Miracle-dz/UniFAR-FTUs huggingface dataset:
HigB of Pseudomonas aeruginosa Enhances Killing of Phagocytes by Up-Regulating the Type III Secretion System in Ciprofloxacin Induced Persister Cells

Bacterial persister cells are dormant and highly tolerant to lethal antibiotics, which are believed to be the major cause of recurring and chronic infections. Activation of toxins of bacterial toxin-antitoxin systems inhibits bacterial growth and plays an important role in persister formation. However, little is known about the overall gene expression profile upon toxin activation. More importantly, how the dormant bacterial persisters evade host immune clearance remains poorly understood. Here we demonstrate that a Pseudomonas aeruginosa toxin-antitoxin system HigB-HigA is required for the ciprofloxacin induced persister formation. Transcriptome analysis of a higA::Tn mutant revealed up regulation of type III secretion systems (T3SS) genes. Overexpression of HigB increased the expression of T3SS genes as well as bacterial cytotoxicity. We further demonstrate that wild type bacteria that survived ciprofloxacin treatment contain higher levels of T3SS proteins and display increased cytotoxicity to macrophage compared to vegetative bacterial cells. These results suggest that P. aeruginosa accumulates T3SS proteins during persister formation, which can protect the persister cells from host clearance by efficiently killing host immune cells.
Status of the optical payload and processor development of ESA's Sentinel 3 mission

In order to meet Earth observation needs of the European Union-ESA Global Monitoring for Environment and Security (GMES) programme, ESA decided to develop the Sentinels as first series of operational satellites. The series of Sentinel-3 satellites will provide global, frequent and near-realtime ocean, ice and land monitoring. It continues Envisat's altimetry, the multispectral, medium-resolution visible and infrared ocean and land-surface observations of ERS, Envisat and Spot, and includes enhancements to meet the operational revisit requirements and to facilitate new products and evolution of services. The first launch is expected in 2012. In this paper the design of the major instruments and their basic performance parameters will be introduced as well as the expected accuracies of the main data products.
Deaf President Now and the Struggle for Deaf Control of Gallaudet University

Deaf President Now, or DPN, should be viewed as a process, not as a single event. The forces that led to the installation of the first deaf president at Gallaudet were set in motion long before 1988, and they continued to be significant through the protests of 2006. Among the many changes wrought by the 1988 DPN movement is a fundamental shift in the demographics of the Gallaudet workforce, such that the percentage of deaf people among the pool of employees has doubled from 25 percent to 50 percent. This article attempts to put DPN in historical context, and it argues that this shift in the Gallaudet work-force has led to profound changes in the institutional culture.
Accessible Online Indoor Maps for Blind and Visually Impaired Users

This paper proposes alternatives for the development and improvement of maps to aid accessibility. Based on our analysis, we present an accessible online indoor map prototype that complies with WCAG 2.0. For the case study, the prototype displays an indoor map that is designed using Scalable Vector Graphics (SVG) format. This format can include information that helps the screen reader to interpret the visual graph information. In addition, the prototype can simulate the route that the users select so they can get an idea of the environment where they will mobilize. We tested the prototype in different browsers with the help of blind people.
Measuring Effectiveness in Transfer Practices For Adult Learners

Sciences and director of the Educational Opportunity Fund Program. Address correspondence to B. Christopher Dougherty, Rutgers University-Camden, Armitage Hall, Room 365, Camden, NJ 08102-1521, USA (E-mail: chrdou@camden.rutgers.edu). The Journal of Continuing Higher Education, 57:54–58, 2009 Copyright © 2009, Association for Con tinu ing Higher Education ISSN 0737-7363 DOI: 10.1080/07377360902839933
Designing and Implementing an Innovative SMS-based alert system (RapidSMS-MCH) to monitor pregnancy and reduce maternal and child deaths in Rwanda

Introduction With the continuous growth of mobile network coverage and unprecedented penetration of mobile devices in the developing world, several mHealth initiatives are being implemented in developing countries. This paper aims to describe requirements for designing and implementing a mobile phone-based communication system aiming at monitoring pregnancy and reducing bottlenecks in communication associated with maternal and newborn deaths; and document challenges and lessons learned. Methods An SMS-based system was developed to improve maternal and child health (MCH) using RapidSMS®, a free and open-sourced software development framework. To achieve the expected results, the RapidSMS-MCH system was customized to allow interactive communication between a community health worker (CHW)following mother-infant pairs in their community, a national centralized database, the health facility and in case of an emergency alert, the ambulance driver. The RapidSMS-MCH system was piloted in Musanze district, Nothern province of Rwanda over a 12-month period. Results A total of 432 CHW were trained and equipped with mobile phones. A total of 35,734 SMS were sent by 432 CHW from May 2010 to April 2011. A total of 11,502 pregnancies were monitored. A total of 362 SMS alerts for urgent and life threatening events were registered. We registered a 27% increase in facility based delivery from 72% twelve months before to 92% at the end of the twelve months pilot phase. Major challenges were telephone maintenance and replacement. Disctrict heath team capacity to manage and supervise the system was strengthened by the end of pilot phase. Highly committed CHWs and effective coordination by the District health team were critical enablers. Conclusion We successully designed and implemented a mobile phone SMS-based system to track pregnancy and maternal and child outcomes in limited resources setting. Implementation of mobile-phone systems at community level could contribute to improving emergency obstetric and neonatal care, yet it requires a well-organized community health structure in limited resource settings.
Efficient construction and simplification of Delaunay meshes

Delaunay meshes (DM) are a special type of triangle mesh where the local Delaunay condition holds everywhere. We present an efficient algorithm to convert an arbitrary manifold triangle mesh M into a Delaunay mesh. We show that the constructed DM has O(Kn) vertices, where n is the number of vertices in M and K is a model-dependent constant. We also develop a novel algorithm to simplify Delaunay meshes, allowing a smooth choice of detail levels. Our methods are conceptually simple, theoretically sound and easy to implement. The DM construction algorithm also scales well due to its O(nK log K) time complexity. Delaunay meshes have many favorable geometric and numerical properties. For example, a DM has exactly the same geometry as the input mesh, and it can be encoded by any mesh data structure. Moreover, the empty geodesic circumcircle property implies that the commonly used cotangent Laplace-Beltrami operator has non-negative weights. Therefore, the existing digital geometry processing algorithms can benefit the numerical stability of DM without changing any codes. We observe that DMs can improve the accuracy of the heat method for computing geodesic distances. Also, popular parameterization techniques, such as discrete harmonic mapping, produce more stable results on the DMs than on the input meshes.
Miners, diggers, ferals and show‐men: school–community projects that affirm and unsettle identities and place?

Many contemporary sociologists suggest that a feature of modern life is that the practices and identities associated with ‘place’ are eroded. The local no longer matters in everyday life as it once did. Some national governments are persuaded of the possibility of an urban dystopia of Orwellian dimensions, and have found a response in theories and rhetorics of social capital, citizenship and communitarianism. They have instituted strategies to address an imaginary of harmonious local communities. In this paper I examine one such government intervention and show how four schools in Tasmania, Australia, took up the invitation to strengthen ties with their local communities. The projects reveal that the local still exists and matters, but they also hint at other possibilities. I argue that by working with a ‘place‐based’ curriculum to assist young people in building local networks and engaging productively with their local neighbourhoods, schools might provide important resources for identity‐building and learning.
Speech-evoked auditory potentials in attention deficit hyperactivity disorder

Abstract Objective: To explore the processing of auditory information through auditory brainstem and higher cortical regions in a sample of children with attention deficit hyperactivity disorder (ADHD) of the combined inattention and hyperactivity subtype (ADHD/C) using auditory evoked potentials. Study Design: Fifteen Arabic speaking ADHD/C children were compared to 15 age-matched normal controls, aged between five and ten years. A Mini-International Neuropsychiatric Interview for Children and Adolescents (Arabic version) was performed to confirm the diagnosis, subtype of ADHD and to exclude comorbid conditions. All children were subjected to Auditory Brainstem Evoked Response (ABR) to click, speech ABR and cortical Mis-Match Negativity (MMN) to speech stimuli. Results: Thirty-three percent of the ADHD/C group showed prolongation of absolute and/or inter-peak wave latencies of the click ABR beyond two standard deviations. The peak latency of the onset waves for speech ABR was abnormal in 87% of the study group. Only three ADHD/C children gave normal MMN. Conclusion: This study demonstrated that abnormal auditory brainstem timing with reduced cortical functions was a characteristic in the studied ADHD/C children. Speech ABR can serve as a biological marker for brainstem neural asynchrony in children with ADHD/C. It might help to organize the highly heterogeneous population of ADHD into more homogeneous subgroups, at least on a particular biological indicator, specifically in individuals who cannot perform the behavioural measures. Further research is needed to determine whether individuals within these subgroups share a similar auditory perceptual profile.
Learning of Detour Problems by Lemurs and Seven Species of Monkeys

40 Ss drawn from 7 species of monkey, and Lemur catta were trained to solve bent-wire detour problems. Old World monkeys were significantly more proficient than New World monkeys or lemurs, but members of the latter two groups did not differ significantly from each other. The results are compared with those obtained with children, apes, and raccoons.
Exploiting Multi-Features to Detect Hedges and their Scope in Biomedical Texts

In this paper, we present a machine learning approach that detects hedge cues and their scope in biomedical texts. Identifying hedged information in texts is a kind of semantic filtering of texts and it is important since it could extract speculative information from factual information. In order to deal with the semantic analysis problem, various evidential features are proposed and integrated through a Conditional Random Fields (CRFs) model. Hedge cues that appear in the training dataset are regarded as keywords and employed as an important feature in hedge cue identification system. For the scope finding, we construct a CRF-based system and a syntactic pattern-based system, and compare their performances. Experiments using test data from CoNLL-2010 shared task show that our proposed method is robust. F-score of the biological hedge detection task and scope finding task achieves 86.32% and 54.18% in in-domain evaluations respectively.
Conceiving Ambiguity: Dynamic Mindreading in Shakespeare’s Twelfth Night

What cognitive process allows a spectator to experience shock and surprise at a character’s actions, yet, a moment later, to decide that the actions presented onstage are coherent and understandable? Drawing upon theories of mindreading and conceptual blending, I offer a dynamic model of character that accounts for surprise, ambiguity, and dramatic shifts of understanding. Subtle changes to one’s perceptions, empathic imagination, and social knowledge—the sort of changes that accumulate throughout the viewing of Shakespeare’s Twelfth Night—can alter one’s understanding of a character in unexpected ways.
On the holomorphicity of genus two Lefschetz fibrations

We prove that any genus-2 Lefschetz fibration without reducible fibers and with “transitive monodromy” is holomorphic. The latter condition comprises all cases where the number of singular fibers µ ∈ 10N is not congruent to 0 modulo 40. This proves a conjecture of the authors in [SiTi1]. An auxiliary statement of independent interest is the holomorphicity of symplectic surfaces in S 2 -bundles over S 2 , of relative degree ≤ 7 over the base, and of symplectic surfaces in CP 2 of degree ≤ 17.
Discovery of Novel Checkpoint Kinase 1 Inhibitors by Virtual Screening Based on Multiple Crystal Structures

Incorporating receptor flexibility is considered crucial for improvement of docking-based virtual screening. With an abundance of crystallographic structures freely available, docking with multiple crystal structures is believed to be a practical approach to cope with protein flexibility. Here we describe a successful application of the docking of multiple structures to discover novel and potent Chk1 inhibitors. Forty-six Chk1 structures were first compared in single structure docking by predicting the binding mode and recovering known ligands. Combinations of different protein structures were then compared by recovery of known ligands and an optimal ensemble of Chk1 structures were selected. The chosen structures were used in the virtual screening of over 60 000 diverse compounds for Chk1 inhibitors. Six novel compounds ranked at the top of the hits list were tested experimentally, and two of these compounds inhibited Chk1 activity-the best with an IC(50) value of 9.6 μM. Further study indicated that achieving a better enrichment and identifying more diverse compounds was more likely using multiple structures than using only a single structure even when protein structures were randomly selected. Taking into account conformational energy difference did not help to improve enrichment in the top ranked list.
Complications of cataract and refractive surgery: a clinicopathological documentation.

PURPOSE To present selected complications of keratorefractive and phakic intraocular lens (IOL) surgery and a series of IOLs that required explantation because of various postimplantation opacification of the IOL optic. METHODS Two specimens obtained after keratorefractive surgery, 2 phakic IOLs, and a total of 23 explanted IOLs from cases in which postimplantation opacification of the IOL optic had occurred were studied. These included 6 Bausch and Lomb (B&L) Hydroview H60 M designs, 9 Medical Developmental Research (MDR) SC60B-OUV designs, and 24 IOLs with rigid PMMA optics that had been implanted in the 1980s and early 1990s. Of the latter, 8 required late explantation because of decreased visual acuity. Analyses performed included gross and light microscopic evaluation, histochemical staining, electron microscopy, and energy-dispersive spectroscopy. RESULTS We provide examples of 3 postrefractive surgery complications: (1) fungal keratitis after LASIK, (2) post-LASIK corneal decompensation, and (3) cataract formation after implantation of phakic posterior chamber IOLs. Regarding the IOL optic opacities, classifications of 3 types are described: (1) a surface calcification of the B&L Hydroview IOL; (2) diffusion of calcium into the substance of the optic of the hydrophilic "acrylic" SC60B-OUV MDR foldable IOL design, sometimes leading to total opacification of the IOL optic and also its haptics; (3) a distinct pattern of intraoptical opacification with rigid PMMA designs that we term a snowflake degeneration. This term is based on the clinical and pathologic appearance of the individual lesions. Each snowflake lesion represents a focal breakdown of PMMA material as opposed to deposition of exogenous material. CONCLUSIONS Analysis of complications of refractive surgery represents a new field of ocular pathology. The clinicopathological reports presented here provide an overview of selected complications after refractive surgery. We also help define 3 newly recognized, clinically significant conditions based on postoperative IOL optic opacification. The calcification processes noted on the 2 modern foldable designs studied here (B&L and MDR lenses) need further review by the manufacturers in order to reassess production processes, especially in terms of polymer selection, manufacturing techniques, and other factors required to produce a safe and effective lens. Any lens not meeting today's high standards should not be marketed. The important fact in recognizing the snowflake complication of PMMA IOLs as described here is to alert surgeons about the nature of the lesion so that they will not alarm patients or require extensive and unnecessary testing in trying to determine its pathogenesis. There is no reason why successful explantation cannot be performed in cases where severe visual decrease or loss has occurred.
Nature of the antigenic complex recognized by T lymphocytes II. T-cell activation by direct modification of macrophage histocompatibility antigens

In order to analyze the molecular structures involved in T-cell recognition we developed an in vitro primary response against alloantisera bound to histocompatibility antigens in which nonimmune guinea pig T cells can be sensitized and subsequently challenged in tissue culture with antisera-treated macrophages. If macrophages were incubated with alloantisera directed against the I-region-associated (Ia) antigens of the guinea pig major histocompatibility complex (MHC) T cells could be sensitized to the antisera bound to macrophage Ia determinants. Anti-Ia-treated syngeneic macrophages in the first and second cultures elicited specific T-cell activation, as measured by increased DNA synthesis, to the antisera-induced immunogenic determinants. Similarly, antiIa-treated allogeneic macrophages also specifically stimulated T cells to antisera bound to allogeneic Ia determinants while reducing the mixed leukocyte reaction. Antisera to the B.1 antigens of the guinea pig MHC, the homologue of the mouse H-2K or H-2D antigens, also elicited specific T-cell activation that did not cross-react with that produced by the anti-Ia alloantisera. Furthermore, the anti-B.1-induced stimulation appeared to be associated with the Ia antigens of the macrophage used for priming since (2 x 13)F1 T cells sensitized with anti-B.1-treated parental macrophages could be restimulated only with the parental macrophage used for initial sensitization, and not with those of the other parent. Since the parental strain 2 and strain 13 guinea pigs express serologically identical B.1 antigens and differ only by Ia antigens of the MHC, this observation suggests that both B.1 and Ia antigens may be included in the immunogenic complex recognized by T cells. However, we cannot rule out the possibility that this restriction is due to other genetic differences between strain 2 and strain 13 guinea pigs that is unrelated to the I-region. We interpret these findings as showing that macrophage Ia antigens may serve to directly present antigens bound to the Ia molecule, and possibly indirectly aid in the presentation of antigens bound to other membrane components, such as the B.1 antigens.
FacB, the Aspergillus nidulans activator of acetate utilization genes, binds dissimilar DNA sequences

The facB gene is required for acetate induction of acetamidase (amdS) and the acetate utilization enzymes acetyl‐CoA synthase (facA), isocitrate lyase (acuD) and malate synthase (acuE) in Aspergillus nidulans. The facB gene encodes a transcriptional activator with a GAL4‐type Zn(II)2Cys6 zinc binuclear cluster DNA‐binding domain which is shown to be required for DNA binding. In vitro DNA‐binding sites for FacB in the 5′ regions of the amdS, facA, acuD and acuE genes have been identified. Mutations in amdS FacB DNA‐binding sites affected expression of an amdS–lacZ reporter in vivo and altered the affinity of in vitro DNA binding. This study shows that the FacB Zn(II)2Cys6 cluster binds to dissimilar sites which show similarity in form but not sequence with DNA‐binding sites of other Zn(II)2Cys6 proteins. Sequences with homology to FacB sites are found in the 5′ regions of genes regulated by the closely related yeast Zn(II)2Cys6 protein CAT8.
Cerebral Cortex Hyperthyroidism of Newborn Mct8-Deficient Mice Transiently Suppressed by Lat2 Inactivation

Thyroid hormone entry into cells is facilitated by transmembrane transporters. Mutations of the specific thyroid hormone transporter, MCT8 (Monocarboxylate Transporter 8, SLC16A2) cause an X-linked syndrome of profound neurological impairment and altered thyroid function known as the Allan-Herndon-Dudley syndrome. MCT8 deficiency presumably results in failure of thyroid hormone to reach the neural target cells in adequate amounts to sustain normal brain development. However during the perinatal period the absence of Mct8 in mice induces a state of cerebral cortex hyperthyroidism, indicating increased brain access and/or retention of thyroid hormone. The contribution of other transporters to thyroid hormone metabolism and action, especially in the context of MCT8 deficiency is not clear. We have analyzed the role of the heterodimeric aminoacid transporter Lat2 (Slc7a8), in the presence or absence of Mct8, on thyroid hormone concentrations and on expression of thyroid hormone-dependent cerebral cortex genes. To this end we generated Lat2-/-, and Mct8-/yLat2 -/- mice, to compare with wild type and Mct8-/y mice during postnatal development. As described previously the single Mct8 KO neonates had a transient increase of 3,5,3′-triiodothyronine concentration and expression of thyroid hormone target genes in the cerebral cortex. Strikingly the absence of Lat2 in the double Mct8Lat2 KO prevented the effect of Mct8 inactivation in newborns. The Lat2 effect was not observed from postnatal day 5 onwards. On postnatal day 21 the Mct8 KO displayed the typical pattern of thyroid hormone concentrations in plasma, decreased cortex 3,5,3′-triiodothyronine concentration and Hr expression, and concomitant Lat2 inactivation produced little to no modifications. As Lat2 is expressed in neurons and in the choroid plexus, the results support a role for Lat2 in the supply of thyroid hormone to the cerebral cortex during early postnatal development.
Predicting Grades in College from the California Psychological Inventory

To forecast four-year, two-year, and single-course grades in college, a California Psychological Inventory (CPI) equation (30.60 - .26Wb + .35Re -. l9Gi + .39Ai + .22Ie + .36Py) was developed. Cross-validational coefficients for scores on the equation were . 38 for 326 males and . 36 for 570 females.
Dual-beam ATI SAR measurements of surface currents in the nearshore ocean

Surface flow is estimated from a dual-beam along-track interferometric synthetic aperture radar at the mouth of a tidally-driven estuary. The measurements show strong variation in the surface flow around jetties and seem to be associated with bathymetry. The surface flow estimates compare well with in situ drifter measurements made around the same time.