Miracle-dz/UniFAR-FTUs huggingface dataset:
Variations in Patient-Centered Medical Home Capacity

Increased interest in the patient-centered medical home (PCMH) among policy makers and practitioners has resulted in a growth of research on the factors that influence its adoption and implementation, yet this research often fails to capture the multidimensional nature of the PCMH and the longitudinal nature of the implementation process. This study documented physician practices’ PCMH capacity across 12 different domains (e.g., extended access, specialist referral, use of patient registry) over a 3-year period (2008-2010). Linear growth models indicated that participation through different types of physician organizations and practice size were associated with different baseline levels of capacity and changes in capacity over time; however, the association varied as a function of the different PCMH dimensions. Differences in PCMH capacity across the 12 domains and time suggest that more attention should be paid to the longitudinal nature of PCMH implementation and the differential challenges associated with its component parts.
Application Heartbeats. A Generic Interface for Expressing Performance Goals and Progress in Self-Tuning Systems

Self-tuning, self-aware, or adaptive computing has been proposed as one method to help application programmers confront the growing complexity of multicore software development. Such systems have been proposed for architectures, compilers, and operating systems to ease the application programmer’s burden by providing services that automatically customize to meet the needs of the application. However, these systems often rely on ad hoc methods for understanding and monitoring an application and thus struggle to incorporate the true performance goals of the applications they are designed to support. This paper presents the Application Heartbeats API which addresses the need to provide a standardized interface for applications to communicate with supportive adaptive systems. The Application Heartbeats framework provides a simple, standard programming interface that applications can use to indicate their performance and which system software can use to query that performance. Several experiments demonstrate the simplicity and efficacy of the Application Heartbeat approach.
Quantitative junctional permeability measurements using the confocal microscope

This paper describes the use of a photobleach method and confocal microscopy to compare the cell‐to‐cell transfer rate of 5,6 carboxyfluorescein in dissociated embryonic chick lens cells with those in the anterior epithelium of the whole embryonic chick lens. The average cell‐to‐cell transfer rates obtained were 7.9 × 10−3 sec−1 in the dissociated cells and 2.6 × 10−3 sec−1 in the anterior epithelium in an intact lens. © 1995 Wiley‐Liss, Inc.
EXPERT-C: A randomized phase II European multicenter trial of neoadjuvant chemotherapy (capecitabine/oxaliplatin) and chemoradiation (CRT) with or without cetuximab followed by total mesorectal excision (TME) in patients with MRI-defined high-risk rectal cancer.

360 Background: We previously demonstrated the feasibility of administering neoadjuvant chemotherapy before CRT and TME in patients with MRI selected poor prognosis rectal cancer (Chua Y J et al Lancet Oncol 2010). This trial evaluates the addition of the anti-EGFR antibody cetuximab to this treatment strategy. KRAS and BRAF mutations have been established as predictive for lack of response to anti-EGFR therapy in metastatic colorectal cancer. METHODS Patients with newly diagnosed, histologically confirmed, MRI defined high risk rectal adenocarcinoma were randomised to receive 4 cycles of capecitabine 1,700mg/m2 with oxaliplatin 130mg/m2 (CAPOX) followed by CRT, 45Gy/25# + 5.4Gy/3# boost with concurrent continuous capecitabine 1,650mg/m2/day, TME and 4 cycles of adjuvant CAPOX (EXPERT) or the same regimen with the addition of cetuximab (400mg/m2 loading dose week 1, followed by 250mg/m2/week) (EXPERT-C). The primary endpoint is complete response (CR) (defined as pathological complete response or radiological complete response in patients who decline surgery) in KRAS and BRAF wild type tumours. Secondary endpoints include radiological response to CRT, CR in both KRAS wild type and mutant patients, R0 resection rates, progression free and overall survival and safety. RESULTS Between 2005-2008, 165 eligible patients were recruited from 15 centres (EXPERT n=81, EXPERT-C n=84). 99% of patients had performance status 0-1, 98% had ≥ T3 disease, 56% had an involved or threatened circumferential resection margin and 72% had evidence of extramural venous invasion determined by MRI. The current median follow up is 30 months. 72/81 (89%) and 79/84 (94%) of patients completed neoadjuvant CRT and 72/81 (89%) and 77/84 (92%) patients underwent curative-intent surgery on the EXPERT and EXPERT-C arms respectively. Two patients declined surgery. CONCLUSIONS The primary and secondary endpoints will be analyzed in October 2010 and will be presented at the meeting. [Table: see text].
GradeViz: Interactive Visual Representation Of Student Grades

We present a visual tool that will help teachers and school administrators assess student grades using multi-dimensional visualization techniques. We use simple two-dimensional geometric objects, “Gsquares” (grade squares) that vary their spatial position, color, and texture properties to encode student grades. The result is a display that can be used by teachers and school administrators to rapidly and accurately analyze, explore, and compare within the grades data. We manage and visualize the grades data in ways that facilitate generation of both high-level overviews and low-level details for subsets of the data. Finally, we plan to validate our visualizations with K-12 teachers and instructors, both to investigate our design choices, and to improve the data representation in GradeViz.
Constraint-Driven Training of Complex Models Using MCMC

Standard machine learning approaches require labeled data, and labeling data for each task, language, and domain of interest is not feasible. Consequently, there has been much interest in developing training algorithms that can leverage constraints from prior knowledge to augment or replace labeled data. Most previous work in this area assumes that there exist efficient inference algorithms for the model being trained. For many NLP tasks of interest, such as entity resolution, complex models that require approximate inference are advantageous. In this paper we study algorithms for training complex models using constraints from prior knowledge. We propose an MCMC-based approximation to Generalized Expectation (GE) training, and compare it to Constraint-Driven SampleRank (CDSR). Sequence labeling experiments demonstrate that MCMC GE closely approximates exact GE, and that GE can substantially outperform CDSR. We then apply these methods to train densely-connected citation resolution models. Both methods yield highly accurate models (up to 94% mean pairwise F1) with only two simple constraints.
Topographic commissural and descending projections of the habenula in the rat

The habenular complex of the epithalamus connects the limbic basal forebrain with numerous neuromodulatory centers in the midbrain. The habenula consists of the medial and lateral nuclei, each of which is speculated to contain multiple subdivisions. Such anatomical arrangements raise the possibility that the habenula accounts for multiple channels of information flow from the limbic forebrain to the midbrain. For understanding whether and, if so, how the multiple streams are organized via the habenula, knowledge of the precise input–output connectivity of each habenular subdivision is essential. In the present study, biotinylated dextran amine and cholera toxin subunit B were used to delineate the differential outputs of various subregions of the medial and lateral nuclei of the habenula in the rat. Both anterograde and retrograde tracing uncovered a heavy commissural connection between the two habenulae on the ipsilateral and contralateral sides. The commissural projection arises primarily in the lateral nucleus and exhibits a fine topography in that a local commissural efferent terminates primarily in the corresponding subregion on the contralateral side. The subregions of the medial and lateral nuclei also give rise to distinct projections to midbrain areas such as the interpeduncular nucleus, the median/paramedian nuclei, and the central gray. These projections produce terminal fields centered in different areas of the targets, supporting the topographically organized descending projections from the habenula. These data together support the organization of multiple channels in the habenula that convey parallel streams of information to the contralateral habenula, midbrain, and brainstem. J. Comp. Neurol. 513:173–187, 2009. © 2009 Wiley‐Liss, Inc.
Optimisation of composite manufacturing processes with computer experiments and Kriging methods

This paper deals with the use of Kriging models in multi-objective optimisation of composite manufacturing processes. A comparative analysis of different optimisation methods was conducted for a case study devoted to resin transfer moulding (RTM) processes. The computerised experiments of composite manufacturing were based on a numerical simulation model of the RTM process. A Latin Hypercube Design (LHD) of the computer experiments was adopted. The computational results from the designed experiments were analysed and a Kriging model was built from the data. Finally, a data envelopment analysis (DEA) was conducted, based on the data generated from the Kriging model to optimise the RTM process. The overall performance of this method was evaluated.
Study on Steroid Induced Ocular Findings in Children with Nephrotic Syndrome.

INTRODUCTION Long term use of corticosteroids in Nephrotic Syndrome (NS) is associated with ocular complications such as Posterior Subcapsular Cataract (PSC), glaucoma, increased intra-ocular pressure, ptosis, mydriasis, eyelid skin atrophy, keratisis, thinning of cornea and sclera, repeated hordeolum exacerbations. AIM To determine ocular abnormalities in children with NS and their association with steroid dosing and duration. MATERIALS AND METHODS Hundred patients with NS in the age group of 2-18 years, with no evidence of other systemic disease, were considered for the study. Group I included cases (66) who took standard steroid regimen for first episode of NS. Group II included cases (34) who took steroid irrationally (daily basis for long time) other than standard regimen. Steroid induced ocular complications were compared in both groups after detailed ophthalmological examination. Statistical analysis was done using Statistical Package for Social Science (SPSS-20.0). RESULTS Ocular abnormalities were found in 12 patients out of 66 in Group I (18%) and 16 patients out of 34 patients in Group II (47%). Out of 12 patients of Group I who had ocular problems, three had myopic astigmatism, eight patients had PSC and one had temporal disc pallor. While in Group II, out of 16 patients who had ocular complications, two patients had raised intra ocular pressure and two patients had myopic astigmatism and 12 patients had posterior sub capsular cataract. The difference in mean cumulative steroid doses in both groups was statistically significant but no such difference was there between duration of steroid intake in both group. CONCLUSION Our study concluded that ocular complications were more common in patients with irrationally steroid intake and cumulative steroid dose intake was also significantly higher in same patients.
Toxin-coregulated pilus, but not mannose-sensitive hemagglutinin, is required for colonization by Vibrio cholerae O1 El Tor biotype and O139 strains

The relative contributions of toxin-coregulated pilus (TCP) and cell-associated mannose-sensitive hemagglutinin (MSHA) to the colonization ability of Vibrio cholerae O1 El Tor biotype strains and O139 Bengal strains was determined by using isogenic parental and in-frame deletion mutant pairs in the infant mouse cholera model. Both the El Tor and O139 tcpA mutant strains showed a dramatic defect in colonization as indicated by their competitive indices, whereas deletion of mshA had a negligible effect on colonization in either background.
SocialSearch - A Social Platform for Web 2.0 Search

In the last decade, social bookmarking services have gained popularity as a way of annotating and categorizing a variety of different web resources. The idea behind this work is to exploit such services for enhancing traditional query expansion techniques. Specifically, the system we propose relies on three-dimensional cooccurrence matrices, where the further dimension is introduced to represent categories of terms sharing the same semantic property. Such categories, named semantic classes, are related to the folksonomy mined from social bookmarking services such as Delicious, Digg, and StumbleUpon. The paper illustrates a comparative experimental evaluation on real datasets, such as the one collected by the Open Directory Project and the TREC 2004. We also include the results of a specific disambiguation analysis aimed to evaluate the effectiveness of our approach in comparison with state-of-the-art techniques when satisfying queries characterized by polysemic and ambiguous terms.
Early Intraocular Complications of Subarachnoid Haemorrhage after Aneurysm Rupture

Abstract The aim of this study was to identify factors predisposing for early intraocular complications of aneurysmal subarachnoid haemorrhage (SAH). The authors analysed 96 selected cases of aneurysmal SAH. Forty patients (42%) demonstrated abnormal fundus findings, including disc swelling (13.5%), retinal haemorrhages (23%), and vitreous haemorrhage (5%). The incidence of intraocular pathologies was significantly higher in patients who lost consciousness at the onset of SAH, were admitted with high scores of the Hunt-Hess and Fisher scales and low score of the Glasgow Coma Scale, as well as in those with arterial hypertension, more sizable aneurysm, and older.
Use of ankle brachial pressure index to predict cardiovascular events and death: a cohort study

Abstract Objective: To determine whether a low ankle brachial pressure index is associated with an increased risk of cardiovascular events and death, and whether the prediction of such events could be improved by including this index. Design: Cohort study. Setting: 11 practices in Edinburgh, Scotland. Subjects: 1592 men and women aged 55–74 years selected at random from the age-sex registers of 11 general practices and followed up for 5 years. Main outcome measures: Incidence of fatal and non-fatal cardiovascular events and all cause mortality. Results: At baseline 90 (5.7%) of subjects had an ankle brachial pressure index </=0.7, 288 (18.2%) had an index </=0.9, and 566 (35.6%) </=1.0. After five years subjects with an index </=0.9 at baseline had an increased risk of non-fatal myocardial infarction (relative risk 1.38, 95% confidence interval 0.88 to 2.16), stroke (1.98, 1.05 to 3.77), cardiovascular death (1.85, 1.15 to 2.97), and all cause mortality (1.58, 1.14 to 2.18) after adjustment for age, sex, coronary disease, and diabetes at baseline. The ability to predict subsequent events was greatly increased by combining the index with other risk factors—for example, hypertensive smokers with normal cholesterol concentrations had a positive predictive value of 25.0%, increasing to 43.8% in subjects with a low index and decreasing to 15.6% in those with a normal index. Conclusion: The ankle brachial pressure index is a good predictor of subsequent cardiovascular events, and improves on predictions by conventional risk factors alone. It is simple and accurate and could be included in routine screening of cardiovascular status. Key messages In this study individuals with a low ankle brachial pressure index had an increased risk of fatal and non-fatal cardiovascular events The index was a good predictor of subsequent cardiovascular events, and improved that of conventional risk factors alone The ankle brachial pressure index could be included in routine screening of cardiovascular status Individuals with a low ankle brachial pressure index require additional monitoring, and might benefit from aspirin or other secondary preventive measures
Multiresolution Features Based Polynomial Kernel Discriminant Analysis for Speaker Recognition

This paper describes polynomial kernel subspace approach to Speaker Recognition systems. Auditory motivated wavelet packet transform is used to derive the desirable speaker features. The nonlinear mapping between the input space and the feature space is implicitly performed using the kernel trick. This nonlinear mapping increases the discrimination capability of a pattern classifier. The use of Mel-scale based and Bark-scale based wavelet packet trees for feature extraction process adds human auditory perception behavior to enhance the classification performance. Experimental results show that the proposed kernel based technique is computationally efficient and performs well with less training data.
Microvascular Thrombosis Models in Venules and Arterioles In Vivo

Platelets are intimately involved in hemostasis and thrombosis. Under physiological conditions, circulating platelets do not interact with microvascular walls. However, in response to microvascular injury, platelet adhesion and subsequent thrombus formation may be observed in venules and arterioles in vivo. Numerous intravital video microscopy techniques have been described to induce and monitor the formation of microvascular thrombi. The mechanisms of microvascular injury vary widely among different models. Some models induce platelet activation with minimal effects on endothelium, others induce endothelial inflammation or injury, while other models lead to thrombus formation associated with endothelial denudation. The molecular mechanisms mediating platelet–vessel wall adhesive interactions differ among various models. In some instances, differences in responses between venules and arterioles are described that cannot be explained solely by hemodynamic factors. Several models for induction of microvascular thrombosis in vivo are outlined in this review, with a focus on the mechanisms of injury and thrombus formation, as well as on differences in responses between venules and arterioles. Recognizing these characteristics should help investigators select an appropriate model for studying microvascular thrombosis in vivo.
Placebo Effects and Informed Consent

The concepts of placebos and placebo effects refer to extremely diverse phenomena. I recommend dissolving the concepts of placebos and placebo effects into loosely related groups of specific mechanisms, including (potentially among others) expectation-fulfillment, classical conditioning, and attentional-somatic feedback loops. If this approach is on the right track, it has three main implications for the ethics of informed consent. First, because of the expectation-fulfillment mechanism, the process of informing cannot be considered independently from the potential effects of treatment. Obtaining informed consent influences the effects of treatment. This provides support for the authorized concealment and authorized deception paradigms, and perhaps even for outright deceptive placebo use. Second, doctors may easily fail to consider the potential benefits of conditioning, leading them to misjudge the trade-off between beneficence and autonomy. Third, how attentional-somatic feedback loops play out depends not only on the content of the informing process but also on its framing. This suggests a role for libertarian paternalism in clinical practice.
Number and phase uncertainties of the q-analog quantized field.

The q-analog coherent states \ensuremath{\Vert}z${\mathrm{〉}}_{\mathit{q}}$ are used to identify some of the canonical physical properties of the single-mode q-analog quantized radiation field in the \ensuremath{\Vert}z${\mathrm{〉}}_{\mathit{q}}$ ``classical limit'' where \ensuremath{\Vert}z\ensuremath{\Vert} is large. In this quantum-optics-like limit, the fractional uncertainties of most physical quantities (momentum, position, amplitude, phase) which characterize the quantum field are shown to be O(1), and only vanish as O(1/\ensuremath{\Vert}z\ensuremath{\Vert}) when q=1. In contrast to this more-quantum-like behavior for q\ensuremath{\ne}1, the fractional uncertainties do still approach zero for the usual number operator, N, and the N-Hamiltonian ${\mathit{H}}_{\mathit{N}}$\ensuremath{\equiv}\ensuremath{\Elzxh}\ensuremath{\omega}(N+1/2) which describes a free q-boson gas. An empirical signature for q-boson counting statistics is that (\ensuremath{\Delta}N${)}^{2}$/〈N〉\ensuremath{\rightarrow}0 as \ensuremath{\Vert}z\ensuremath{\Vert}\ensuremath{\rightarrow}\ensuremath{\infty}. Properties of the q-analog generalizations of the phase operators of Susskind and Glogower (SG) and of the phase operator \ensuremath{\varphi}${\mathrm{^}}_{\mathit{q}}$ of Pegg and Barnett are investigated. In contrast to the manifest q deformed properties of SG operators for moderate \ensuremath{\Vert}z${\mathrm{\ensuremath{\Vert}}}^{2}$, the ``Hermitian'' phase operator \ensuremath{\varphi}${\mathrm{^}}_{\mathit{q}}$ still exhibits almost normal classical behavior in the \ensuremath{\Vert}z${\mathrm{〉}}_{\mathit{q}}$ basis. In particular, the conventional (approximate) number-phase uncertainty relation \ensuremath{\Delta}N\ensuremath{\Delta}\ensuremath{\varphi}${\mathrm{^}}_{\mathit{q}}$\ensuremath{\ge}1/2 and approximate commutation relation [N,\ensuremath{\varphi}${\mathrm{^}}_{\mathit{q}}$]=i are found to follow for the single-mode q-analog quantized field. So N and \ensuremath{\varphi}${\mathrm{^}}_{\mathit{q}}$ are almost canonically conjugate operators in the \ensuremath{\Vert}z${\mathrm{〉}}_{\mathit{q}}$ classical limit. The \ensuremath{\Vert}z${\mathrm{〉}}_{\mathit{q}}$ coherent states minimize this uncertainty relation for moderate \ensuremath{\Vert}z${\mathrm{\ensuremath{\Vert}}}^{2}$. q-analog generalizations of the P, Q, and W phase-space representations are treated in the Appendix.
Genetic Analysis of SCO2997, Encoding a TagF Homologue, Indicates a Role for Wall Teichoic Acids in Sporulation of Streptomyces coelicolor A3(2)

ABSTRACT Streptomyces coelicolor contains two gene clusters putatively involved in wall teichoic acid biosynthesis. Inactivation of the tagF homologue SCO2997 or SCO2584, a component of the Streptomyces spore wall synthesizing complex, affected sporulation. The mutant phenotypes resembled those of mre mutants, suggesting a function of wall teichoic acids in the differentiation of Streptomyces.
Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size

We investigate the distribution of sizes of fragments obtained from the amplified fragment length polymorphism (AFLP) marker technique. We find that empirical distributions obtained in two plant species, Phaseolus lunatus and Lolium perenne, are consistent with the expected distributions obtained from analytical theory and from numerical simulations. Our results indicate that the size distribution is strongly asymmetrical, with a much higher proportion of small than large fragments, that it is not influenced by the number of selective nucleotides nor by genome size but that it may vary with genome‐wide GC‐content, with a higher proportion of small fragments in cases of lower GC‐content when considering the standard AFLP protocol with the enzyme MseI. Results from population samples of the two plant species show that there is a negative relationship between AFLP fragment size and fragment population frequency. Monte Carlo simulations reveal that size homoplasy, arising from pulling together nonhomologous fragments of the same size, generates patterns similar to those observed in P. lunatus and L. perenne because of the asymmetry of the size distribution. We discuss the implications of these results in the context of estimating genetic diversity with AFLP markers.