specialization with some required for either competence (FimT) and others for twitching (ComE). The protein that transports DNA across the inner membrane (ComA) specializes in competence, while signal transduction proteins (PilG, PilS, and PilR) specialize in twitching. Taken together our results suggest that the function of accessory proteins should not be based on homology alone. In addition the results suggest that in A. baylyi the mechanisms of natural transformation and twitching are mediated by the same set of core Type IV pilus proteins with distinct specialized proteins required for each phenotype. Finally, since competence requires multiple pilins as well as both pilus retraction motors PilU and PilT, this suggests that A. baylyi employs a pilus in natural transformation.