Miracle-dz/UniFAR-FTUs huggingface dataset:
Trypsin‐ligand binding free energies from explicit and implicit solvent simulations with polarizable potential

We have calculated the binding free energies of a series of benzamidine‐like inhibitors to trypsin with a polarizable force field using both explicit and implicit solvent approaches. Free energy perturbation has been performed for the ligands in bulk water and in protein complex with molecular dynamics simulations. The binding free energies calculated from explicit solvent simulations are well within the accuracy of experimental measurement and the direction of change is predicted correctly in all cases. We analyzed the molecular dipole moments of the ligands in gas, water and protein environments. Neither binding affinity nor ligand solvation free energy in bulk water shows much dependence on the molecular dipole moments of the ligands. Substitution of the aromatic or the charged group in the ligand results in considerable change in the solvation energy in bulk water and protein whereas the binding affinity varies insignificantly due to cancellation. The effect of chemical modification on ligand charge distribution is mostly local. Replacing benzene with diazine has minimal impact on the atomic multipoles at the amidinium group. We have also utilized an implicit solvent based end‐state approach to evaluate the binding free energies of these inhibitors. In this approach, the polarizable multipole model combined with Poisson‐Boltzmann/surface area (PMPB/SA) provides the electrostatic interaction energy and the polar solvation free energy. Overall the relative binding free energies obtained from the MM‐PMPB/SA model are in good agreement with the experimental data. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009
STRATEGIC HUMAN RESOURCE MANAGEMENT IN SERVICE CONTEXT: TAKING CARE OF BUSINESS BY TAKING CARE OF EMPLOYEES AND CUSTOMERS

Integrating the strategic human resource management research with the multiple-stakeholder view of organizational climate, in this study we propose that the human resource management practices of a high-performance work system enhance a business unit's market performance in the service context by facilitating 2 types of strategically targeted organizational climate: concern for customers and concern for employees, which further encourage employees to engage in cooperative behaviors with customers (service performance) and coworkers (helping behavior) that are essential in achieving superior market performance. The results based on the data collected from multiple sources of 133 stores in Taiwan in 2 phases largely supported the proposed theoretical framework and shed light on the influence mechanism of high-performance work system on organizational effectiveness in the service context.
Genital warts in men: a large population-based cross-sectional survey of Danish men

Objectives To estimate the occurrence of and risk factors associated with genital warts in Danish men Methods We conducted a cross-sectional, questionnaire-based study among almost 23 000 men aged 18–45 years, randomly sampled from the general population of Denmark. Data was collected on self-reported clinically diagnosed genital warts, and various lifestyle habits. Results Ever having had clinically diagnosed genital warts was reported by 7.9% of the men. The median age at first occurrence was 22 years. Genital warts within the previous 12 months were reported by 0.92% of the men, with a peak of 1.83% among men aged 21–24 years. The likelihood of reporting genital warts was strongly correlated with the lifetime number of sex partners (OR 8.0; 95% CI 6.0 to 10.8 for ≥15 partners vs 1–2 partners). Other factors associated with an increased risk for genital warts included ever having smoked and having had other sexually transmitted infections. Conclusions Almost 8% of Danish men aged 18–45 years reported having had a diagnosis of genital warts. The results provide baseline information for developing and monitoring prevention strategies against genital warts, such as vaccination against human papillomavirus types 6 and 11.
Issues in Multiple Regression

Controlling for variables implies conceptual distinctness between the control and zero-order variables. However, there are different levels of distinctness, some more subtle than others. These levels are determined by the theoretical context of the research. Failure to specify the theoretical context creates ambiguity as to the level of distinctness, and leads to the partialling fallacy, in which one controls for variables that are distinct in terms of appropriate theory. Although this can occur in using any control procedure, it is especially likely to occur in multiple regression, where high-order partial regression coefficients are routinely obtained in order to determine the relative importance of variables. Four major ways in which these regression coefficients can be seriously misleading are discussed. Although warnings concerning multicollinearity are to be found in statistics texts, they are insufficiently informative to prevent the mistakes described here. This is because the problem is essentially one of substantive interpretation rather than one of mathematical statistics per se.
Assessing the Relative Ages of Admixture in the Bovine Hybrid Zones of Africa and the Near East Using X Chromosome Haplotype Mosaicism

Historical hybridization events between the two subspecies of cattle, Bos taurus and B. indicus, have occurred in several regions of the world, while other populations have remained nonadmixed. We typed closely linked X chromosome microsatellites in cattle populations with differing histories of admixture from Africa, Europe, the Near East, and India. Haplotype breakdown will occur as admixed populations age, and longer ancestral haplotypes will remain intact in more recently admixed populations compared to older ones. We genotyped male animals from these populations, obtaining unambiguous haplotypes, and measured levels of linkage disequilibrium (LD) and ancestral mosaicism. Extensive LD, likely to be the result of ongoing admixture, was discovered in hybrid cattle populations from the perimeter of the tsetse zone in West Africa. A Bayesian method to assign microsatellite allele ancestry was used to designate the likely origin of each chromosomal segment and assess the relative ages of admixture in the populations. A gradient of the age of admixture in the African continent emerged, where older admixture has produced more fragmented haplotypes in the south, and longer intact haplotypes, indicating more recent hybridization, feature in the northwest.
The (un)making of opposition coalitions and the challenge of democratization in Ethiopia, 1991–2011

Abstract A key challenge in the consolidation of a democratic system in transitional countries is the lack of effective opposition political parties to counter the dominance of incumbent regimes. In the case of Ethiopia, to be described in this article, opposition parties are weak, fragmented, and mutually antagonistic. Hence, in order to counter the dominance of the Ethiopian Peoples' Revolutionary Democratic Front (EPRDF), coalitions and alliances have been used by the opposition parties. But opposition coalitions remain unstable and prone to fragmentation due to both internal and external factors. This study analyses the factors responsible to the often repeated fragmentation of opposition coalitions in Ethiopia.
Management of 1000 vestibular schwannomas (acoustic neuromas): clinical presentation.

OBJECTIVE Despite good knowledge of the key symptoms of vestibular schwannomas and their significance for surgical results, the evolution of symptoms and signs and their relation to tumor extension still need thorough investigation. METHODS From 1978 to 1993, operations were performed by the same surgeon (M.S.) on 1000 vestibular schwannomas at the Neurosurgical Department of Nordstadt Hospital. The vestibular schwannomas were diagnosed in 962 patients, including 522 female patients (54%) and 440 male patients (46%); the mean age was significantly higher in female patients (47.6 yr) than in men (45.2 yr). We focused our analysis on the incidence of subjective disturbances versus objective morbidity, on the sequence of symptom onset, and on symptom duration and symptomatology versus tumor size and extension. RESULTS The most frequent clinical symptoms were disturbances of the acoustic (95%), vestibular (61%), trigeminal (9%), and facial (6%) nerves. Symptom duration was 3.7 years for hearing loss, 1.9 years for facial paresis, and 1.3 years for trigeminal disturbances. Symptom incidence and duration did not strictly correlate with tumor size. Key symptoms of various tumor extension classes precipitated the diagnosis, such as trigeminal disturbances in large tumors with brain stem compression or tinnitus in small neuromas. In cases of trigeminal or facial nerve symptoms, the overall duration of symptomatology was much shorter. According to the subjective perception of the patients, between only one- and two-thirds of nerve disturbances were noticed. Patients with preoperative deafness had become deaf either chronically (23%) or suddenly (3%); even in cases of moderate hearing deficit that lasts a long time, deafness can occur suddenly. The rate of tinnitus was higher in hearing than in deaf patients; however, deafness does not mean relief from tinnitus, because this symptom persists in 46% of preoperatively deaf patients. Vestibular disturbances most often occur as some unsteadiness while walking or as vertigo, and the symptoms frequently are fluctuating, not constant. CONCLUSION Differences in tumor biology can be underestimated and are not visible on radiological scans. For example, intrameatal tumors, despite their small size, present with a duration of symptoms that is representative of the larger tumors and are most frequently associated with vestibular symptoms and with tinnitus. Large tumors with brain stem compression present with relatively shorter symptom durations and at a younger age; both factors are suggestive of especially fast tumor growth. The clinical findings presented in this study promote new consideration of the dynamics of tumor growth and of the affected neural tissues.
Early parenteral penicillin in meningococcal disease.

EDITOR, -There cannot be many general practitioners who, if asked about their worst waking nightmares, would not include the presentation of a child with early meningococcal meningitis. General practitioners would expect to encounter this once in 25 years on average, yet it will haunt them every time they see an unwell child with a fever. Similarly, there cannot be. many who are not aware of the need to give parenteral benzylpenicillin in this situation. Why then had about half of patients who had and were suspected to have the disease not been given the treatment, and how can the figures be improved? ' I believe that had these questions been put to a general practitioner rather than an epidemiologist more useful answers would have been given in an editorial.2 Very rare threatening events that are difficult to deal with classically produce denial. Doctors are as subject to this phenomenon as anyone, and this combined with the random practical difficulties (sod's law decrees that the day you need it you left the bag at the surgery while you nipped out to do the extra visit) suggests that a 50% treatment rate is understandable. Further exhortation and penalty reinforce denial. The answer lies in a mixture of these with reduction of the threat by the provision of more relevant information (about the management of sick children) from credible educators and positive feedback about the results of efforts. This means a joint effort by paediatricians and general practitioners to understand more systematically the early management of unwell children in the community (perhaps the equivalent of the Baby Check for parents) and a confidential inquiry system for serious morbidity and mortality in children.
Biomedical Informatics and Granularity

An explicit formal-ontological representation of entities existing at multiple levels of granularity is an urgent requirement for biomedical information processing. We discuss some fundamental principles which can form a basis for such a representation. We also comment on some of the implicit treatments of granularity in currently available ontologies and terminologies (GO, FMA, SNOMED CT).
Music and Language in Degenerative Disease of the Brain

Music and language functions were studied in two musicians with degenerative disease. Both patients were tested on a standardized language battery and a series of music tasks. In the first case with left cortical atrophy and primary progressive aphasia, expressive music functions were spared with impaired reception of rhythm. The second case with posterior cortical atrophy, greater on the right, was nonaphasic, had spatial agraphia, a visuopractic deficit, and severe expressive music deficits, but intact rhythm repetition. The aphasic patient showed dissociations between music and language in fluency and content; continuous, organized, although reiterative music production was contrasted with nonfluent language. The nonaphasic patient showed the opposite pattern of deficits; unmusical production with impaired melody and rhythm organization that was contrasted with fluent, intelligible language. The double dissociation between language and music functions supports the existence of independent cognitive systems, one consistent with conventional left lateralization models of language, temporal sequence, and analytic music processing and another with a right lateralization model of implicit music cognition.
A context-aware and QoS-aware telehomecare system. (Un système de télésanté contextuel avec support de qualité de service pour le maintien à domicile)

This thesis is a thesis CIFRE between LORIA and the MEDETIC Company and focuses on the design of telehomecare system for the elderly.In addition to the design of a remote surveillance architecture “Vill’Âge ®” based on networks of heterogeneous sensor (home automation, IEEE802.15.4/Zigbee, Wifi, Bluetooth), thesis has contributed essentially on the proposal of a clustering and routing protocol in the network of wireless sensors with an approach to fuzzy logic, and of a middleware for the collection and processing of data from sensors with the management of the quality of service as a special feature.A first platform was developed at Colmar (MEDETIC) and a second who is more complete is under development at LORIA (http://infositu.loria.fr/). By using this system, MEDeTIC, offers a new concept of smart homes for the senior citizens, named in French “Maisons Vill’Âge”. The first housing schemes are being built in 2 departments of France. A flat is entirely equipped to act as a demonstrator and as laboratory of research and development.The system is designed for the elderly who wish to spend their old age in their own home, because of its potential to increase independence and quality of life. This would not only benefit the elderly who want to live in their own home, but also the national health care system by cutting costs significantly. Based on this PhD thesis, MPIGate, a “Multiprotocol Interface and Gateway for for telecare, environment”, has been developed. MPIGate was awarded in the competition of the Ministry of Higher Education and Research and OSEO 2010
Microtubule-assisted altered trafficking of astrocytic gap junction protein connexin 43 is associated with depletion of connexin 47 during mouse hepatitis virus infection

Gap junctions (GJs) are important for maintenance of CNS homeostasis. GJ proteins, connexin 43 (Cx43) and connexin 47 (Cx47), play a crucial role in production and maintenance of CNS myelin. Cx43 is mainly expressed by astrocytes in the CNS and forms gap junction intercellular communications between astrocytes-astrocytes (Cx43–Cx43) and between astrocytes-oligodendrocytes (Cx43–Cx47). Mutations of these connexin (Cx) proteins cause dysmyelinating diseases in humans. Previously, it has been shown that Cx43 localization and expression is altered due to mouse hepatitis virus (MHV)-A59 infection both in vivo and in vitro; however, its mechanism and association with loss of myelin protein was not elaborated. Thus, we explored potential mechanisms by which MHV-A59 infection alters Cx43 localization and examined the effects of viral infection on Cx47 expression and its association with loss of the myelin marker proteolipid protein. Immunofluorescence and total internal reflection fluorescence microscopy confirmed that MHV-A59 used microtubules (MTs) as a conduit to reach the cell surface and restricted MT-mediated Cx43 delivery to the cell membrane. Co-immunoprecipitation experiments demonstrated that Cx43–β-tubulin molecular interaction was depleted due to protein–protein interaction between viral particles and MTs. During acute MHV-A59 infection, oligodendrocytic Cx47, which is mainly stabilized by Cx43 in vivo, was down-regulated, and its characteristic staining remained disrupted even at chronic phase. The loss of Cx47 was associated with loss of proteolipid protein at the chronic stage of MHV-A59 infection.
Brain activity correlates of consumer brand choice shift associated with television advertising

This study uses brain activity measures to examine the relationship between television advertising and changes in consumer brand preference. Prior to and after viewing a television programme that included grocery advertisements 198 right-handed females selected six ‘door prizes’ from six grocery categories. One of the advertisements featured a jam that was available as a door prize. Steady-state topography (SST) was used to estimate brain activity at eight scalp sites, including left and right lateral prefrontal sites previously shown to index the strength of long-term memory (LTM) encoding. Our hypothesis, that lateral prefrontal activity would be higher during branding for the 18 participants who shifted to the advertised jam compared to those consistently selecting the competitor jam, was confirmed, but only for the left hemisphere. Our findings suggest that SST activity at lateral prefrontal sites during television advertisement branding may be a useful indicator of advertising effectiveness.
Simplification of multibody models by parameter reduction

Model selection methods are used in different scientific contexts to represent a characteristic data set in terms of a reduced number of parameters. Apparently, these methods have not found their way into the literature on multibody systems dynamics. Multibody models can be considered parametric models in terms of their dynamic parameters, and model selection techniques can then be used to express these models in terms of a reduced number of parameters. These parameter-reduced models are expected to have a smaller computational complexity than the original one and still preserve the desired level of accuracy. They are also known to be good candidates for parameter estimation purposes. In this work, simulations of the actual model are used to define a data set that is representative of the system's standard working conditions. A parameter-reduced model is chosen and its parameter values estimated so that they minimize the prediction error on these data. To that end, model selection heuristics and normalized error measures are proposed. Using this methodology, two multibody systems with very different characteristic mobility are analyzed. Highly considerable reductions in the number of parameters and computational cost are obtained without compromising the accuracy of the reduced model too much. As an additional result, a generalization of the base parameter concept to the context of parameter-reduced models is proposed.
Race differences in sexual activity among adolescent women: role of neighborhood characteristics.

A sociologist applied individual and aggregate-level 1982 data on 11620 observations and 1180 first intercourse events to multivariate hazard models to examine the role of neighborhood characteristics in determining racial differences in nonmarital sexual activity of US adolescents. The hypothesis is that racially-differentiated community environments generate and maintain race differences in fertility-related behaviors. The dependent variable is risk of nonmarital first intercourse. Socioeconomic status of the neighborhood (p < 0.05) and labor market experiences of neighborhood women (p < 0.001) were very important determinants of the strong race difference in risk of first intercourse. Both white and black female adolescents were more likely to have nonmarital sexual intercourse when the potential consequences of this sexual activity (as evidenced by the economic characteristics of the neighborhood and the experiences and behaviors of neighborhood adults) appeared rather low. When these potential costs appeared high however they tended to delay first intercourse. There were no cross-level race interactions suggesting that black and white female teens respond alike to structural constraints and opportunities. These findings indicate that race differences in adolescent sexual activity and its negative consequences will continue as long as the US has segregated housing patterns.
Comparison of Membrane Targeting Strategies for the Accumulation of the Human Immunodeficiency Virus p24 Protein in Transgenic Tobacco

Membrane anchorage was tested as a strategy to accumulate recombinant proteins in transgenic plants. Transmembrane domains of different lengths and topology were fused to the cytosolic HIV antigen p24, to promote endoplasmic reticulum (ER) residence or traffic to distal compartments of the secretory pathway in transgenic tobacco. Fusions to a domain of the maize seed storage protein γ-zein were also expressed, as a reference strategy that leads to very high stability via the formation of large polymers in the ER lumen. Although all the membrane anchored constructs were less stable compared to the zein fusions, residence at the ER membrane either as a type I fusion (where the p24 sequence is luminal) or a tail-anchored fusion (where the p24 sequence is cytosolic) resulted in much higher stability than delivery to the plasma membrane or intermediate traffic compartments. Delivery to the tonoplast was never observed. The inclusion of a thrombin cleavage site allowed for the quantitative in vitro recovery of p24 from all constructs. These results point to the ER as suitable compartment for the accumulation of membrane-anchored recombinant proteins in plants.
Integration of Positive and Negative Affective Stimuli

The research reported in this article examines how multiple affective stimuli of differing valence (i.e., both positive and negative) are integrated into an overall affective response. Prior research on the integration of positive and negative information has not focused on affect, and previous affect integration research has not considered both positive and negative feelings. Two experiments investigate how positive and negative affective stimuli combine to influence overall affective responses to an advertisement, content-specific beliefs, and overall ad evaluations. Both recency and contrast effects were observed on positive affective response and positive beliefs, but comparable effects on negative affective response and negative beliefs were not evident. The results support a motivational influence of affect on judgments.