Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of highly active antiretroviral therapy on the molecular epidemiology of newly diagnosed HIV infections

Objective:To evaluate HIV-1 transmission trends and the impact of highly active antiretroviral therapy (HAART) on newly diagnosed HIV infections in Geneva, Switzerland. Design:Retrospective molecular epidemiology analysis of all newly HIV-diagnosed individuals between 2008 and 2010. Methods:Phylogenetic analyses were performed using pol sequences of 780 newly HIV-1 diagnosed individuals between 2000 and 2010 (mandatory reporting) and 1058 individuals diagnosed before 2000. All clusters (bootstrap value >98%) including individuals diagnosed in 2008–2010 were analyzed. Recent HIV infections (<1 year) were determined by documented seroconversion and/or fraction of ambiguous nucleotides. Median viral load and HAART coverage during the study period were obtained from patients included in the Swiss HIV Cohort Study (SHCS). Results:Among 142 newly diagnosed individuals during 2008–2010, 49% had a recent infection and 42% were included in transmission clusters. Among the latter, two-thirds were included in new clusters and one-third expanded previously known clusters. MSM carrying resistant strains were more frequently included in clusters. Only 1.8% of individuals diagnosed before 2000 and 10.8% diagnosed during 2000–2008 were included in clusters involving individuals diagnosed between 2008 and 2010. During 2008–2010, the median population viral load of SHCS-enrolled individuals was significantly lower for individuals diagnosed before 2000 than for those diagnosed during 2000–2008 and 2008–2010 and HAART coverage significantly higher. Conclusions:MSM with recent HIV infection are a significant source of onward transmission. Individuals diagnosed before 2000 were only exceptionally related to newly diagnosed infections between 2008 and 2010. Prevention campaigns need to be focused on improving diagnosis for recently infected individuals.
Effects of Hydrogen Peroxide and Ultrasound on Biomass Reduction and Toxin Release in the Cyanobacterium, Microcystis aeruginosa

Cyanobacterial blooms are expected to increase, and the toxins they produce threaten human health and impair ecosystem services. The reduction of the nutrient load of surface waters is the preferred way to prevent these blooms; however, this is not always feasible. Quick curative measures are therefore preferred in some cases. Two of these proposed measures, peroxide and ultrasound, were tested for their efficiency in reducing cyanobacterial biomass and potential release of cyanotoxins. Hereto, laboratory assays with a microcystin (MC)-producing cyanobacterium (Microcystis aeruginosa) were conducted. Peroxide effectively reduced M. aeruginosa biomass when dosed at 4 or 8 mg L−1, but not at 1 and 2 mg L−1. Peroxide dosed at 4 or 8 mg L−1 lowered total MC concentrations by 23%, yet led to a significant release of MCs into the water. Dissolved MC concentrations were nine-times (4 mg L−1) and 12-times (8 mg L−1 H2O2) higher than in the control. Cell lysis moreover increased the proportion of the dissolved hydrophobic variants, MC-LW and MC-LF (where L = Leucine, W = tryptophan, F = phenylalanine). Ultrasound treatment with commercial transducers sold for clearing ponds and lakes only caused minimal growth inhibition and some release of MCs into the water. Commercial ultrasound transducers are therefore ineffective at controlling cyanobacteria.
On the mechanism of cytotoxicity of silver and copper amalgams in a cell culture system.

– Silver and copper amalgams show a pronounced cytotoxic effect on monolayer cultures of human epithelial cells (NCTG 2544). Analyses of the medium from silver amalgam cultures showed that, zinc was released in substantial amounts (14 μg/ml after incubation for 24 h). Small amounts of mercury and possibly also some silver were released, whereas release of copper and tin could not be. detected. Toxicity tests showed that 10 μg Zn2+/ml reduced the number of cells by 96% after incubation for 24 h. In the copper amalgam cultures about. 100 μg copper and 5 μg, cadmium per ml medium were found after 24 h. Only small amounts of mercury were released, Toxicity tests showed an increasing effect of Cu2+ and Cd2+ with tune. With 50 μg Cu2+/ml the number of cells was reduced by 73% after incubation for 24 h, and after 3 d a similar effect was found with 25 μg/ml. With 10 μg Cd2+/ml no cells were left after 24 h, whereas after 3 d 1μg/ml reduced cell growth by more than 80 %.
Clinical Pharmaceutical Services in Retail Practice. I. Pharmacists' Willingness and Abilities to Provide Services

The expansion of service levels in traditional community pharmacies in the face of structural and process impediments as well as the lack of reinforcement that would be provided by demand and reimbursement for such services requires a highly dedicated professional. As a result, this research had the goals of (1) investigating the relationship between service provision and pharmacist willingness and competency, and (2) characterizing pharmacists who presently do or do not provide expanded levels of service. A census of South Carolina community pharmacists was carried out using a self-administered, mail questionnaire. Analysis of the 890 responses representing 63.4 percent of the sample revealed that there is a significant relationship between pharmacists' willingness and ability and the extent to which they provide expanded levels of service. Pharmacists providing services were not only more willing and able to do so, but worked longer hours, tended to work in apothecary or independent pharmacies, held advanced degrees, and were more involved in continuing education. The results generally support the hypothesis that both willingness and competency may serve as barriers to the extension of clinical services into traditional community pharmacy settings.
Modeling zinc in biomolecules with the self consistent charge‐density functional tight binding (SCC‐DFTB) method: Applications to structural and energetic analysis

Parameters for the zinc ion have been developed in the self‐consistent charge density functional tight‐binding (SCC‐DFTB) framework. The approach was tested against B3LYP calculations for a range of systems, including small molecules that contain the typical coordination environment of zinc in biological systems (cysteine, histidine, glutamic/aspartic acids, and water) and active site models for a number of enzymes such as alcohol dehydrogenase, carbonic anhydrase, and aminopeptidase. The SCC‐DFTB approach reproduces structural and energetic properties rather reliably (e.g., total and relative ligand binding energies and deprotonation energies of ligands and barriers for zinc‐assisted proton transfers), as compared with B3LYP/6‐311+G** or MP2/6‐311+G** calculations. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 565–581, 2003
Using Genetic Programming to Predict the Macroporosity of Woven Cotton Fabrics

This paper reports the effect of woven fabric construction on macroporosity properties. The area of a macropore's cross section, equivalent, maximum, and minimum pore diameters, pore density, and open porosity are observed in this research involving woven fabric construction parameters—yarn linear density, fabric tightness, weave type, and denting. Predictive models, determined by genetic programming, are derived to describe the influence of fabric construction. The results show very good agreement between the experimental and predicted values. This work provides guidelines for engineering staple- yarn cotton fabrics in a grey state in terms of macroporosity properties.
Extracellular matrix mineralization is regulated locally; different roles of two gla-containing proteins

Extracellular matrix mineralization (ECMM) is a physiologic process in the skeleton and in teeth and a pathologic one in other organs. The molecular mechanisms controlling ECMM are poorly understood. Inactivation of Matrix gla protein (Mgp) revealed that MGP is an inhibitor of ECMM. The fact that MGP is present in the general circulation raises the question of whether ECMM is regulated locally and/or systemically. Here, we show that restoration of Mgp expression in arteries rescues the arterial mineralization phenotype of Mgp−/− mice, whereas its expression in osteoblasts prevents bone mineralization. In contrast, raising the serum level of MGP does not affect mineralization of any ECM. In vivo mutagenesis experiments show that the anti-ECMM function of MGP requires four amino acids which are γ-carboxylated (gla residues). Surprisingly, another gla protein specific to bone and teeth (osteocalcin) does not display the anti-ECMM function of MGP. These results indicate that ECMM is regulated locally in animals and uncover a striking disparity of function between proteins sharing identical structural motifs.
Estimating the design effort of Web applications

We focus on the effort needed for designing Web applications. The effort required for the design phase is an important part of the total development effort of a Web application, whose implementation can be (partially) automated by tools. We carried out an empirical study with the students of an advanced university class that used W2000, as the special-purpose object-oriented design notation for the design of Web applications. We investigated the impact of a number of attributes (e.g., size, complexity) of the W2000 design artifacts built during the design phase on the total effort needed to design Web applications and we identified a few attributes that may be related to the total design effort. In addition, we carried out a finer-grain analysis, by studying which of these attributes have an impact on the effort devoted to the steps of the design phase that are followed when using W2000.
The relationship between creativity and mood disorders

Research designed to examine the relationship between creativity and mental illnesses must confront multiple challenges. What is the optimal sample to study? How should creativity be defined? What is the most appropriate comparison group? Only a limited number of studies have examined highly creative individuals using personal interviews and a noncreative comparison group. The majority of these have examined writers. The preponderance of the evidence suggests that in these creative individuals the rate of mood disorder is high, and that both bipolar disorder and unipolar depression are quite common. Clinicians who treat creative individuals with mood disorders must also confronta variety of challenges, including the fear that treatment may diminish creativity, in the case of bipolar disorder, hovt/ever, it is likely that reducing severe manic episodes may actually enhance creativity in many individuals.
A retrospective cohort study of mode of delivery among public and private patients in an integrated maternity hospital setting

Objective To examine the associations between mode of delivery and public versus privately funded obstetric care within the same hospital setting. Design Retrospective cohort study. Setting Urban maternity hospital in Ireland. Population A total of 30 053 women with singleton pregnancies who delivered between 2008 and 2011. Methods The study population was divided into those who booked for obstetric care within the public (n=24 574) or private clinics (n=5479). Logistic regression analyses were performed to examine the associations between operative delivery and type of care, adjusting for potential confounding factors. Main outcome measures Caesarean section (scheduled or emergency), operative vaginal delivery (vacuum or forceps), indication for caesarean section as classified by the operator. Results Compared with public patients, private patients were more likely to be delivered by caesarean section (34.4% vs 22.5%, OR 1.81; 95% CI 1.70 to 1.93) or operative vaginal delivery (20.1% vs 16.5%, OR 1.28; 95% CI 1.19 to 1.38). The greatest disparity was for scheduled caesarean sections; differences persisted for nulliparous and parous women after controlling for medical and social differences between the groups (nulliparous 11.9% vs 4.6%, adjusted (adj) OR 1.82; 95% CI 1.49 to 2.24 and parous 26% vs 12.2%, adj OR 2.08; 95% CI 1.86 to 2.32). Scheduled repeat caesarean section accounted for most of the disparity among parous patients. Maternal request per se was an uncommonly reported indication for caesarean section (35 in each group, p<0.000). Conclusions Privately funded obstetric care is associated with higher rates of operative deliveries that are not fully accounted for by medical or obstetric risk differences.
Improved stability analysis of nonlinear networked control systems over multiple communication links

In this paper, we consider a nonlinear networked control system (NCS) in which controller, sensors and actuators are connected via several communication links. In Each link, networking effects such as the transmission delays, packet loss, sampling jiiter and data packet miss-ordering are captured by time-varying delays. Stability analysis is carried out based on the Lyapunov-Krasovskii method to obtain conditions for stability of the nonlinear NCS in the form of linear matrix inequality (LMI). The results are applied to a two degrees of freedom robot arm NCS which shows a considerable improvement with respect to the previous works.
Learning Social Affordance for Human-Robot Interaction

In this paper, we present an approach for robot learning of social affordance from human activity videos. We consider the problem in the context of human-robot interaction: Our approach learns structural representations of human-human (and human-object-human) interactions, describing how body-parts of each agent move with respect to each other and what spatial relations they should maintain to complete each sub-event (i.e., sub-goal). This enables the robot to infer its own movement in reaction to the human body motion, allowing it to naturally replicate such interactions. We introduce the representation of social affordance and propose a generative model for its weakly supervised learning from human demonstration videos. Our approach discovers critical steps (i.e., latent sub-events) in an interaction and the typical motion associated with them, learning what body-parts should be involved and how. The experimental results demonstrate that our Markov Chain Monte Carlo (MCMC) based learning algorithm automatically discovers semantically meaningful interactive affordance from RGB-D videos, which allows us to generate appropriate full body motion for an agent.
Certain new aspects of etiology and pathogenesis of Alzheimer’s disease

The research focuses on the possibility of early detection of AD-specific vascular and atrophic brain changes in families which have a tendency to inherit the disease. The research includedthree families with AD inheritance. All patientsunderwent: cognitive function assessment(MMSE),determination of dementia severity(CDR) and AD stages (TDR), computed tomography (CT), magnetic resonance imaging (MRI), scintigraphy of the brain (SG), rheoencephalography (REG), and cerebral multigated angiography (MUGA). All patients with different AD stages, as well as their descendants, have specific atrophic changes in the temporal lobes of the brain. The degree of these changes increases as AD becomes more severe and ranges from 4% - 8% (TDR-0) to 33% - 62% (TDR-3) of the total mass of a healthy person’s temporal lobes. Simultaneously, thepatients examined have changes of microcirculation manifested by reduction of the capillarybed in the temporal and frontalparietal regions,the development of multiple arteriovenousshunts in the same areas, early venous dumping, anomalous expansion of venoustrunks that receive blood from the arterialvenous shunts, venous stasis on the frontoparietal boundary. Similar changes are found among AD patients’ descendants aged 8 - 11, the only difference being in the degree of temporal lobes atrophy which is 4.7%. This proves that microcirculatory disorders are primary and atrophic changes of the temporal lobes are secondary in AD development. The data obtained indicate that the examination of AD patients’ relatives should begin well before the possible manifestations of the disease, even in childhood. It will allow to reveal the possibility of inheritance and the signs of the disease at the earliest possible stage and to begin its treatment in time.
Improved Bounds for Topological Cliques in Graphs of Large Girth

We prove that every graph of minimum degree at least $r$ and girth at least 27 contains a subdivision of $K_{r+1}$. This implies that the conjecture of Hajos, that every graph of chromatic number at least $r$ contains a subdivision of $K_r$, is true for graphs of girth at least 27. This conjecture is known to be false in general.
Prevalence of Carotid Artery Stenosis in Patients With Coronary Artery Disease in Japanese Population

Background and Purpose— Prevalence of carotid artery stenosis in patients with coronary artery disease (CAD) is unknown in Japanese population. Methods— The study populations consisted of 632 consecutive patients who underwent coronary angiography because of suspicion of CAD. All patients underwent carotid ultrasonography to screen carotid artery stenosis before coronary angiography. We defined echographic carotid stenosis as area stenosis of >50% or peak systolic velocity of >200 cm/s. Results— Echographic carotid stenosis was observed in 124 patients (19.6%). Coronary angiography revealed 433 patients had CAD. Prevalence of echographic carotid artery stenosis was 14 of 199 (7.0%), 18 of 124 (14.5%), 28 of 131 (21.4%), and 64 of 178 (36.0%) in patients with 0-, 1-, 2-, and 3-vessel CAD, respectively (P<0.0001). The prevalence rate with carotid stenosis and CAD was 25.4%. Multivariate stepwise logistic regression analysis showed that age and the extent of CAD were independently related to the presence of carotid stenosis (P=0.0002 and <0.0001, respectively). Conclusions— Prevalence of carotid stenosis in patients with CAD is high in Japan as well as in Western countries. Screening of carotid artery stenosis is recommended especially in older patients with multivessel CAD.
Mental health status and leisure-time physical activity contribute to fatigue intensity in patients with spondylarthropathy.

OBJECTIVE To examine the relationship between disease-related variables, leisure-time physical activity (LTPA), and mental health status with fatigue severity in patients with spondylarthropathy (SpA). METHODS Sixty-six SpA patients completed questionnaires assessing disease activity (Bath Ankylosing Spondylitis Disease Activity Index [BASDAI]), functional ability (Bath Ankylosing Spondylitis Functional Index), and health-related quality of life (Short Form 36). LTPA patterns, demographics, and disease-related data were obtained by interview. A clinical examination determined tender point count. Fatigue was assessed with the BASDAI fatigue item. RESULTS The mean BASDAI fatigue score was 5.5 (SD=2.7) with 59% of the sample obtaining a score > or =5. Disease activity, functional disability, and worse mental health contributed to greater fatigue (R2=0.56). The relationship between exercise duration and fatigue intensity was moderated by mental health status. For patients with poorer mental health scores, exercise did not influence fatigue severity. However, for patients reporting better mental health status, engaging in more LTPA decreased fatigue severity. CONCLUSION In addition to increased disease activity and functional disability, greater fatigue severity in SpA is associated with poorer mental health status. Integrating regular leisure physical activity into the comprehensive treatment of SpA may be useful for modulating fatigue.
The serine/arginine-rich protein SF2/ASF regulates protein sumoylation

Protein modification by conjugation of small ubiquitin-related modifier (SUMO) is involved in diverse biological functions, such as transcription regulation, subcellular partitioning, stress response, DNA damage repair, and chromatin remodeling. Here, we show that the serine/arginine-rich protein SF2/ASF, a factor involved in splicing regulation and other RNA metabolism-related processes, is a regulator of the sumoylation pathway. The overexpression of this protein stimulates, but its knockdown inhibits SUMO conjugation. SF2/ASF interacts with Ubc9 and enhances sumoylation of specific substrates, sharing characteristics with already described SUMO E3 ligases. In addition, SF2/ASF interacts with the SUMO E3 ligase PIAS1 (protein inhibitor of activated STAT-1), regulating PIAS1-induced overall protein sumoylation. The RNA recognition motif 2 of SF2/ASF is necessary and sufficient for sumoylation enhancement. Moreover, SF2/ASF has a role in heat shock-induced sumoylation and promotes SUMO conjugation to RNA processing factors. These results add a component to the sumoylation pathway and a previously unexplored role for the multifunctional SR protein SF2/ASF.
Preventative and therapeutic vaccines for fungal infections: from concept to implementation

Many challenges confront the development of fungal vaccines for humans including differences in host susceptibility, varied pathogenic mechanisms employed by the different species of fungi and mechanisms of host resistance. Hence, no single antigen can be expected to serve as a pan fungal vaccine. Instead, it is likely that progress for fungal vaccines will have to be made at the level of each individual organism. In recent years, tremendous strides have been made in understanding the immunopathogenesis of medically important fungal infections and identifying putative vaccine candidates. Such discoveries will facilitate the introduction of fungal vaccines into the therapeutic armamentarium of clinicians. The fungi under discussion in this review include Candida spp. , Aspergillus spp. , Cryptococcus neoformans, Coccidioides spp. , Histoplasma capsulatum, Blastomyces dermatitidis, Paracoccidioides brasiliensis and Pneumocystis jirovecii.
A Knowledge-Based Approach to Network Security: Applying Cyc in the Domain of Network Risk Assessment

CycSecure™ is a network risk assessment and network monitoring application that relies on knowledge-based artificial intelligence technologies to improve on traditional network vulnerability assessment. CycSecure integrates public reports of software faults from online databases, data gathered automatically from computers on a network and hand-ontologized information about computers and computer networks. This information is stored in the Cyc® knowledge base (KB) and reasoned about by the Cyc inference engine and planner to provide detailed analyses of the security (and vulnerability) of networks.