Miracle-dz/UniFAR-FTUs huggingface dataset:
Increase in Fitness of Streptococcus pneumoniae Is Associated With the Severity of Necrotizing Pneumonia

Background: The incidence of necrotizing pneumococcal pneumonia has increased during the past 2 decades. We hypothesized that increased pneumococcal load or augmented inflammatory cytokine production might lead to destructive pneumococcal lung disease. Methods: This study enrolled prospectively 0- to 18-year-old children with a diagnosis of community-acquired pneumonia with pleural effusion admitted to 6 medical centers from March 2010 to April 2012. Children were diagnosed with pneumococcal empyema if the pleural fluid tested positive for quantitative pneumococcal (lytA) detection by real-time polymerase chain reaction. Pneumococcal empyema cases were further divided into 4 groups according to necrosis severity: (0) nonnecrosis, (1) mild necrosis, (2) cavitation and (3) bronchopleural fistula. Nasopharyngeal and pleural pneumococcal load, as well as levels of proinflammatory cytokines (TNF-&agr;, IL-1&bgr;, IL-6, IL-8), Th1-(IL-2, IFN-&ggr;), Th2-(IL-4, IL-10) and Th17-cytokines (IL-17), in the pleural fluid was measured. Results: Serotypes 19A and 3 accounted for 69.4% and 12.5%, respectively, of 72 cases of pneumococcal empyema. Pleural pneumococcal load was significantly higher in serotypes 19A and 3 infection than in the other strains causing infection (P = 0.006). There was a correlation between nasopharyngeal and pleural pneumococcal load (&rgr; = 0.35; P = 0.05). In multivariate ordinal logistic regression analysis, pleural pneumococcal load (adjusted odds ratio: 1.79; 95% confidence interval: 1.03–3.06) and IL-8 (adjusted odds ratio: 2.64; 95% confidence interval: 1.21–5.75) were independent factors associated with the severity of lung necrosis. Conclusions: Evolution of Streptococcus pneumoniae toward increased fitness in their interaction with host and exaggerated IL-8 expression may be responsible for the increase of necrotizing pneumococcal pneumonia.
Supporting Teacher Intervention in Unpredictable Learning Environments

Modern teaching tools, such as educational robotics, require new learning environments. The teacher especially needs to be supported in novel ways. Conflative learning environment is based on the agents collecting data from the learning process. The teacher can build a support environment based on his or her empirical observations from the classroom. An implementation of the conflative learning environment is described and two case studies about the use of system are reported. The results show that agents are useful and efficient in data collection, and that the Empirical Modelling environment can be used to construct the working classroom models.
Expression of the Tick-Associated Vtp Protein of Borrelia hermsii in a Murine Model of Relapsing Fever

Borrelia hermsii, a spirochete and cause of relapsing fever, is notable for its immune evasion by multiphasic antigenic variation within its vertebrate host. This is based on a diverse repertoire of surface antigen genes, only one of which is expressed at a time. Another major surface protein, the Variable Tick Protein (Vtp), is expressed in the tick vector and is invariable at its genetic locus. Given the limited immune systems of ticks, the finding of considerable diversity among the Vtp proteins of different strains of B. hermsii was unexpected. We investigated one explanation for this diversity of Vtp proteins, namely expression of the protein in mammals and a consequent elicitation of a specific immune response. Mice were infected with B. hermsii of either the HS1 or CC1 strain, which have antigenically distinctive Vtp proteins but otherwise have similar repertoires of the variable surface antigens. Subsequently collected sera were examined for antibody reactivities against Vtp and other antigens using Western blot analysis, dot blot, and protein microarray. Week-6 sera of infected mice contained antibodies that were largely specific for the Vtp of the infecting strain and were not attributable to antibody cross-reactivities. The antibody responses of the mice infected with different strains were otherwise similar. Further evidence of in vivo expression of the vtp gene was from enumeration of cDNA sequence reads that mapped to a set of selected B. hermsii genes. This measure of transcription of the infecting strain’s vtp gene was ~10% of that for the abundantly-expressed, serotype-defining variable antigen gene but similar to that of genes known for in vivo expression. The findings of Vtp expression in a vertebrate host and elicitation of a specific anti-Vtp antibody response support the view that balancing selection by host adaptive immunity accounts in part for the observed diversity of Vtp proteins.
Maritime route of colonization of Europe

Significance The question of colonization of Europe by Neolithic people of the Near East and their contribution to the farming economy of Europe has been addressed with extensive archaeological studies and many genetic investigations of extant European and Near Eastern populations. Here, we use DNA polymorphisms of extant populations to investigate the patterns of gene flow from the Near East to Europe. Our data support the hypothesis that Near Eastern migrants reached Europe from Anatolia. A maritime route and island hopping was mainly used by these Near Eastern migrants to reach Southern Europe. The Neolithic populations, which colonized Europe approximately 9,000 y ago, presumably migrated from Near East to Anatolia and from there to Central Europe through Thrace and the Balkans. An alternative route would have been island hopping across the Southern European coast. To test this hypothesis, we analyzed genome-wide DNA polymorphisms on populations bordering the Mediterranean coast and from Anatolia and mainland Europe. We observe a striking structure correlating genes with geography around the Mediterranean Sea with characteristic east to west clines of gene flow. Using population network analysis, we also find that the gene flow from Anatolia to Europe was through Dodecanese, Crete, and the Southern European coast, compatible with the hypothesis that a maritime coastal route was mainly used for the migration of Neolithic farmers to Europe.
Collective Action and Knowledge Contribution in Electronic Networks of Practice

Although there has been a significant increase in networked communication and a growing interest in virtual organizing, to date researchers have yet to establish consistent terminology and have paid little attention to how specific characteristics of the electronic network influence social dynamics such as knowledge contribution. To address this gap, we develop a theoretical model and a set of propositions that explain knowledge contribution in voluntary, computer-mediated, very large and open networks focused on knowledge exchange around a specific practice. We base our model on theories of social networks and collective action to explain how a social network of volunteers sustains productive exchanges between individuals, such as the exchange of knowledge. We utilize the concept of a network of practice to illustrate how the macrostructural properties of the communication media, network size, access to the network, and mode of participation affect network dynamics and knowledge contribution. We then develop a model and a set of propositions to suggest that knowledge contribution within an electronic network of practice is dependent upon 1) the
Preoperative evaluation of cervical lymph nodes for metastasis in patients with oral squamous cell carcinoma: A comparative study of efficacy of palpation, ultrasonography and computed tomography

Introduction: Oral cancer is a major health threat in a country like India, where patients frequently present with advanced disease with regional dissemination to cervical lymph nodes. The management and prognosis depend on the status of cervical lymph nodes. Thus, it becomes imperative to diagnose and evaluate them preoperatively. Aim: This study aims to compare the efficacy of palpation, ultrasonography (USG) and computed tomography (CT) in the preoperative evaluation of cervical lymph node for metastasis in patients with oral squamous cell carcinoma. Settings: Department of Oral and Maxillofacial Surgery, SCB Dental College and Hospital, Cuttack, Odisha, India. Methodology: A total of thirty patients of either sex of age group 20–70 years, diagnosed with oral cancer were randomly selected for the study and subjected to palpation, USG and computer tomography followed by histopathology for confirmation. The results were evaluate statistically by sensitivity, specificity, positive predictive value, and negative predictive value and accuracy. Results: For level IA palpation, USG and CT were equally sensitive (100%) and specific (100%). Although palpation, USG and CT were equally sensitive (80%) for level IB, the specificity of palpation (70%) <USG (95%) = CT (95%). For level II sensitivity of palpation (25%) <USG (75%) <CT (100%) whereas specificity was CT (84.6%) <palpation (92.3%) <USG (100%). Conclusion: CT (96.1%) and USG (97.7%) were more accurate than palpation (92.7%), for detection of metastasis in cervical lymph nodes in patients with oral squamous cell carcinoma. CT along with USG should be used for accurate preoperative evaluation of cervical lymph node.
Fundamental evaluation of moisture damage in warm-mix asphalts

Warm-mix asphalt (WMA) technologies have been used extensively in the last decade. The benefits of WMA have motivated stakeholders to expedite the implementation of this technology. However, some research studies have raised concerns regarding WMA laboratory performance in terms of resistance to moisture damage, while WMA has demonstrated good performance in the field. These experiences led to further research to understand the fundamental characteristics of WMA. This study conducted a comprehensive evaluation of WMA prepared using different aggregate sources, asphalt binders, and WMA additives. A dynamic mechanical analyser was used to test the mastic phase of conventional hot-mix asphalt and WMA. The test specimens were evaluated at different conditions – dry and wet – and at different ageing stages – unaged and three-month aged – in a controlled environmental room (i.e. 60°C). A fracture mechanics approach was used to analyse the test results. This approach incorporated fundamental material properties, including adhesive bond energy between aggregates and asphalt binder. The results show that WMA performance improved with ageing and the overall performance of the WMA can be improved if the selection of materials (i.e. aggregate source, asphalt binder, WMA technology) is optimised based on the compatibility of their surface energy. In addition, surface energy results were able to explain some findings from the mechanical testing related to moisture susceptibility of WMA.
Control of the superior colliculus by the lateral prefrontal cortex

Several decades of patient, functional imaging and neurophysiological studies have supported a model in which the lateral prefrontal cortex (PFC) acts to suppress unwanted saccades by inhibiting activity in the oculomotor system. However, recent results from combined PFC deactivation and neural recordings of the superior colliculus in monkeys demonstrate that the primary influence of the PFC on the oculomotor system is excitatory, and stands in direct contradiction to the inhibitory model of PFC function. Although erroneous saccades towards a visual stimulus are commonly labelled reflexive in patients with PFC damage or dysfunction, the latencies of most of these saccades are outside of the range of express saccades, which are triggered directly by the visual stimulus. Deactivation and pharmacological manipulation studies in monkeys suggest that response errors following PFC damage or dysfunction are not the result of a failure in response suppression but can best be understood in the context of a failure to maintain and implement the proper task set.
Molecular Complexity and Its Impact on the Probability of Finding Leads for Drug Discovery

Using a simple model of ligand-receptor interactions, the interactions between ligands and receptors of varying complexities are studied and the probabilities of binding calculated. It is observed that as the systems become more complex the chance of observing a useful interaction for a randomly chosen ligand falls dramatically. The implications of this for the design of combinatorial libraries is explored. A large set of drug leads and optimized compounds is profiled using several different properties relevant to molecular recognition. The changes observed for these properties during the drug optimization phase support the hypothesis that less complex molecules are more common starting points for the discovery of drugs. An extreme example of the use of simple molecules for directed screening against thrombin is provided.
Neural evidence for description dependent reward processing in the framing effect

Human decision making can be influenced by emotionally valenced contexts, known as the framing effect. We used event-related brain potentials to investigate how framing influences the encoding of reward. We found that the feedback related negativity (FRN), which indexes the “worse than expected” negative prediction error in the anterior cingulate cortex (ACC), was more negative for the negative frame than for the positive frame in the win domain. Consistent with previous findings that the FRN is not sensitive to “better than expected” positive prediction error, the FRN did not differentiate the positive and negative frame in the loss domain. Our results provide neural evidence that the description invariance principle which states that reward representation and decision making are not influenced by how options are presented is violated in the framing effect.
Peptide transport in yeast: utilization of leucine- and lysine-containing peptides by Saccharomyces cerevisiae

A variety of leucine-containing di- and tripeptides and two lysine-containing dipeptides supported the growth of strain Z1-2D, a leucine, lysine auxotroph of Saccharomyces cerevisiae. However, (Lys)2, (Lys)3, (Lys)4, and (Lys)5 as well as Gly-Leu-Gly, three tetra- and one pentapeptide containing leucine were not utilized by the mutant. Cellular peptidases released leucine or lysine from all of these non-growth-supporting peptides, suggesting that the failure of strain Z1-2D to utilize these compounds reflects their failure to enter the yeast. Competition studies employing phenylalanine or non-leucine-containing peptides showed that the uptake of peptides into S. cerevisiae Z1-2D is distinct from that of amino acids and that di- and oligopeptides may share a common transport system. The failure of strain Z1-2D to utilize any peptide larger than (Leu)3 may indicate a transport size limit. Such a size limit would influence the construction of models that explain the action of yeast mating factors.
Apolipoprotein E4 Domain Interaction Induces Endoplasmic Reticulum Stress and Impairs Astrocyte Function*

Domain interaction, a structural property of apolipoprotein E4 (apoE4), is predicted to contribute to the association of apoE4 with Alzheimer disease. Arg-61 apoE mice, a gene-targeted mouse model specific for domain interaction, have lower brain apoE levels and synaptic, functional, and cognitive deficits. We hypothesized that domain interaction elicits an endoplasmic reticulum (ER) stress in astrocytes and an unfolded protein response that targets Arg-61 apoE for degradation. Primary Arg-61 apoE astrocytes had less intracellular apoE than wild-type astrocytes, and unfolded protein response markers OASIS (old astrocyte specifically induced substance), ATF4, and XBP-1 and downstream effectors were up-regulated. ER stress appears to cause global astrocyte dysfunction as glucose uptake was decreased in Arg-61 apoE astrocytes, and astrocyte-conditioned medium promoted neurite outgrowth less efficiently than wild-type medium in Neuro-2a cell cultures. We showed age-dependent up-regulation of brain OASIS levels and processing in Arg-61 apoE mice. ER stress and astrocyte dysfunction represent a new paradigm underlying the association of apoE4 with neurodegeneration.
Heterogeneity of the Hypoxic State in Perfused Rat Heart

SUMMARY Tissue oxygen gradients were examined in the saline-perfused rat heart by NADH fluorescence photography. In high flow hypoxia, where the coronary flow was maintained and the arterial oxygen tension was gradually reduced, oxygen extraction was virtually complete before oxygen consumption was significantly diminished. Inadequate oxygen delivery resulted in a well defined pattern of anoxic zones. The anoxic zones were several hundred microns in width, an order of magnitude greater than intercapillary distances. In low flow hypoxia (ischemia), where the arterial oxygen tension remained at its control value and the coronary flow was diminished, anoxic zones also developed, following the same pattern as in high flow hypoxia. However, in ischemia, the anoxic areas developed while the effluent oxygen tension was significantly greater than zero. Whereas respiratory acidosis between pH 7.3 and 6.9 resulted in vasodilation, below pH 6.8 there was a marked increase in vascular resistance. Anoxic zones appeared despite only a slight change in effluent oxygen tension from the control. In high flow hypoxia, ischemia, and acidosis-induced ischemia, the anoxic zones disappeared when control perfusion conditions were restored. The data demonstrate that tissue oxygen gradients are very steep in the hypoxic state, so that ischemia and hypoxia result in discrete heterogeneous areas of anoxic tissue bounded by sharp areas where the oxygen supply is sufficient to maintain normal mitochondrial oxidative function. In these states in which oxygen delivery is less than oxygen demand, coronary perfusion appears to be regulated at the level of the arterioles rather than the capillaries.
Title : Testosterone and cortisol jointly modulate risk-taking

Recent theories propose that testosterone should be positively related to risk-taking, but empirical support is mixed. Building on the dual-hormone hypothesis, the present research tested whether testosterone’s role in risk-taking depends on cortisol. Study 1 (N = 115) tested this hypothesis in a mixed-sex sample with self and informant reports of risk-taking. Study 2 (N = 165) tested this hypothesis in a male-only sample with the Balloon Analog Risk Task, a behavioral measure of risk-taking. Across both studies, there was a positive association between basal testosterone and risk-taking among individuals low in basal cortisol but not individuals high in basal cortisol. This pattern emerged in both males and females and across multiple measures of risk-taking (self reports, informant reports, behavior). These studies provide novel empirical support for the claim that testosterone and cortisol jointly regulate risk-taking. Discussion focuses on putative mechanisms as well as implications for real-world risk-taking behaviors.
Deconvolution of Blood Microarray Data Identifies Cellular Activation Patterns in Systemic Lupus Erythematosus

Systemic Lupus Erythematosus (SLE) is a systemic autoimmune disease with a complex spectrum of cellular and molecular characteristics including several dramatic changes in the populations of peripheral leukocytes. These changes include general leukopenia, activation of B and T cells, and maturation of granulocytes. The manifestation of SLE in peripheral blood is central to the disease but is incompletely understood. A technique for rigorously characterizing changes in mixed populations of cells, microarray expression deconvolution, has been applied to several areas of biology but not to SLE or to blood. Here we demonstrate that microarray expression deconvolution accurately quantifies the constituents of real blood samples and mixtures of immune-derived cell lines. We characterize a broad spectrum of peripheral leukocyte cell types and states in SLE to uncover novel patterns including: specific activation of NK and T helper lymphocytes, relationships of these patterns to each other, and correlations to clinical variables and measures. The expansion and activation of monocytes, NK cells, and T helper cells in SLE at least partly underlie this disease's prominent interferon signature. These and other patterns of leukocyte dynamics uncovered here correlate with disease severity and treatment, suggest potential new treatments, and extend our understanding of lupus pathology as a complex autoimmune disease involving many arms of the immune system.
Current version:

Rationale: With the current dizzying array of study abroad options available to our majors, the Spanish Department would like to streamline its major to make it more flexible so that students who study abroad and receive “No Equivalent” hours may more easily complete the requirements for the major. These courses are usually worth 2, 4, or 6 hours rather than the standard 3. Such students often find it difficult to fit their foreign coursework into the restrictive framework of the current major. Therefore we propose a single program of study which allows for a wider variety of elective possibilities.
Integrated Analysis of Gene Copy Number, Copy Neutral LOH, and microRNA Profiles in Adult Acute Lymphoblastic Leukemia

We adopted an integrated analysis of gene copy number alterations (CNAs), copy number neutral loss of heterozygosity (CNN LOH), and microRNA (miRNA) profiling in 21 adult acute lymphoblastic leukemia (ALL) patients. This study revealed the most frequent CNAs to be at chromosomes 9p, 7, and 17 and recurrent CNN LOH at 5p, 9p, and Xq. As for the most differentially expressed miRNAs, they included 8 upregulated and 14 downregulated miRNAs, of which miR-148a at 7p15.2, miR-22 at 17p13.3, miR-223 at Xq12, as well as miR-101-2 at 9p24.1 exhibited recurrent CNAs or CNN LOH. miR-101-2 was recurrently downregulated, and although the related CNN LOH was detected only in BCR-ABL1 negative cases (2/14), deletions of miR-101-2 were observed solely in BCR-ABL1 positive cases (4/7). Finally, BCR-ABL1 positive cases, in contrast to negative ones, were characterized by slightly, but still significantly, higher expression levels of miR-29b.
Healing the healer: A tool to encourage student reflection towards health

Background: Research has demonstrated that students’ health falters while in medical school with healthy behaviors continuing to deteriorate during residency. Medical education can be focused toward helping students find health for themselves. Physicians who are most likely to practice healthy lifestyles are more likely to encourage their patients to do so. Aims: Create a tool that encourages self-reflection, education and self-care for physicians-in-training. Method: Users completed a web-based tool that helped them create a personal health plan focusing on the themes of nutrition, lifestyle choices, family history, mind-body influences and spiritual connection. A six-question survey was completed by 500 users. Results: The results support the main objectives of the tool, which were to encourage self-reflection, positive lifestyle habits and education towards key aspects of health and well-being. Conclusion: Having medical students and residents develop their own health plans can be an efficient method towards encouraging self-care, understanding foundational health concepts and instilling skills to teach health promotion to their patients.