Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of Chlamydia trachomatis omp1 Genotypes among Sexually Transmitted Disease Patients in Sweden

ABSTRACT A method for detection and genotyping of genital Chlamydia trachomatis infections based on omp1 gene amplification and sequencing was developed. DNA was extracted from urogenital or urine samples using a Chelex-based method, and an approximately 1,100-bp-long fragment from the omp1 gene was directly amplified and sequenced. Genotyping was performed by BLAST similarity search, and phylogenetic tree analysis was used to illustrate the evolutionary relationships between clinical isolates and reference strains. The method was used to determine the genotypes ofC. trachomatis in 237 positive urogenital and/or urine specimens collected at a Swedish sexually transmitted disease clinic during 1 year. The most common genotypes corresponded to serotypes E (47%) and F (17%). The omp1 gene was highly conserved for genotype E (106 of 112 samples without any mutation) and F (41 of 42 samples without any mutation) strains but appear slightly less conserved for genotypes G (n = 6) and H (n = 6), where the sequences displayed one to four nucleotide substitutions relative to the reference sequence. Genotyping of samples collected at the follow-up visit indicated that two patients had become reinfected, while three other patients suffered treatment failure or reinfection. One woman appeared to have a mixed infection with two different C. trachomatis strains. Thisomp1 genotyping method had a high reproducibility and could be used for epidemiological characterization of sexually transmitted Chlamydia infections.
Enforced pointing gesture can indicate invisible objects behind a wall

The pointing gesture is regarded as indicating an object or location in the environment. People sometimes point to invisible objects, but the inferential mechanism is not known. This study examined comprehension of pointing with a bent index finger at an invisible object behind a wall. The experimenter pointed at an object using either typical pointing or “enforced pointing” behind a wall that was either opaque or transparent. In enforced pointing, the experimenter moved his arm in an arc movement. The participants guessed which object was being denoted. The wall was also either relatively high or relatively low. When the participants looked at typical pointing, they thought that objects both in front of the wall and behind the wall were being denoted. However, when they looked at enforced pointing, they more frequently thought that objects behind the wall were denoted. People seemed to use pragmatic knowledge on this “enforced” pointing gesture.
Mechanism of Substrate Recognition by Drug-Resistant Human Immunodeficiency Virus Type 1 Protease Variants Revealed by a Novel Structural Intermediate

ABSTRACT Human immunodeficiency virus type 1 (HIV-1) protease processes and cleaves the Gag and Gag-Pol polyproteins, allowing viral maturation, and therefore is an important target for antiviral therapy. Ligand binding occurs when the flaps open, allowing access to the active site. This flexibility in flap geometry makes trapping and crystallizing structural intermediates in substrate binding challenging. In this study, we report two crystal structures of two HIV-1 protease variants bound with their corresponding nucleocapsid-p1 variant. One of the flaps in each of these structures exhibits an unusual “intermediate” conformation. Analysis of the flap-intermediate and flap-closed crystal structures reveals that the intermonomer flap movements may be asynchronous and that the flap which wraps over the P3 to P1 (P3-P1) residues of the substrate might close first. This is consistent with our hypothesis that the P3-P1 region is crucial for substrate recognition. The intermediate conformation is conserved in both the wild-type and drug-resistant variants. The structural differences between the variants are evident only when the flaps are closed. Thus, a plausible structural model for the adaptability of HIV-1 protease to recognize substrates in the presence of drug-resistant mutations has been proposed.
Universals of tone rules: 30 years later

Over 30 years ago, Hyman & Schuh (1974) surveyed a number of West African tone systems and determined that the most common forms of tone rules were tone spreading and (contour) tone simplification. Since then the study of tone has undergone dramatic development both in terms of theory as well as descriptive coverage of the world’s languages. In this paper I reexamine and elaborate on the major findings of the earlier study. Drawing on a wider range of tone systems, I show that Hyman & Schuh’s claims are confirmed in languages outside West Africa as well. Concerning the perseverative bias of tone spreading, cases of tone anticipation in Eastern Bantu are shown to originate at the right edge of a domain, originally triggered by a final boundary tone. Contour tone simplification is systematically examined in context, revealing that the process may be sensitive to the nature of the preceding and/or following tone. At various points a distinction is made between the articulatory vs. perceptual factors motivating recurrent tone rules. These findings cohere with the tendencies in F0 alignment documented in intonational systems as well.
Distinct Mechanisms Control Human Naive and Antigen-Experienced CD8+ T Lymphocyte Proliferation1

Human Ag-specific CD8+ T lymphocytes are heterogeneous and include functionally distinct populations. In this study, we report that at least two distinct mechanisms control the expansion of circulating naive, memory, and effector CD8+ T lymphocytes when exposed to mitogen or Ag stimulation. The first one leads to apoptosis and occurs shortly after in vitro stimulation. Susceptibility to cell death is prominent among primed T cell subsets, and it is inversely correlated with the size of the ex vivo Bcl-2high population within these subsets. Importantly, the Bcl-2high phenotype is associated to the proportion of responsive CD8+ T cells, independently of their differentiation stage. The second one depends on the expression of newly synthesized cyclin-dependent kinase inhibitor p16INK4a that occurs in a significant fraction of T cells that had been actively cycling, leading to their cell cycle arrest upon stimulation. Strikingly, accumulation of p16INK4a protein preferentially occurs in naive as opposed to primed derived T lymphocytes and is not related to apoptosis. Significant levels of p16 are readily detectable in a small number of ex vivo CD8+ T cells. Our observations reveal that activation-induced p16 expression represents an alternative process to apoptosis, limiting the proliferation potential of activated naive derived T lymphocytes.
Finding and Classifying Product Relationships using Information from the Public Web

Relationships between products such as accessory or successor products are hard to find on the Web or have to be inserted manually in product information systems. Finding and classifying such relations automatically using information from the public Web only offers great value for customers and vendors as it helps to improve the buying process at low cost. We present and evaluate algorithms and methods for product relationship extraction on the Web requiring only a set of clustered product names as input. The solution can be easily implemented in different product information systems most useful in but not necessarily restricted to the application domain of online shopping.
Controle op Nederlandse wijze in Vlaamse gemeenten: pure science fiction of realistisch toekomstscenario?

Het Nieuw Publiek Management (verder NPM), een containerbegrip voor een brede waaier van moderniseringen en hervormingsinitiatieven tijdens de laatste decennia, bracht het concept van ‘controle’ in lokale besturen opnieuw SAMENVATTING Ondanks het feit dat er recent verschillende controle-instrumenten (rapportages gekoppeld aan de beleidsen beheerscyclus (BBC), interne controle, externe audit . ) zijn geïntroduceerd in de Vlaamse gemeenten, geven raadsleden zelf aan hun controlerende rol ten opzichte van het college van burgemeester en schepenen niet ten volle uit te spelen. Controleactiviteiten maken echter integraal deel uit van de versterkte gemeenteraad die men hiermee hoopte te realiseren. Ingegeven door een aantal contextuele factoren zoals dualisering en schaalvergroting, is de controlepraktijk in Nederlandse gemeenten veel sterker uitgebouwd, onder meer door de installatie van een rekenkamerfunctie en een griffie. In dit artikel gaan we op basis van literatuuronderzoek en eigen ervaringen na of de Vlaamse lokale bestuurders lessen kunnen trekken uit de wijze waarop Nederlandse raadsleden hun college controleren. Naast een bespreking van het beschikbare instrumentarium focussen we op het werkelijk gebruik van de controleinstrumenten in beide landen. Daaruit blijkt dat een uitgebreid controle-instrumentarium niet automatisch resulteert in uitgebreide controleactiviteiten door raadsleden. Contextuele en politieke factoren zoals schaalgrootte en openheid vanuit de meerderheid en het college vormen kritische randvoorwaarden om tot een gedegen controlepraktijk vanuit de gemeenteraad te komen.
Pressor effects following microinjection of 5‐HT1A receptor agonists into the raphe obscurus of the anaesthetized rat

1 The effects of electrical stimulation and microinjections (90 nl) of the 5‐HT1A receptor agonists, flesinoxan and 8‐hydroxy‐2‐(di‐n‐propylamino) tetralin (8‐OH‐DPAT), and glutamate into the raphe obscurus on blood pressure, heart rate and phrenic nerve activity (central inspiratory drive) were investigated in rats anaesthetized with α‐chloralose. 2 Electrical stimulation of the raphe obscurus caused a rise in blood pressure which was associated with bradycardia, while glutamate (2.7 nmol) caused only a rise in blood pressure. 3 Flesinoxan (1.3 nmol) and 8‐OH‐DPAT (0.7 nmol) increased blood pressure by 9 ± 1 and 14 ± 2 mmHg, respectively and did not affect heart rate. For both agonists the effect on blood pressure was shown to be dose‐dependent; again no effect on the heart rate was observed over the dose‐ranges chosen. 4 Microinjections of the non‐selective 5‐HT1A receptor antagonists, (±)‐pindolol (2.7 nmol) or methiothepin (5.2 nmol), into the raphe obscurus prevented the increase in blood pressure caused by microinjection of flesinoxan. However, (±)‐pindolol caused a sustained rise in blood pressure of 15 ± 1 mmHg while methiothepin caused a transient rise in blood pressure. Neither drugs affected heart rate. The ability of methiothepin to attenuate the pressor effect of flesinoxan was found to be partially reversed after 30 min. 5 It is suggested that activation of 5‐HT1A receptors within the raphe obscurus can cause sympathoexcitation.
Pattern of thyroid disorders in the southwestern region of Nigeria.

OBJECTIVE Thyroid disorders were thought to be rare in Africans in the early 1960s. However the 1970s witnessed an upsurge in reported cases of thyroid disorders in Africans. In endocrinology clinics in Nigeria, thyroid disorders are the second most common endocrine disorders seen. This study attempts to describe the patterns of thyroid disorders, clinical features, and complications as seen in Nigerians. DESIGN/SUBJECTS This is a descriptive study that took place from June 2004 to August 2005 in the Department of Medicine of the Lagos State University Teaching Hospital, Ikeja, Nigeria. The demographic data, anthropometric indices, clinical features and associated complications of thyroid disorders were documented. Patients were categorized into three broad groups according to symptoms and biochemical profile as being euthyroid, thyrotoxic and hypothyroid. RESULTS The total number of patients with thyroid disorders seen in a 15-month period was 78. The female:male ratio was 5:1. The mean (standard deviation) age of all the subjects studied was 40 (12.4) years. The female:male ratio of those with thyrotoxicosis was 5.6:1. Cardiovascular complications of thyrotoxicosis, namely heart failure and atrial fibrillation, were the most common reasons for prolonged morbidity and hospitalizations. Hypothyroidism was present in five (7%), Graves disease/hyperthyroidism in 63 (84%), and euthyroid in 10 (9%). Obstructive symptoms were documented in eight (13%) of the subjects with palpable goiters. CONCLUSION Thyroid disorders in Nigerians are a significant cause of cardiovascular morbidity. Public awareness of thyroid disorders and their potential complications could lead to improved diagnostic and therapeutic facilities.
Cholesterol increases kinetic, energetic, and mechanical stability of the human β2-adrenergic receptor

The steroid cholesterol is an essential component of eukaryotic membranes, and it functionally modulates membrane proteins, including G protein-coupled receptors. To reveal insight into how cholesterol modulates G protein-coupled receptors, we have used dynamic single-molecule force spectroscopy to quantify the mechanical strength and flexibility, conformational variability, and kinetic and energetic stability of structural segments stabilizing the human β2-adrenergic receptor (β2AR) in the absence and presence of the cholesterol analog cholesteryl hemisuccinate (CHS). CHS considerably increased the kinetic, energetic, and mechanical stability of almost every structural segment at sufficient magnitude to alter the structure and functional relationship of β2AR. One exception was the structural core segment of β2AR, which establishes multiple ligand binding sites, and its properties were not significantly influenced by CHS.
Analysis of Patient-reported Outcomes of Quality of Life and Functioning Before and After Treatment of Major Depressive Disorder Comorbid With Alcohol Use Disorders.

OBJECTIVE Alcohol use disorders (AUDs) are common among persons with major depressive disorder (MDD) and have an adverse impact on course of illness and patient outcomes. The aim of this study was to examine whether AUD adversely impacted patient-centered outcomes in a sample of research subjects evaluated as part of a large clinical trial for depression. The outcomes of interest to this post hoc analysis are quality of life (QOL), functioning, and depressive symptom severity. METHODS We analyzed 2280 adult MDD outpatient research subjects using data from the Sequenced Treatment Alternatives to Relieve Depression trial. We compared entry and post-selective serotonin reuptake inhibitors (SSRI) treatment QOL, functioning, and depressive symptom severity scores between 121comorbid MDD with AUD (MDD + AUD) subjects and 2159 MDD-no-AUD subjects, and also differences between subjects categorized as remitters versus nonremitters within each group at exit. RESULTS At entry, MDD + AUD subjects reported similar QOL, functioning, and depressive symptom severity compared with the MDD-no-AUD subjects. After treatment with citalopram, both groups showed significant improvements throughout treatment; however, 36% to 55% of subjects still suffered from severely impaired QOL and functioning at exit. CONCLUSIONS The overall study population demonstrated a significant response to treatment with large effect sizes in depressive symptom reduction, but to a lesser extent in QOL and functioning. Findings suggest that subjects with MDD + AUD benefited equally as MDD-no-AUD from treatment with selective serotonin reuptake inhibitors (SSRI) medication, yet both groups continue to experience reduced QOL and functioning after treatment. Monitoring QOL and functioning is critical to determine whether interventions that improve clinical outcomes also impact patient-centered outcomes, and our analysis suggests that there is a pressing need for innovative interventions that effectively improve these outcomes.
Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes

Research in autophagy continues to accelerate,(1) and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose. (2,3) There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.
Experimental study of Taylor’s hypothesis in a turbulent soap film

An experimental study of Taylor’s hypothesis in a quasi-two-dimensional turbulent soap film is presented. A two-probe laser Doppler velocimeter enables a nonintrusive simultaneous measurement of the velocity at spatially separated points. Using the cross correlation between a pair of points displaced in both space and time, the velocity coherence is measured to be better than 90% for scales less than the integral scale. Taylor’s hypothesis is confirmed insofar as the lower moments of the longitudinal velocity difference are equal whether measured with or without invoking the hypothesis. A quantitative study of the decorrelation beyond the integral scale is also presented.
Fluid simulation: SIGGRAPH 2007 course notesVideo files associated with this course are available from the citation page

Animating fluids like water, smoke, and fire by physics-based simulation is increasingly important in visual effects and is starting to make an impact in real-time games. This course goes from the basics of 3D fluid flow to the state of the art in graphics. We will begin with an intuitive explanation of the important concepts in fluid simulation, and as we progress demonstrate how to implement an effective smoke and water simulation system, complete with irregular curved boundaries and surface tension. The last half of the course will cover advanced topics such as fire and explosions, adaptive grid methods, real-time-capable algorithms together with the latest technology in hardware acceleration, and non-Newtonian fluids like sand. Intuition and implementation details will be underscored throughout.
Auditor Evaluation of Others’ Credibility: A Review of Experimental Studies on Determinants and Consequences

I synthesize the extant experimental literature examining auditor evaluation of others’ credibility published in six top accounting journals over the last three-and-a-half decades. I adapt the original definition of credibility by Hovland, Janis, and Kelley (1953): the extent of perceiving someone as competent and trustworthy. Audit guidance requires auditors to consider credibility of management, internal auditors, and staff, yet the research literature on auditor evaluation of others’ credibility is fragmented and scarce, limiting our understanding of determinants and consequences of auditor evaluations. I develop a framework for analysis of research on auditor evaluation of others’ credibility and review extant literature by types of examined effects (determinants of credibility vs. consequences of credibility) and by examined credibility components (competence, trustworthiness, or both). Throughout the literature review I suggest areas for future research.
Dimensions of Teacher Self-Efficacy and Relations with Strain Factors, Perceived Collective Teacher Efficacy, and Teacher Burnout.

In this study, the authors developed and factor analyzed the Norwegian Teacher Self-Efficacy Scale. They also examined relations among teacher self-efficacy, perceived collective teacher efficacy, external control (teachers' general beliefs about limitations to what can be achieved through education), strain factors, and teacher burnout. Participants were 244 elementary and middle school teachers. The analysis supported the conceptualization of teacher self-efficacy as a multidimensional construct. They found strong support for 6 separate but correlated dimensions of teacher self-efficacy, which were included in the following subscales: Instruction, Adapting Education to Individual Students' Needs, Motivating Students, Keeping Discipline, Cooperating With Colleagues and Parents, and Coping With Changes and Challenges. They also found support for a strong 2nd-order self-efficacy factor underlying the 6 dimensions. Teacher self-efficacy was conceptually distinguished from perceived collective teacher efficacy and external control. Teacher self-efficacy was strongly related to collective teacher efficacy and teacher burnout.
Modeling Information Systems Using Objects, Agents, and Task-Based Problem Solving Adapters

A surge control fluid delivery system is described particularly adapted for pumping of high-viscosity substances from a reservoir for dispensing. The system includes a manifold which is connected to an outlet line of a pump. A vent circuit for returning fluid from the manifold to the reservoir is also provided. Surge control is achieved through a control system which modulates the fluid supply pump and further activates a valve in the vent return line to maintain the pressure of the fluid within the manifold to within adjustable upper and lower limits. The system further includes means for automatically switching from one source of fluid to another upon depletion of the first source.
High perceptual load causes inattentional blindness and deafness in drivers

ABSTRACT Perceptual load theory of attention predicts that the level of perceptual load in a primary task affects the processing of additional stimuli. Given the lack of ecologically valid evidence for the model, the current study assessed the effect of perceptual load on driver awareness during simulated driving tasks. The results showed that perceptual load dramatically affected driver awareness for visual and auditory stimuli, even those that were driving relevant and safety critical (e.g. pedestrians or the sound of a car horn). The results support load theory and suggest that perceptual load may be an important factor in driver safety.