Miracle-dz/UniFAR-FTUs huggingface dataset:
Reciprocal Teaching of Comprehension-Fostering and Comprehension-Monitoring Activities

Two instructional studies directed at the comprehension-fostering and comprehension-monitoring activities of seventh grade poor comprehenders are reported. The four study activities were summarizing (self-review), questioning, clarifying, and predicting. The training method was that of reciprocal teaching, where the tutor and students took turns leading a dialogue centered on pertinent features of the text. In Study 1, a comparison between the reciprocal teaching method and a second intervention modeled on typical classroom practice resulted in greater gains and maintenance over time for the reciprocal procedure. Reciprocal teaching, with an adult model guiding the student to interact with the text in more sophisticated ways, led to a significant improvement in the quality of the summaries and questions. It also led to sizable gains on criterion tests of comprehension, reliable maintenance over time, generalization to classroom comprehension tests, transfer to novel tasks that tapped the trained skills of.
Enfuvirtide Resistance Mutations: Impact on Human Immunodeficiency Virus Envelope Function, Entry Inhibitor Sensitivity, and Virus Neutralization

ABSTRACT Enfuvirtide (ENF/T-20/Fuzeon), the first human immunodeficiency virus (HIV) entry inhibitor to be licensed, targets a structural intermediate of the entry process. ENF binds the HR1 domain in gp41 after Env has bound CD4, preventing conformational changes needed for membrane fusion. Mutations in HR1 that confer ENF resistance can arise following ENF therapy. ENF resistance mutations were introduced into an R5- and X4-tropic Env to examine their impact on fusion, infection, and sensitivity to different classes of entry inhibitors and neutralizing antibodies. HR1 mutations could reduce infection and fusion efficiency and also delay fusion kinetics, likely accounting for their negative impact on viral fitness. HR1 mutations had minimal effect on virus sensitivity to other classes of entry inhibitors, including those targeting CD4 binding (BMS-806 and a CD4-specific monoclonal antibody [MAb]), coreceptor binding (CXCR4 inhibitor AMD3100 and CCR5 inhibitor TAK-779), or fusion (T-1249), indicating that ENF-resistant viruses can remain sensitive to other entry inhibitors in vivo. Some HR1 mutations conferred increased sensitivity to a subset of neutralizing MAbs that likely target fusion intermediates or with epitopes preferentially exposed following receptor interactions (17b, 48D, 2F5, 4E10, and IgGb12), as well as sera from some HIV-positive individuals. Mechanistically, enhanced neutralization correlated with reduced fusion kinetics, indicating that, in addition to steric constraints, kinetics may also limit virus neutralization by some antibodies. Therefore, escape from ENF comes at a cost to viral fitness and may confer enhanced sensitivity to humoral immunity due to prolonged exposure of epitopes that are not readily accessible in the native Env trimer. Resistance to other entry inhibitors was not observed.
Hepatic Resection for Metastatic Tumors From Gastric Cancer

ObjectiveTo assess the surgical results and clinicopathologic features of hepatic metastases from gastric adenocarcinoma to identify patients with a better probability of survival. Summary Background DataMany studies have reported the benefit of hepatic resection for metastatic tumors from colorectal cancer. However, indications for a surgical approach for gastric adenocarcinoma involving the liver have not been clearly defined. MethodsNinety (11%) of 807 patients with primary gastric cancer were diagnosed with synchronous (n = 78) or metachronous (n = 12) hepatic metastases. Of these, 19 underwent 20 resections intended to cure the metastatic lesion in the liver. The clinicopathologic features of the hepatic metastases in, and the surgical results for, the 19 patients were analyzed. ResultsThe actuarial 1-year, 3-year, and 5-year survival rates after hepatic resection were, respectively, 77%, 34%, and 34%, and three patients survived for more than 5 years after surgery. Solitary and metachronous metastases were significant determinants for a favorable prognosis after hepatic resection. Pathologically, a fibrous pseudocapsule between the tumor and surrounding hepatic parenchyma was found in 13 of the 19 patients (68%). The presence of a peritumoral fibrous pseudocapsule and a well-differentiated histologic type of metastatic nodule were significant prognostic factors. Factors associated with the primary lesion were not significant prognostic determinants in patients who underwent curative resection of the primary cancer. ConclusionsSolitary and metachronous metastases from gastric cancer should be treated by a surgical approach and confer a better prognosis. A new prognostic factor, the presence of a pseudocapsule, may be helpful in defining indications for postoperative adjuvant treatment.
Gustatory neural processing in the hindbrain.

Sensory neurophysiology must account for sensation and perception. Given the richness and complexity of our auditory and visual worlds, this remains a daunting charge even after decades of sophist icated visual and auditory neurophysiology. Taste, on th� other hand, should be easy. It contains little of the spatial and tempQral dimensions found in vision, audition, or somesthesis, and humans report only a few taste categories or qualities. In English, the most common are sweet, salty, sour , and bitter . Given this apparently simpler task, how does gustatory neurophysiology acquit itself? Gustatory neurophysiological data, primarily from rodents, match human quality judgments moderately well, but the degree of this success or failure depends upon the theoretical bias of the beholder , as well as on the scope of the gustatory responses included. Taste per se may have only a few sensory categories, but other attributes contribute complexity and richness to the sensory experience that leaves present neurophysiological data far behind. The absence of obvious stimulus dimensions continues to impede neuro­ physiological analysis of gustatory sensibility. The molecules that elicit similar verbal reports of taste from humans and neural activity in gustatory afferent nerves often bear little chemical relation to one another . Sugars,
Ad Hoc Cooperation for the Cellular Uplink with Capacity Constrained Backhaul

Base station cooperation is a promising solution to the interference limitation of today's cellular networks. The capacity and fairness gains shown by information theoretical analysis of base station cooperation in cellular networks are huge. However, a major downside of base station cooperation is the additional information exchange among base stations which is the motivation for recent work on backhaul efficient cooperation schemes. In this paper, we show how imperfect channel knowledge which is caused by a scheduling delay affects the performance of a backhaul constrained base station cooperation scheme. Using the example of a distributed antenna system, we investigate the benefits of a cooperation scheme which takes the varying channel state into account to make ad-hoc decisions about the required accuracy of exchanged information. Ad hoc cooperation is shown to give very good results, and is thus an effective means to counteract the influence of outdated channel information of the scheduler.
Diffusion bonding of hot rolled 7075 aluminium alloy

AbstractDiffusion bonding studies of hot rolled 7075 aluminium alloy have been carried out in vacuum on a Gleeble 1500 test machine over a range of temperatures, pressures, and times. A new surface treatment procedure was used in which the surfaces to be joined were coated with an organic solution immediately after the removal of surface oxides. Bond quality was asssessed using optical microscopy, tensile strength measurements, and scanning electron microscopy of the surfaces of the fractured tensile specimens. Bonds with parent metal strength and microstructure were obtained and the optimum bonding conditions were identified. The characteristics of the surface treatment method and the bonding mechanism are discussed
Ectopic retinoic acid signaling affects outflow tract cushion development through suppression of the myocardial Tbx2-Tgfβ2 pathway

The progress of molecular genetics has enabled us to identify the genes responsible for congenital heart malformations. However, recent studies suggest that congenital heart diseases are induced not only by mutations in certain genes, but also by abnormal maternal factors. A high concentration of maternal retinoic acid (RA), the active derivative of vitamin A, is well known as a teratogenic agent that can cause developmental defects. Our previous studies have shown that the maternal administration of RA to mice within a narrow developmental window induces outflow tract (OFT) septum defects, a condition that closely resembles human transposition of the great arteries (TGA), although the responsible factors and pathogenic mechanisms of the TGA induced by RA remain unknown. We herein demonstrate that the expression of Tbx2 in the OFT myocardium is responsive to RA, and its downregulation is associated with abnormal OFT development. We found that RA could directly downregulate the Tbx2 expression through a functional retinoic acid response element (RARE) in the Tbx2 promoter region, which is also required for the initiation of Tbx2 transcription during OFT development. Tgfb2 expression was also downregulated in the RA-treated OFT region and was upregulated by Tbx2 in a culture system. Moreover, defective epithelial-mesenchymal transition caused by the excess RA was rescued by the addition of Tgfβ2 in an organ culture system. These data suggest that RA signaling participates in the Tbx2 transcriptional mechanism during OFT development and that the Tbx2-Tgfβ2 cascade is one of the key pathways involved in inducing the TGA phenotype.
A Computer-Based Model for Studying the Effects of Lasers on the Retina

A computer-based model has been developed to explore the effects of lasers on the eye. The model was developed using a technique known as BioFusion®, which embodies a software engineering and knowledge acquisition methodology. The technique provides a formal means for developing a model by gathering, organizing, analyzing, documenting, synthesizing, and implementing the vast amount of knowledge needed about a biological process into a working computer simulation. The resulting PC-based model can then be used to explore questions in an in silico environment, and to work synergistically with in vitro and in vivo experiments.
Delay-Induced Consensus and Quasi-Consensus in Multi-Agent Dynamical Systems

This paper studies consensus and quasi-consensus in multi-agent dynamical systems. A linear consensus protocol in the second-order dynamics is designed where both the current and delayed position information is utilized. Time delay, in a common perspective, can induce periodic oscillations or even chaos in dynamical systems. However, it is found in this paper that consensus and quasi-consensus in a multi-agent system cannot be reached without the delayed position information under the given protocol while they can be achieved with a relatively small time delay by appropriately choosing the coupling strengths. A necessary and sufficient condition for reaching consensus in multi-agent dynamical systems is established. It is shown that consensus and quasi-consensus can be achieved if and only if the time delay is bounded by some critical value which depends on the coupling strength and the largest eigenvalue of the Laplacian matrix of the network. The motivation for studying quasi-consensus is provided where the potential relationship between the second-order multi-agent system with delayed positive feedback and the first-order system with distributed-delay control input is discussed. Finally, simulation examples are given to illustrate the theoretical analysis.
Progress in spatial robot juggling

The authors review their progress to date in eliciting dynamically dexterous behaviors from a 3-d.o. f. direct drive robot manipulator whose real-time stereo cameras provide 60 Hz sampled images of multiple freely falling bodies in highly structured lighting conditions. At present, the robot is capable of forcing a single ping-pong ball into a specified steady-state (near) periodic vertical motion by repeated controlled impacts with a rigid paddle. The robot sustains the steady-state behavior over long periods (typically many thousands of impacts) and is capable of recovering from significant unexpected adversarial perturbations of the ball's flight phase. Gain tuning experiments corroborate the authors' contention that the stability mechanism underlying the robot's reliability can be attributed to the same nonlinear dynamics responsible for analogous behavior in a previous 1-d.o. f. robot. <<ETX>>
Vibration Control of a Laminated Plate with Piezoelectric Sensor/Actuator: Finite Element Formulation and Modal Analysis

The combined effects of passive and active control on the vibration control of a com posite laminated plate with piezoelectric sensors/actuators are investigated. Finite element formula tion and modal analysis are presented. Classical laminated plate theory with the induced strain ac tuation and Hamilton's principle are used to formulate the equation of motion of the system. The total charge developed on the sensor layer is calculated from the direct piezoelectric equation. The equa tions of motion and the total charge are discretized with 4-node, 12-degree of freedom quadrilateral plate bending elements. The stiffness and damping property changes of composite structures by varying the layer angles are used as a passive control method. Piezoelectric sensors/actuators with negative velocity feedback control are used as an active control method. By numerical simulation, the effects of stiffness and damping property changes of composite structures and the effects of sen sor/actuator division on the response of the structure and the performance of the vibration control are investigated. Since active control and passive control affect each other, the active control and the passive control should be considered simultaneously in designing the efficient adaptive structures.
Phased‐Array Intracardiac Echocardiography During Pulmonary Vein Isolation and Linear Ablation for Atrial Fibrillation

Phased‐Array Intracardiac Echocardiography for AF Ablation. Introduction: Fluoroscopic imaging provides limited anatomic guidance for left atrial structures. The aim of this study was to determine the utility of real‐time, phased‐array intracardiac echocardiography during radiofrequency ablation for atrial fibrillation.
The Robert Gordon University's HARD Track Experiments at TREC 2004

The High Accuracy Retrieval from Documents (HARD) track explores methods of improving the accuracy of document retrieval systems. As part of this track, the participants have investigated how information about a searcher’s context can be used to improve retrieval performance [Allan, 2003; Allan, 2004]. Searchers, referred to as assessors in this track, produce TREC-style search topics. Additionally, assessors are asked to specify values from pre-defined categories of metadata, that relate to the context of the search, as opposed to the topic of the search. The categories and values of the metadata used for the HARD track in 2004 are:
Percutaneous lung biopsies: a survey of UK practice based on 5444 biopsies.

Percutaneous transthoracic lung biopsies are commonly performed for the investigation of lung masses. We describe current practice and complication rates in the UK. A postal questionnaire was sent to all centres in the British Thoracic Society directory. 157 replies (61% response rate) were received, providing data on 5444 biopsies. Mean number of biopsies performed per annum was 30.5 per centre; 8% of centres did not perform biopsies, 36% performed <25 biopsies per annum, 34% <50, 16% <100 and 6% >100. Consultant radiologists perform 91% of biopsies. Written consent was obtained at all centres. The operator obtained consent at 50% of centres. Written information for patients was provided at 35 (24%) centres. Biopsies are performed on a day case basis at 103 (71%) centres. Prior to biopsy the following were obtained routinely: CT scan (73% of centres), platelet count (73%), full clotting screen (70%), lung function (55%). Complications included pneumothorax (20.5% of biopsies), pneumothorax requiring chest drain (3.1%), haemoptysis (5.3%) and death (0.15%). The timing of post-procedure chest radiography was variable. Those centres that performed predominantly cutting needle biopsies had similar pneumothorax rates to centres performing mainly fine needle biopsies (18.9% vs 18.3%). There is great variation in practice throughout the UK. Most procedures are performed on a daycase basis. Small pneumothoraces are common but infrequently require treatment. National guidelines are needed to ensure consistency of standards.
Inference of protein kinetics by stochastic modeling and simulation of fluorescence recovery after photobleaching experiments

MOTIVATION Fluorescence recovery after photobleaching (FRAP) is a functional live cell imaging technique that permits the exploration of protein dynamics in living cells. To extract kinetic parameters from FRAP data, a number of analytical models have been developed. Simplifications are inherent in these models, which may lead to inexhaustive or inaccurate exploitation of the experimental data. An appealing alternative is offered by the simulation of biological processes in realistic environments at a particle level. However, inference of kinetic parameters using simulation-based models is still limited. RESULTS We introduce and demonstrate a new method for the inference of kinetic parameter values from FRAP data. A small number of in silico FRAP experiments is used to construct a mapping from FRAP recovery curves to the parameters of the underlying protein kinetics. Parameter estimates from experimental data can then be computed by applying the mapping to the observed recovery curves. A bootstrap process is used to investigate identifiability of the physical parameters and determine confidence regions for their estimates. Our method circumvents the computational burden of seeking the best-fitting parameters via iterative simulation. After validation on synthetic data, the method is applied to the analysis of the nuclear proteins Cdt1, PCNA and GFPnls. Parameter estimation results from several experimental samples are in accordance with previous findings, but also allow us to discuss identifiability issues as well as cell-to-cell variability of the protein kinetics. IMPLEMENTATION All methods were implemented in MATLAB R2011b. Monte Carlo simulations were run on the HPC cluster Brutus of ETH Zurich. CONTACT lygeros@control.ee. ethz.ch or lygerou@med.upatras. gr SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Maximum Size and Throughput of SOA-Based Optical Burst Switching Nodes With Limited Tuning-Range Wavelength Converters and FDL Buffers

In this paper, we show the physical limitations of semiconductor optical amplifier (SOA)-based switching nodes for optical burst switching (OBS). The investigation covers one basic tune-and-select (TAS) architecture, as well as extensions with wavelength converters of limited tuning range (LTR) and dedicated and shared fiber delay line (FDL) buffers. Their maximum size and throughput are analyzed for nodes with four input/output fibers at different bit rates. As main impairments for signal degradation amplifier noise and crosstalk are considered. It is shown that the advanced contention resolution functionality leads to smaller-sized nodes due to higher losses and noise. Among the considered node architectures the highest maximum throughput can be achieved with TAS-LTR due to the smaller number of SOA noise contributions.
Stepwise Development of MAIT Cells in Mouse and Human

Mucosal-associated invariant T (MAIT) cells display two evolutionarily conserved features: an invariant T cell receptor (TCR)α (iTCRα) chain and restriction by the nonpolymorphic class Ib major histocompatibility complex (MHC) molecule, MHC-related molecule 1 (MR1). MR1 expression on thymus epithelial cells is not necessary for MAIT cell development but their accumulation in the gut requires MR1 expressing B cells and commensal flora. MAIT cell development is poorly known, as these cells have not been found in the thymus so far. Herein, complementary human and mouse experiments using an anti-humanVα7. 2 antibody and MAIT cell-specific iTCRα and TCRβ transgenic mice in different genetic backgrounds show that MAIT cell development is a stepwise process, with an intra-thymic selection followed by peripheral expansion. Mouse MAIT cells are selected in an MR1-dependent manner both in fetal thymic organ culture and in double iTCRα and TCRβ transgenic RAG knockout mice. In the latter mice, MAIT cells do not expand in the periphery unless B cells are added back by adoptive transfer, showing that B cells are not required for the initial thymic selection step but for the peripheral accumulation. In humans, contrary to natural killer T (NKT) cells, MAIT cells display a naïve phenotype in the thymus as well as in cord blood where they are in low numbers. After birth, MAIT cells acquire a memory phenotype and expand dramatically, up to 1%–4% of blood T cells. Finally, in contrast with NKT cells, human MAIT cell development is independent of the molecular adaptor SAP. Interestingly, mouse MAIT cells display a naïve phenotype and do not express the ZBTB16 transcription factor, which, in contrast, is expressed by NKT cells and the memory human MAIT cells found in the periphery after birth. In conclusion, MAIT cells are selected by MR1 in the thymus on a non-B non-T hematopoietic cell, and acquire a memory phenotype and expand in the periphery in a process dependent both upon B cells and the bacterial flora. Thus, their development follows a unique pattern at the crossroad of NKT and γδ T cells.
The Scirtothrips dorsalis Species Complex: Endemism and Invasion in a Global Pest

Invasive arthropods pose unique management challenges in various environments, the first of which is correct identification. This apparently mundane task is particularly difficult if multiple species are morphologically indistinguishable but accurate identification can be determined with DNA barcoding provided an adequate reference set is available. Scirtothrips dorsalis is a highly polyphagous plant pest with a rapidly expanding global distribution and this species, as currently recognized, may be comprised of cryptic species. Here we report the development of a comprehensive DNA barcode library for S. dorsalis and seven nuclear markers via next-generation sequencing for identification use within the complex. We also report the delimitation of nine cryptic species and two morphologically distinguishable species comprising the S. dorsalis species complex using histogram analysis of DNA barcodes, Bayesian phylogenetics, and the multi-species coalescent. One member of the complex, here designated the South Asia 1 cryptic species, is highly invasive, polyphagous, and likely the species implicated in tospovirus transmission. Two other species, South Asia 2, and East Asia 1 are also highly polyphagous and appear to be at an earlier stage of global invasion. The remaining members of the complex are regionally endemic, varying in their pest status and degree of polyphagy. In addition to patterns of invasion and endemism, our results provide a framework both for identifying members of the complex based on their DNA barcode, and for future species delimiting efforts.