Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure-based Pharmacophore and Virtual Screening for Bacterial MexB Efflux Pump Inhibitors

Pseudomonas aeruginosa shows high degree of intrinsic resistance to a wide variety of antimicrobial agents. Efflux pump is a major mechanism of resistance exhibited by P. aeruginosa. The benefits of broad-spectrum efflux pump inhibitors (EPIs) led to the screening of synthetic and natural product databases for identifying inhibitors of the Mex pumps from P. aeruginosa. In the present study, pharmacophore based virtual screening of databases was used, in an effort to identify compounds that could possess activity against the MexB protein of P. aeruginosa. A pharmacophore hypothesis was created for the known inhibitor MC-207,110. This hypothesis was used to screen a total of 392 natural compounds and 1,95,000 synthetic compounds from Phase database. The compounds shortlisted based on the fitness score were docked against the target protein, MexB using Glide_XP. The compounds shortlisted based on Glide score showed interaction with active site residues. These compounds have to be validated in vitro for their potential efflux inhibitory activity. Keywords-Psuedomonas aeruginosa; MexAB-OprM efflux pump; e-pharmacophore; efflux pump inhibitors
Intentions to move, residential preferences and mobility behaviour: a longitudinal perspective

This book is about the discrepancy between individuals’ stated intentions to move and their actual mobility behaviour. Do people move when they say they are willing to do so? And if so, to what extent do they realise or adjust their initial residential preferences? Does the spatial context matter to the extent to which mobility intentions and residential preferences are realised? How important are anticipated and unanticipated life course changes to the mobility behaviour of intended movers? And do unanticipated life events trigger people to move unexpectedly? Through five complementary studies, this book seeks to uncover the mechanisms contributing to behavioural inconsistencies in the individual mobility decision-making processes. Using an innovative longitudinal data set in which housing survey data from a large-scale sample for the Netherlands are enriched with longitudinal register data, it is shown that many people do not behave according to their prior stated attitude towards moving. Most intended movers do not change residence within two years and some people move despite having no initial intention to do so. Anticipated and unanticipated life course changes may provide an additional or unexpected stimulus to change residence. The results also demonstrate the relevance of the context in which residential choices are made. A high housing market pressure is accompanied by a lower rate of success in two ways: both intentions to move and residential preferences are less frequently realised.
Secrecy DoF of Blind MIMOME Wiretap Channel With Delayed CSIT

We study the Gaussian multiple-input multiple-output multiple-eavesdropper wiretap channel where a transmitter wishes to communicate a confidential message to a legitimate receiver in the presence of eavesdroppers. Each node in the network is equipped with an arbitrary number of antennas. Furthermore, channels are time varying, and there is no channel state information available at the transmitter (CSIT) with respect to eavesdroppers’ channels; and transmitter only has access to delayed CSIT of the channel to the legitimate receiver. The secure degrees of freedom (SDoF) for such a network has only been characterized for special cases, and is unknown in general. We completely characterize the SDoF of this network for all antenna configurations. In particular, we strictly improve the state-of-the-art achievable scheme for this network by proposing more efficient artificial noise alignment at the receivers. Furthermore, we develop a tight upper bound by utilizing three important inequalities that provide lower bounds on the received signal dimensions at receivers which supply delayed CSIT or no CSIT. These inequalities together allow for analysis of signal dimensions in networks with heterogeneous CSIT; and as a result, we present a converse proof that leads to characterization of SDoF for all possible antenna configurations.
A Computational Model of Word Learning from Multimodal Sensory Input

How do infants segment continuous streams of speech to discover words of their language? Current theories emphasize the role of acoustic evidence in discovering word boundaries (Cutler 1991; Brent 1999; de Marcken 1996; Friederici & Wessels 1993; see also Bolinger & Gertsman 1957). To test an alternate hypothesis, we recorded natural infant-directed speech from caregivers engaged in play with their pre-linguistic infants centered around common objects. We also recorded the visual context in which the speech occurred by capturing images of these objects. We analyzed the data using two computational models, one of which processed only acoustic recordings, and a second model which integrated acoustic and visual input. The models were implemented using standard speech and vision processing techniques enabling the models to process sensory data. We show that using visual context in conjunction with spoken input dramatically improves learning when compared with using acoustic evidence alone. These results demonstrate the power of inter-modal learning and suggest that infants may use evidence from visual and other non-acoustic context to aid in speech segmentation and spoken word discovery.
Research Note: Punish and Rehabilitate? Public Attitudes Toward Six Common Crimes

Opinion polls show increasing punitiveness among the public toward criminals. However, methodological issues raise questions about the use of such polls in developing public policy. To provide a more accurate description of attitudes toward crime, a telephone survey of 397 adults was conducted in which punitive and rehabilitative sentiments toward six common crimes were examined. Respondents expressed a strong punishment orientation toward all six offenses, this punitiveness being relatively uniform across a variety of demographic and attitudinal subpopulations within the sample. However, strong support was also expressed for rehabilitative programs, particularly among the young, poor, and minority populations.
Gender role stress and burnout in chinese human service professionals in Hong Kong

Abstract Three hundred and seventy-four Chinese human service professionals were surveyed to examine the associations between burnout and gender role stress. Gender role stress refers to people's gender-based cognitive appraisal of specific situations that are role dystonic and stressful. Results showed that gender role stress was the best predictor for emotional exhaustion and depersonalization, while professional type was the best predictor for personal accomplishment. Masculine gender role stress was related to emotional exhaustion and depersonalization for both male and female professionals, whereas feminine gender role stress was related to similar burnout dimensions for male professionals only. Gender role stress and burnout associations were found only in gender-typed professions of police officers and nurses, but not in a nongender-typed profession of secondary school teacher. Among the three groups, nurses experienced a higher level of gender role stress and lack of personal accomplishment than p.
An improved NOESY simulation program for partially relaxed spectra: BIRDER.

An improved 2D NOESY simulation program, BIRDER (back-calculation considering incomplete recovery and differential external relaxation), has been developed. BIRDER has the following features: (1) It allows for differential external relaxation rates for protons with different chemical environments, (2) it automatically accounts for incomplete recovery of z magnetization between scans, and (3) it incorporates anisotropic tumbling motional modes for nonspherical molecules. It was found that a lower R factor is obtained if differential external relaxation rates are used in the NOESY spectrum simulation. The method for experimentally determining these external relaxation rates is discussed. In practice, the ability to account for incomplete recovery of z magnetization is very useful in the quantitative analysis of 2D NOESY spectra of spin systems with long longitudinal relaxation times (T1). For example, the T1's of some protons in RNA duplexes are approximately 4-6 s. Thus, a more than 15 s relaxation delay is needed to allow the z magnetization to return to thermal equilibrium between scans, requiring more than a week to obtain a single NOESY spectrum. Unless incomplete recovery of z magnetization is explicitly considered, distance errors may arise when shorter relaxation delays are used. The situation is further complicated in studies of DNA:RNA hybrid or DNA-RNA chimeric duplexes in which the DNA protons relax much faster than the RNA protons. It is shown that BIRDER successfully corrects for the incomplete recovery of z magnetization and makes it possible to save spectrometer time by using shorter relaxation delays without introducing serious errors. The nonsymmetrical nature of NOESY spectra when the spin system is not fully relaxed is discussed. (ABSTRACT TRUNCATED AT 250 WORDS)
How Open Should Open Source Be?

Many open-source projects land security fixes in public repositories before shipping these patches to users. This paper presents attacks on such projects - taking Firefox as a case-study - that exploit patch metadata to efficiently search for security patches prior to shipping. Using access-restricted bug reports linked from patch descriptions, security patches can be immediately identified for 260 out of 300 days of Firefox 3 development. In response to Mozilla obfuscating descriptions, we show that machine learning can exploit metadata such as patch author to search for security patches, extending the total window of vulnerability by 5 months in an 8 month period when examining up to two patches daily. Finally we present strong evidence that further metadata obfuscation is unlikely to prevent information leaks, and we argue that open-source projects instead ought to keep security patches secret until they are ready to be released.
Luminal cholinergic signalling in airway lining fluid: a novel mechanism for activating chloride secretion via Ca2+‐dependent Cl‐ and K+ channels

BACKGROUND AND PURPOSE Recent studies detected the expression of proteins involved in cholinergic metabolism in airway epithelial cells, although the function of this non‐neuronal cholinergic system is not known in detail. Thus, this study focused on the effect of luminal ACh as a regulator of transepithelial ion transport in epithelial cells.
I am more than just a TA!

This article is based on the findings of a funded research project. It examines the perspectives of teaching assistants (TAs) and higher-level teaching assistants (HLTAs) on their responsibilities and their views on leadership and management to see how they might have a role in leadership and management. The sample (N = 58) was drawn from schools in the English Midlands. The research followed a sequential mixed method approach which involved a survey and follow-up semi-structured interviews respectively. No major differences were found between the views of TAs and HLTAs. They believed leadership is centred on the support they get from their workplace/colleagues and their engagement in decision-making. They have a preference for the collaborative form of leadership. Although the findings show how TAs and HLTAs perceive leadership and management, which might illuminate some ideas about engaging them in this process, schools have to decide how to meet their own needs.
The antileishmanial agent licochalcone A interferes with the function of parasite mitochondria

Our previous studies have shown that licochalcone A, an oxygenated chalcone, has antileishmanial (M. Chen, S.B. Christensen, J. Blom, E. Lemmich, L. Nadelmann, K. Fich, T.G. Theander, and A. Kharazmi, Antimicrob, Agents Chemother. 37:2550-2556, 1993; M. Chen, S.B. Christensen, T.G. Theander, and A. Khrazmi, Antimicrob. Agents Chemother. 38:1339-1344, 1994) and antimalarial (M. Chen, T.G. Theander, S.B. Christensen, L. Hviid, L. Zhai, and A. Kaharazmi, Antimicrob. Agents Chemother. 38:1470-1475, 1994) activities. We have observed that licochalcone A alters the ultrastructure of the mitochondria of Leishmania promastigotes (Chen et al., Antimicrob. Agents Chemother. 37:2550-2556, 1993). The present study was designed to examine this observation further and investigate the mechanism of action of antileishmanial activity of licochalcone A. Electron microscopic studies showed that licochalcone A altered the ultrastructure of Leishmania major promastigote and amastigote mitochondria in a concentration-dependent manner without damaging the organelles of macrophages or the phagocytic function of these cells. Studies on the function of the parasite mitochondria showed that licochalcone A inhibited the respiration of the parasite by the parasites. Moreover, licochalcone A inhibited the activity of the parasite mitochondrial dehydrogenase. The inhibition of the activity of the parasite mitochondrial enzyme correlated well with the changes in the ultrastructure of the mitochondria shown by electron microscopy. These findings demonstrate that licochalcone A alters the ultrastructure and function of the mitochondria of Leishmania parasites.
Open Access Research

which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Research A prospective observational study of the relationship of critical illness associated hyperglycaemia in medical ICU patients and subsequent development of type 2 diabetes Abstract Introduction: Critical illness is commonly complicated by hyperglycaemia caused by mediators of stress and inflammation. Severity of disease is the main risk factor for development of hyperglycaemia, but not all severely ill develop hyperglycemia and some do even in mild disease. We hypothesised that acute disease only exposes a latent disturbance of glucose metabolism which puts those patients at higher risk for developing diabetes. Methods: Medical patients with no history of impaired glucose metabolism or other endocrine disorder admitted to an intensive care unit between July 1998 and June 2004 were considered for inclusion. Glucose was measured at least two times a day, and patients were divided into the hyperglycaemia group (glucose ≥7.8 mmol/l) and normoglycaemia group. An oral glucose tolerance test was performed within six weeks after discharge to disclose patients with unknown diabetes or pre-diabetes who were excluded. Patients treated with corticosteroids and those terminally ill were also excluded from the follow-up which lasted for a minimum of five years with annual oral glucose tolerance tests. Results: A five-year follow-up was completed for 398 patients in the normoglycaemia group, of which 14 (3.5%) developed type 2 diabetes. In the hyperglycaemia group 193 patients finished follow-up and 33 (17.1%) developed type 2 diabetes. The relative risk for type 2 diabetes during five years after the acute illness was 5.6 (95% confidence interval (CI) 3.1 to 10.2). Conclusions: Patients with hyperglycaemia during acute illness who are not diagnosed with diabetes before or during the hospitalization should be considered a population at increased risk for developing diabetes. They should, therefore, be followed-up, in order to be timely diagnosed and treated. Introduction Hyperglycaemia commonly occurs in the course of any critical illness. This now generally known fact, first described by Claude Bernard in 1878 [1], became widely accepted after studies had shown its association with worse outcomes [2,3] and the positive effects of tight glucose control in the critically ill [4,5]. The issue is still focussed on after later studies [6] opened up a debate on how tight the control of glycaemia should be [7,8]. The
Discovering Emotions in Filipino Laughter Using Audio Features

Laughter is one important aspect when it comes to non-verbal communication. Though laughter is often associated with the feeling of happiness, it may not always be the case; laughter may also portray different kinds of emotions. We infer that a variety of other emotions exist during laughter and occurrence and therefore investigate this phenomenon. It is the objective of this research to be able to identify the underlying emotions in Filipino laughter. This research focuses on studying existing machine learning techniques on emotion identification through audio signals from laughter in order to derive more suitable solutions. In this research, we present a comparative study of the performances of Multilayer Perceptron (MLP) and Support Vector Machines (SVM) using our system. Manual segmentation was done on recorded audio and pre- processing was implemented using low-pass filters. The 13 Mel-frequency cepstral coefficients (MFCCs) and prosodic features (pitch, intensity and formants), were extracted from audio signals and were separately fed to the machine classifier. Results had shown that highest rate of correctly classified instances is achieved using prosodic features only. MLP yielded a 44.4444% rate while SVM has a 18.5185% rate.
Power quality disturbances classification Based on multi-class classification SVM

this paper used the multi-class classification for support vector machine and combined with the good amplitude-frequency characteristic of fourier transform,the good time-frequency characteristics of wavelet transform and the excellent statistical learning ability of support vector machine to make the classification and recognition to the disturbances of power quality. Mathematical modeling for the 8 kinds of common power quality disturbances, namely voltage swell, voltage sag, voltage interruption, harmonic, voltage fluctuation, transient oscillation , transient pulse and frequency deviation, and then use fourier transform and wavelet transform to extract the characteristics of the waveform of the generated samples, and input the characteristic value to the osu_svm and do the quality disturbances Multi-class Classification. The example shows that this method has a high recognition accuracy, a few training samples and training time is short, a good real-time performance, and is not sensitive to noise, etc. It is an effective method for Power quality disturbances classification.
Comparative study of six rotary nickel-titanium systems and hand instrumentation for root canal preparation.

AIM To compare ex vivo various parameters of root canal preparation using a manual technique and six different rotary nickel-titanium (Ni-Ti) instruments (FlexMaster, System GT, HERO 642, K3, ProTaper, and RaCe). METHODOLOGY A total of 147 extracted mandibular molars were divided into seven groups (n = 21) with equal mean mesio-buccal root canal curvatures (up to 70 degrees), and embedded in a muffle system. All root canals were prepared to size 30 using a crown-down preparation technique for the rotary nickel-titanium instruments and a standardized preparation (using reamers and Hedströem files) for the manual technique. Length modifications and straightening were determined by standardized radiography and a computer-aided difference measurement for every instrument system. Post-operative cross-sections were evaluated by light-microscopic investigation and photographic documentation. Procedural errors, working time and time for instrumentation were recorded. The data were analysed statistically using the Kruskal-Wallis test and the Mann-Whitney U-test. RESULTS No significant differences were detected between the rotary Ni-Ti instruments for alteration of working length. All Ni-Ti systems maintained the original curvature well, with minor mean degrees of straightening ranging from 0.45 degrees (System GT) to 1.17 degrees (ProTaper). ProTaper had the lowest numbers of irregular post-operative root canal diameters; the results were comparable between the other systems. Instrument fractures occurred with ProTaper in three root canals, whilst preparation with System GT, HERO 642, K3 and the manual technique resulted in one fracture each. Ni-Ti instruments prepared canals more rapidly than the manual technique. The shortest time for instrumentation was achieved with System GT (11.7 s). CONCLUSIONS Under the conditions of this ex vivo study all Ni-Ti systems maintained the canal curvature, were associated with few instrument fractures and were more rapid than a standardized manual technique. ProTaper instruments created more regular canal diameters.
Inside a Digital Experiment: Co-producing Telecare Services for Older People

The problem of the user remains central to information systems research and practice, more so given the importance now given to user-led innovation. Telecare is a much-vaunted example of e-enabled health and social care which, over the past decade or more has received considerable policy attention and investment in Europe and beyond. However, it appears that the technological opportunities offered have not been taken-up in everyday practice and that the engagement of users-service providers and end users-has been identified as a major barrier. This article presents the experience of a European level project that sought to use a form of co-production to engage users in the development of a telecare system for older people. The outcome was a platform with infrastructural properties and a service-orientated architecture better able to support subsequent innovation in use.
Sequence Type and emm Type Diversity in Streptococcus pyogenes Isolates Causing Invasive Disease in Norway between 1988 and 2003

ABSTRACT The incidence of invasive group A streptococcal disease has increased in Norway since the 1980s. Analysis of 100 isolates recovered from 1988 to 2003 showed an increased genotypic diversity over time, while the prevalence of the strain that dominated in 1988, sequence type (ST)-28/emm-1, decreased. Necrotizing fasciitis was often associated with ST-15/emm-3.
Human Identification Based on the Palmar Surface of the Hand

In this paper, we investigate a new multimodal biometric approach for personal recognition, based on two different biometrics computed from the same hand image: palmprint and fingerprint surface. The detection of these modalities is conducted with no constraints imposed on the subject. In addition, this approach has the particularity of using a new fusion scheme based on the rank level integration method to consolidate the results obtained from the different biometric instances. Rank level fusion is a relatively new fusion approach. It is not a well-studied research problem, yet it has a high potential for efficient consolidation of multiple unimodal biometric outputs matching. To the best of our knowledge, we present the first application of the rank level fusion to consolidate the rank information produced by the five individual fingerprint surface and the palmprint. The achieved experimental results have shown that the designed system achieves an excellent recognition rate and provides more security than unimodal biometric system.
Analysis of Plasmid and Chromosomal DNA of Multidrug-Resistant Salmonella enterica Serovar Typhi from Asia

ABSTRACT Molecular analysis of chromosomal DNA from 193 multidrug-resistant (MDR) Salmonella enterica serovar Typhi isolates from 1990 to 1995 from Pakistan, Kuwait, Malaysia, Bangladesh, and India produced a total of five major different pulsed-field gel electrophoresis (PFGE) patterns. Even within a particular country MDR S. entericaserovar Typhi DNA was found to be in different PFGE groups. Similar self-transferable 98-MDa plasmids belonging to either incompatibility group incHI1 or incHI1/FIIA were implicated in the MDR phenotype inS. enterica serovar Typhi isolates from all the locations except Quetta, Pakistan, where the majority were of incFIA. A total of five different PFGE genotypes with six different plasmids, based on incompatibility and restriction endonuclease analysis groups, were found among these MDR S. enterica serovar Typhi isolates.