Miracle-dz/UniFAR-FTUs huggingface dataset:
Study of site controlled quantum dot formation on focused ion beam patterned GaAs substrate

In this project, we combine Ga+ focused ion beam (FIB) patterning and self-assembly of InGaAs quantum dots in order to produce regular quantum dot (QD) arrays. The GaAs substrate is patterned before transporting into molecular beam epitaxy growth chamber to do anneal and overgrowth. The thickness of deposited InAs is precisely controlled. Quantum dots are expected to nucleate at specific locations, where the ion beam has previously implanted gallium atoms. The properties of the quantum dots formed are related to the FIB beam parameters, which include accelerating voltage, probe current, dwell time and pitch. We studied and statistically analyzed the relationship, focusing on their diameter, height and distribution. Scanning electronic microscope (SEM) and atomic force microscope (AFM) images have been used to analyze the patterns and QDs before and after overgrowth. Micro-PL study was performed to test the QD opto-electronic property. Scanning transmission electron microscope (STEM) cross sectional analysis and X-ray mapping is performed.
The Effectiveness of Daily Mindful Breathing Practices on Test Anxiety of Students

The present study examined the effectiveness of daily mindful breathing practices on test anxiety of university students. A total of 36 participants were randomly assigned to one of three conditions: a training mindful breathing condition (n = 12), a training cognitive reappraisal condition (contrast group, n = 12), and a non-training condition (control group, n = 12). Each of the participants trained by themselves for 6 days after they had taken one session of education for mindful or cognitive reappraisal practices. They wrote their experiences on daily worksheets and sent it by mobile with taking pictures that were confirmed by the researcher. Before and after training, each of the participants completed a questionnaire to assess: test anxiety, positive thought, and positive affect. The results of the study showed that both mindful breathing practice and cognitive reappraisal practice yielded large effect sizes in reducing test anxiety. In addition, the mindful breathing condition scored significantly higher on positive thoughts than the cognitive reappraisal and control conditions. The findings of this study suggest that both daily mindful breathing and cognitive reappraisal practices were effective in reducing test anxiety; however, mindful breathing increased positive automatic thoughts to a greater extent than cognitive reappraisal.
Viral Activation of MK2-hsp27-p115RhoGEF-RhoA Signaling Axis Causes Cytoskeletal Rearrangements, P-body Disruption and ARE-mRNA Stabilization

Kaposi's sarcoma-associated herpesvirus (KSHV) is the infectious cause of several AIDS-related cancers, including the endothelial cell (EC) neoplasm Kaposi's sarcoma (KS). KSHV-infected ECs secrete abundant host-derived pro-inflammatory molecules and angiogenic factors that contribute to tumorigenesis. The precise contributions of viral gene products to this secretory phenotype remain to be elucidated, but there is emerging evidence for post-transcriptional regulation. The Kaposin B (KapB) protein is thought to contribute to the secretory phenotype in infected cells by binding and activating the stress-responsive kinase MK2, thereby selectively blocking decay of AU-rich mRNAs (ARE-mRNAs) encoding pro-inflammatory cytokines and angiogenic factors. Processing bodies (PBs) are cytoplasmic ribonucleoprotein foci in which ARE-mRNAs normally undergo rapid 5′ to 3′ decay. Here, we demonstrate that PB dispersion is a feature of latent KSHV infection, which is dependent on kaposin protein expression. KapB is sufficient to disperse PBs, and KapB-mediated ARE-mRNA stabilization could be partially reversed by treatments that restore PBs. Using a combination of genetic and chemical approaches we provide evidence that KapB-mediated PB dispersion is dependent on activation of a non-canonical Rho-GTPase signaling axis involving MK2, hsp27, p115RhoGEF and RhoA. PB dispersion in latently infected cells is likewise dependent on p115RhoGEF. In addition to PB dispersion, KapB-mediated RhoA activation in primary ECs caused actin stress fiber formation, increased cell motility and angiogenesis; these effects were dependent on the activity of the RhoA substrate kinases ROCK1/2. By contrast, KapB-mediated PB dispersion occurred in a ROCK1/2-independent manner. Taken together, these observations position KapB as a key contributor to viral reprogramming of ECs, capable of eliciting many of the phenotypes characteristic of KS tumor cells, and strongly contributing to the post-transcriptional control of EC gene expression and secretion.
Evaluation of patient handoff methods on an inpatient teaching service.

BACKGROUND The patient handoff process can be a highly variable and unstructured period at risk for communication errors. The morning sign-in process used by resident physicians at teaching hospitals typically involves less rigorous handoff protocols than the resident evening sign-out process. Little research has been conducted on best practices for handoffs during morning sign-in exchanges between resident physicians. Research must evaluate optimal protocols for the resident morning sign-in process. METHODS Three morning handoff protocols consisting of written, electronic, and face-to-face methods were implemented over 3 study phases during an academic year. Study participants included all interns covering the internal medicine inpatient teaching service at a tertiary hospital. Study measures entailed intern survey-based interviews analyzed for failures in handoff protocols with or without missed pertinent information. Descriptive and comparative analyses examined study phase differences. RESULTS A scheduled face-to-face handoff process had the fewest protocol deviations and demonstrated best communication of essential patient care information between cross-covering teams compared to written and electronic sign-in protocols. CONCLUSION Intern patient handoffs were more reliable when the sign-in protocol included scheduled face-to-face meetings. This method provided the best communication of patient care information and allowed for open exchanges of information.
Fast Hinge Detection Algorithms for Flexible Protein Structures

Analysis of conformational changes is one of the keys to the understanding of protein functions and interactions. For the analysis, we often compare two protein structures, taking flexible regions like hinge regions into consideration. The Root Mean Square Deviation (RMSD) is the most popular measure for comparing two protein structures, but it is only for rigid structures without hinge regions. In this paper, we propose a new measure called RMSD considering hinges (RMSDh) and its variant RMSDh(k) for comparing two flexible proteins with hinge regions. We also propose novel efficient algorithms for computing them, which can detect the hinge positions at the same time. The RMSDh is suitable for cases where there is one small hinge region in each of the two target structures. The new algorithm for computing the RMSDh runs in linear time, which is the same as the time complexity for computing the RMSD and is faster than any of previous algorithms for hinge detection. The RMSDh(k) is designed for comparing structures with more than one hinge region. The RMSDh(k) measure considers at most k small hinge region, i.e., the RMSDh(k) value should be small if the two structures are similar except for at most k hinge regions. To compute the value, we propose an O(kn2)-time and O(n)-space algorithm based on a new dynamic programming technique. With the same computational time and space, we can enumerate the predicted hinge positions. We also test our algorithms against actual flexible protein structures, and show that the hinge positions can be correctly detected by our algorithms.
Do factors in the psychosocial work environment mediate the effect of socioeconomic position on the risk of myocardial infarction? Study from the Copenhagen Centre for Prospective Population Studies

Aim: To investigate whether the effect of socioeconomic position on risk of myocardial infarction (MI) is mediated by differential exposure or differential susceptibility to psychosocial work environment. Methods: Data were used from three prospective population studies conducted in Copenhagen. A total of 16 214 employees, 44% women, aged 20–75 years, with initial examination between 1974 and 1992 were followed until 1996 for incident (hospital admission or death) MI. Register based information on job categories was used. Psychosocial job exposures were measured indirectly by means of a job exposure matrix based on the Danish Work Environment Cohort Study 1990. Results: During follow up, 731 subjects were diagnosed with an MI: 610 men and 121 women (35% fatal). The hazards by socioeconomic position showed a graded effect with a hazard ratio (HR) of 1.57 (95% CI 1.23 to 2.03) for unskilled workers compared to executive managers. Despite a strong and graded association in risk of MI related to decision authority and skill discretion, only skill discretion mediated the effect of socioeconomic position. The HR for unskilled workers was reduced to 1.47 (0.93 to 2.31) after adjustment for decision authority and other cardiovascular risk factors, and to 1.07 (0.72 to 1.60) after adjustment for skill discretion and cardiovascular risk factors. No sign of synergy was found. Conclusions: Decision authority and skill discretion were strongly related to socioeconomic position; and the effect on risk of MI was partially mediated by skill discretion. Improvements in psychosocial work environment, especially possibilities for skill discretion, might contribute to reducing the incidence of MI and social inequality in MI.
Strategies to Combat Mycosphaerella Leaf Disease in Eucalyptus globulus Plantations in Northern Spain

Eucalyptus globulus is widely planted in temperate regions to produce pulp for its high performance but few studies of the impact of Mycosphaerella Leaf Disease (MLD) have been documented. This study aimed to explore and provide knowledge on disease in the management of young Eucalyptus globulus stands in the north of Spain. The influences of subspecies, cloning, and fertilization on the degree of severity of the disease were analyzed. The study was conducted with different material plants of Eucalyptus globulus, of Australian origin, from other sources, open-pollinated families, clones, and families of controlled pollination. Each series tested different vegetal material, except for a number of control codes that were used as reference samples for MLD evaluation. Severity, height at which foliage changes from juvenile to adult, total height, and volume were all measured. There were significant correlations in the average MLD severity of families and provenances obtained from the different trials. ANOVA revealed important differences between subspecies of E. globulus. A correlation was found between the percentage of adult leaf and the severity. There were differences in the impact of MLD between plant material non-selected and selected by its tolerance (p < 0.0001). There was a significant effect on the severity between mature cuttings and families from seed non-selected in their tolerance to MLD. Their tolerance was lower than that achieved from seed selected by its tolerance to MLD. Genetic selection was shown as the best strategy since there are individuals exceptionally tolerant to MLD.
Why doctors leave rural practice.

Retention of rural doctors remains difficult because of complex factors that influence decisions of medical families. This study explores the reasons why Queensland rural doctors left their communities during 1995. Semi-structured interviews were conducted with contactable former rural doctors who claimed that they had entered rural practice with the intention to stay for a substantial period of time. The interviews were audiotaped, transcribed and analysed using NUD.IST software. Participants appeared to be subject to a dynamic balance between opposing pressures to stay and pressures to leave. In time, they became susceptible to 'triggers' to leave. These triggers were sometimes locality-specific and could be difficult to address, particularly without early intervention. We believe that it should be possible to develop strategies that address specific concerns of rural doctors, particularly if they are identified early. The optimum period of stay in rural practice should be reconsidered, such that moderate stays should be rewarded in a way that retains the doctors in some form of rural, or near-rural practice.
Re-assessing the relationship between sporozoite dose and incubation period in Plasmodium vivax malaria: a systematic re-analysis

SUMMARY Infections with the malaria parasite Plasmodium vivax are noteworthy for potentially very long incubation periods (6–9 months), which present a major barrier to disease elimination. Increased sporozoite challenge has been reported to be associated with both shorter incubation and pre-patent periods in a range of human challenge studies. However, this evidence base has scant empirical foundation, as these historical analyses were limited by available analytic methods, and provides no quantitative estimates of effect size. Following a comprehensive literature search, we re-analysed all identified studies using survival and/or logistic models plus contingency tables. We have found very weak evidence for dose-dependence at entomologically plausible inocula levels. These results strongly suggest that sporozoite dosage is not an important driver of long-latency. Evidence presented suggests that parasite strain and vector species have quantitatively greater impacts, and the potential existence of a dose threshold for human dose-response to sporozoites. Greater consideration of the complex interplay between these aspects of vectors and parasites are important for human challenge experiments, vaccine trials, and epidemiology towards global malaria elimination.
Analysis of Memory B Cell Responses and Isolation of Novel Monoclonal Antibodies with Neutralizing Breadth from HIV-1-Infected Individuals

Background The isolation of human monoclonal antibodies (mAbs) that neutralize a broad spectrum of primary HIV-1 isolates and the characterization of the human neutralizing antibody B cell response to HIV-1 infection are important goals that are central to the design of an effective antibody-based vaccine. Methods and Findings We immortalized IgG+ memory B cells from individuals infected with diverse clades of HIV-1 and selected on the basis of plasma neutralization profiles that were cross-clade and relatively potent. Culture supernatants were screened using various recombinant forms of the envelope glycoproteins (Env) in multiple parallel assays. We isolated 58 mAbs that were mapped to different Env surfaces, most of which showed neutralizing activity. One mAb in particular (HJ16) specific for a novel epitope proximal to the CD4 binding site on gp120 selectively neutralized a multi-clade panel of Tier-2 HIV-1 pseudoviruses, and demonstrated reactivity that was comparable in breadth, but distinct in neutralization specificity, to that of the other CD4 binding site-specific neutralizing mAb b12. A second mAb (HGN194) bound a conserved epitope in the V3 crown and neutralized all Tier-1 and a proportion of Tier-2 pseudoviruses tested, irrespective of clade. A third mAb (HK20) with broad neutralizing activity, particularly as a Fab fragment, recognized a highly conserved epitope in the HR-1 region of gp41, but showed striking assay-dependent selectivity in its activity. Conclusions This study reveals that by using appropriate screening methods, a large proportion of memory B cells can be isolated that produce mAbs with HIV-1 neutralizing activity. Three of these mAbs show unusual breadth of neutralization and therefore add to the current panel of HIV-1 neutralizing antibodies with potential for passive protection and template-based vaccine design.
Interaction of Nitrogen Supply, Sea Level Rise, and Elevation on Species Form and Composition of Salt Marsh Plants.

Supply of nitrogen (1), elevation within the intertidal range (2), and changes in sea level (3) are among the many factors that structure the vegetation of salt marshes. Here, we examine interactions between these three factors in long-term experimental plots maintained in Great Sippewissett Marsh since 1970 (1). The vegetation of Great Sippewissett Marsh is dominated by Spartina alterniflora and a few other species. The distribution of forms of S. alterniflora varies along the intertidal gradient in salt marshes, with the shorter forms found above creek banks on the high parts of the marsh and the taller form lower in the intertidal and along creek banks. The intermediate form lies between the short and tall forms in the marsh. The higher parts of the marsh support a few other species including Spartina patens, Distichlis spicata, Salicornia europaea, and Iva frutes-
Acute pulmonary disease and sickle cell anemia.

Seventy-five of 166 patients with sickle cell anemia were hospitalized one or more times for a clinical illness indistinguishable from bacterial pneumonia. Although bacteriologic confirmation by culture of blood, respiratory tract secretions, or stool was obtained in only 84 (50 per cent) of these episodes, the clinical and radiographic similarity of proved, presumptive, and possible cases, the young age of most of the patients, the frequency of involvement of the upper, middle, or both of these lobes, the lack of association with clinical crises, and the known propensity for pneumococcal disease in this population, all suggested that the events represented pneumonia rather than pulmonary infarction. The high risk and the multiple episodes suggested that this population might be benefited by pneumococcal vaccine. Pulmonary infarction was a far less frequent complication that occurred in only 5 patients and was generally distinguished by the older age of the patients, involvement of a single lower lobe, an.
Development and Validation of a Specific Radioimmunoassay for Somatostatin in Human Plasma

Little is known about the factors controlling somatostatin secretion in man, and data are not available on the changes in circulating levels in various human physiological or pathophysiological states. This is mainly a consequence of the technical difficulties involved in measuring somatostatin in plasma. In the presence of plasma, binding of somatostatin tracer to antibody was consistently decreased by about 20%, and this could not be abolished by the addition of EDTA and aprotinin or by the use of specially prepared somatostatin-free plasma. Furthermore, in the presence of plasma, endogenous somatostatin does not dilute in parallel with synthetic cyclic somatostatin standard. We have, therefore, developed and validated a radioimmunoassay for somatostatin using prior extraction of the peptide onto leached silica glass. Tyrosine-11 somatostatin was iodinated using lactoperoxidase and purified on ODS silica. This method is superior to iodination using chloramine-T with CMC cellulose purification, and gives a highly purified preparation with a shelf-life of at least eight weeks. Using this tracer and a specific antiserum, the limit of sensitivity of the assay was 10 pg/ml, with an intra-assay coefficient of variation of 12% (n = 16) and inter-assay coefficient of variation of 15% (n = 10). Parallelism has been demonstrated between standard synthetic cyclic somatostatin and all extracted plasma samples. The mean recovery of exogenous somatostatin from plasma was 78%. The fasting level of immunoreactive somatostatin at 0900 hours in 40 normal subjects ranged from 17 to 81 pg/ml. Care is needed, however, when comparing these values with those obtained from other laboratories since standard preparations of somatostatin vary considerably in their immunopotency.
Simulating vibrational energy flow in proteins: Relaxation rate and mechanism for heme cooling in cytochrome c

The rate and mechanism of the kinetic energy relaxation of directly excited heme in cytochrome c was investigated using classical molecular dynamics simulation. The kinetic energy relaxation was found to be a biphasic exponential decay process with relaxation time constants of 1.5 ps for the fast process and 10.1 ps for the slow process. Approximately 60% of the kinetic energy relaxes on the short time scale. Energy flow from the heme to the protein is found to occur “through bond” via (1) covalent linkages of the heme to the Cys14, Cys17, His18, and Met80 protein residues and (2) hydrogen bonds to Tyr48, Thr49, Asn52, and Thr78 protein residues and nearby water molecules and “through space” via nonbonded collisional energy transfer to nearby heme pocket residuesArg38, Thr40, Gly41, and Phe46. In a previous simulation study by Sagnella and Straub, heme “cooling” in myoglobin was found to proceed via a spatially anisotropic “funneling” mechanism as a single-exponential process with a time constant of 5.9 p.
Prospective evaluation of flexible ureteroscopes with a novel evaluation tool.

INTRODUCTION Assess the function and handling in the clinical setting of three different types of reusable or disposable ureteroscopes using a novel, comprehensive flexible ureteroscope evaluation tool. MATERIALS AND METHODS Urologists used a fiberoptic (Olympus URF-P5/P6), digital reusable (Storz Flex Xc), or a new digital disposable ureteroscope (Boston Scientific LithoVue) during ureteroscopic laser lithotripsy. An investigator-designed evaluation tool was used to prospectively assess the performance and handling of the ureteroscopes related to user comfort, maneuverability, efficiency, and various mechanical qualities. After each procedure, surgeons involved in each case who used the ureteroscope completed the written evaluation of the ureteroscope he/she used independently of one another. RESULTS We reviewed 79 evaluations that were completed after 34 surgical cases; residents and post-graduate MDs were involved in each case. On the characteristics evaluated, significant differences between ureteroscopes were noted. The Storz reusable digital ureteroscope received the highest ratings overall while the new LithoVue disposable ureteroscope generally scored lowest. Our evaluation tool demonstrated good internal consistency, suggesting reliable results. Ureteroscope maneuverability correlated most to overall satisfaction. CONCLUSION The clinical evaluation of flexible ureteroscopes for stone removal is critical in equipment purchase decision-making and in planning surgical approaches. We created a comprehensive evaluation tool to standardize and quantify the assessment of ureteroscopes used at our institution. Results revealed significant differences between ureteroscopes for several user and performance characteristics and good reliability of the evaluation tool itself.
Effective web crawling

The key factors for the success of the World Wide Web are its large size and the lack of a centralized control over its contents. Both issues are also the most important source of problems for locating information. The Web is a context in which traditional Information Retrieval methods are challenged, and given the volume of the Web and its speed of change, the coverage of modern search engines is relatively small. Moreover, the distribution of quality is very skewed, and interesting pages are scarce in comparison with the rest of the content.