Miracle-dz/UniFAR-FTUs huggingface dataset:
Accuracy of Self-Reported Breast Cancer Information among Women from the Ontario Site of the Breast Cancer Family Registry

Obtaining complete medical record information can be challenging and expensive in breast cancer studies. The current literature is limited with respect to the accuracy of self-report and factors that may influence this. We assessed the agreement between self-reported and medical record breast cancer information among women from the Ontario site of the Breast Cancer Family Registry. Women aged 20–69 years diagnosed with incident breast cancer 1996–1998 were identified from the Ontario Cancer Registry, sampled on age and family history. We calculated kappa statistics, proportion correct, sensitivity, specificity, and positive and negative predictive values and conducted unconditional logistic regression to examine whether characteristics of the women influenced agreement. The proportions of women who correctly reported having received a broad category of therapy (hormone therapy, chemotherapy, radiation, or surgery) as well as sensitivity and specificity were above 90%, and the kappa statistics were above 0.80. The specific type of hormonal or chemotherapy was reported with low-to-moderate agreement. Aside from recurrence, no factors were consistently associated with agreement. Thus, most women were able to accurately report broad categories of treatment but not necessarily specific treatment types. The finding of this study can aid researchers in the use and design of self-administered treatment questionnaires.
In vitro model of cerebrospinal fluid outflow through human arachnoid granulations.

PURPOSE To describe and validate an in vitro model of the arachnoid granulation (AG) outflow pathway for cerebrospinal fluid (CSF), by using human AG cells grown on a filter membrane support and perfused in a modified Ussing chamber at pressures analogous to normal human intracranial pressures. METHODS Human AG cells were grown, characterized, seeded onto filter membranes, and perfused in the physiologic (basal to apical, B-->A) or nonphysiologic (apical to basal, A-->B) directions. Cells were fixed under pressure after perfusion and prepared for electron microscopy (EM). RESULTS The average cellular hydraulic conductivity in the B-->A direction (10 total) was 4.52 +/- 0.43 microL/min per mm Hg/cm(2) with an average transcellular pressure decrease of 3.13 +/- 0.09 mm Hg. The average cellular hydraulic conductivity in the A-->B direction (six total) was 0.29 +/- 0.16 microL/min per mm Hg/cm(2) with an average transcellular decrease in pressure of 3.33 +/- 0.16 mm Hg. Cells perfused nonphysiologically showed a large number of dead and dying cells. EM postperfusion analysis showed that AG cells were integrally attached to the underlying filter membrane. Large extracellular cisternal spaces were visible between overlapping AG cells and vacuoles within the cytoplasm. It is possible that these spaces within and between cells represent pathways for transcellular and paracellular transport of fluid. CONCLUSIONS The results demonstrate that AG cells in vitro show a statistically significant greater flow rate and cellular hydraulic conductivity when perfused in the physiologic versus the nonphysiologic direction under normal intracranial pressures. These results suggest that this in vitro model of the AGs can accurately replicate the unidirectional flow of CSF in vivo.
Deletion Derivatives of the MuDR Regulatory Transposon of Maize Encode Antisense Transcripts but Are Not Dominant-Negative Regulators of Mutator Activities Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.014605.

The maize MuDR/Mu transposable elements are highly aggressive, and their activities are held in check by host developmental and epigenetic mechanisms. The Mutator regulatory element, MuDR, produces both sense and antisense transcripts. We have investigated the impact of the presence of antisense transcripts on the abundance of the corresponding sense messages and on the regulation of Mutator activities. We report that internal deletions in MuDR arise frequently in somatic tissues; preferential loss of the 3′ untranslated region of mudrA and/or mudrB containing the intergenic region is correlated with chimeric sense mudrA/antisense mudrB and sense mudrB/antisense mudrA transcripts. Heritable internal deletions are extremely frequent (>10−2 per element), and the resulting defective MuDR elements also encode antisense transcripts. Expression of endogenous or additional transgene-encoded antisense transcripts neither decreases sense transcript levels nor inhibits Mutator excision activity over the three generations examined. We propose that antisense transcripts produced by MuDR deletions are not dominant-negative regulators of Mutator activities.
Empirical Price of Fairness in Failure-Aware Kidney Exchange

Fielded kidney exchanges typically use utilitarian or near-utilitarian matching rules, potentially at great cost to certain classes of hardto-match patients. Dickerson, Procaccia, and Sandholm [6] recently adapted the price of fairness, a measure of the tradeoff between fairness and efficiency, to kidney exchange; they showed that the price of fairness is small in theory but often non-negligible in practice. We extend their work by directly comparing fairness in two models of kidney exchange—where edges either can or cannot fail after an algorithmic match but before transplantation. On real and simulated data, even matching under strict fairness constraints in the model with edge failure results in significantly more expected transplants than matching efficiently in the deterministic model.
Modelling noise-induced fibre-orientation error in diffusion-tensor MRI

Diffusion-tensor MRI can be used to measure fibre orientation within the brain. Several studies have proposed methods to reconstruct known white matter fibre tracts in the brain. These methods are known as tractography. However, the measured fibre orientations are subject to error, which leads tractography methods to fail or define false connections. Probabilistic tractography methods use a model of the probability density function (PDF) of the local fibre orientation in each voxel, to calculate the likelihood of any potential fibre pathway through a DT data set. We propose the Watson distribution as a new fibre orientation PDF to replace ad hoc models used previously. We compare the probabilistic index of connectivity (PICo) tractography method using three candidate PDFs and show that the Watson PDF compares favourably to the ad hoc models.
On the Complexity of Scheduling Problems for Parallel/Pipelined Machines

The problem of optimal scheduling of a job system for two dedicated processors is presented. A machine model with two functional units which can be either sequential or pipelined is considered. The complexity of optimal scheduling for a set of expressions on such machines is investigated. Some previous NP-completeness results are reviewed and several new ones are presented. For one restricted case, a polynomial-time algorithm is described and analyzed. >
UB at TREC 12: HARD and Genomics Tracks

University at Buffalo (UB) participated in TREC-12 in Genomics and High Accuracy Retrieval from Documents (HARD) tracks. We explored some techniques that combine Information Retrieval and Information Extraction to perform the TREC tasks. We used an Information Extraction engine InfoXtract [3] from Cymfony Inc. to enhance retrieval results. For the Genomics primary task, documents retrieved using a vector space model with relevance feedback are reweighted based on the biomedical named entities discovered by InfoXtract. For the secondary task, extracted information along with cue words for text snippets that describe functionality is used for generating GeneRIFs for given Gene name and PubMed abstract. A language modeling approach that incorporates keyword and non-keyword features are used for the HARD task. Features extracted by InfoXtract from the HARD corpus are used to rank documents and/or passages as answers to the HARD queries. Cymfony’s InfoXtract [3] is a customizable Information Extraction engine that performs syntactic and semantic parsing of a document to identify features like named entities, relationships and events in them. The baseline InfoXtract engine has been trained for the general English and news domain, It can be customized to recognize new named entities like Gene Names and Gene Function. Biomedical Customization of InfoXtract is briefly presented in Section 2.2.
Natural Language Direction Following for Robots in Unstructured Unknown Environments

Abstract : Robots are increasingly performing collaborative tasks with people in homes, workplaces, and outdoors, and with this increase in interaction comes a need for e cient communication between human and robot teammates. One way to achieve this communication is through natural language, which provides a exible and intuitive way to issue commands to robots without requiring specialized interfaces or extensive user training. One task where natural language understanding could facilitate humanrobot interaction is navigation through unknown environments, where a user directs a robot toward a goal by describing \201in natural language\202 the actions necessary to reach the destination. Most existing approaches to following natural language directions assume that the robot has access to a complete map of the environment ahead of time. This assumption severely limits the potential environments in which a robot could operate, since collecting a semantically labeled map of the environment is expensive and time consuming. Following directions in unknown environments is much more challenging, as the robot must now make decisions using only information about the parts of the environment it has observed so far. In other words, absent a full map the robot must incrementally build up its map \201using sensor measurements\202, and rely on this partial map to follow the direction. Some approaches to following directions in unknown environments do exist, but they implicitly restrict the structure of the environment, and have so far only been applied in simulated or highly structured environments. To date, no solution exists to the problem of real robots following natural directions through unstructured and unknown environments. We address this gap by formulating the problem of following directions in unstructured unknown environments as one of sequential decision making under uncertainty. In this setting, a policy reasons about the robot's knowledge of the world so far, and predicts a sequ
Duration and breaks in sedentary behaviour: accelerometer data from 1566 community-dwelling older men (British Regional Heart Study)

Background Sedentary behaviours are increasingly recognised as raising the risk of cardiovascular disease events, diabetes and mortality, independently of physical activity levels. However, little is known about patterns of sedentary behaviour in older adults. Methods Cross-sectional study of 1566/3137 (50% response) men aged 71–91 years from a UK population-based cohort study. Men wore a GT3x accelerometer over the hip for 1 week in 2010–2011. Mean daily minutes of sedentary behaviours, percentage of day in sedentary behaviours, sedentary bouts and breaks were calculated and summarised by health and demographic characteristics. Results 1403 ambulatory men aged 78.4 years (SD=4.6 years) with ≥600 min of accelerometer wear on ≥3 days had complete data on covariables. Men spent on average 618 min (SD=83), or 72% of their day in sedentary behaviours (<100 counts/min). On average, men accumulated 72 spells of sedentary behaviours per day, with 7 breaks in each sedentary hour. Men had on average 5.1 sedentary bouts of ≥30 min, which accounted for 43% of sedentary time, and 1.4 bouts of ≥60 min, which accounted for 19% of daily sedentary time. Men who were over 80 years old, obese, depressed and had multiple chronic conditions accumulated more sedentary time and spent more time in longer sedentary bouts. Conclusions Older men spend nearly three quarters of their day in sedentary behaviours, mostly accumulated in short bouts, although bouts lasting ≥30 min accounted for nearly half of the sedentary time each day. Men with medical risk factors were more likely to also display sedentary behaviour.
Beryllium carcinogenesis. I. Inhalation exposure of rats to beryllium sulfate aerosol.

One hundred fifty rats (with equal number of controls) were exposed to the inhalation of beryllium sulfate aerosol at a mean atmospheric concentration of 34.25 µg of Be/cu m, and sacrificed in monthly groups during 72 weeks of exposure. Average lung weight towards the end of exposure was 4.25 times normal. Histopathologic examination disclosed 2 gradually developing pathologic processes: ( a ) an inflammatory response chiefly characterized by marked accumulation of histiocytic elements forming clusters of macrophages in the alveolar spaces; and ( b ) a proliferative response, progressing from early epithelial hyperplasia of the alveolar surfaces, through metaplasia and anaplasia, to lung cancer. The first tumors were found after 9 months of exposure, the incidence rapidly rising, and reaching 100% at 13 months ( vs. 0% in controls). All tumors appeared to be alveolar adenocarcinomas, in some instances with focal intermixture of other types. Out of 56 tumors studied, 3 reached a very large size comparatively early. Females appeared to be more vulnerable to the exposure than males in terms of attritional mortality and body weight loss.
Pulmonary effects of nebivolol

The pharmacological control of arterial hypertension is a very frequent issue in clinical practice and some critical aspects can arise in particular circumstances and with particular molecules. In the case of hypertensive subjects with respiratory comorbidities, when first introduced, these β-adrenergic receptor antagonists were described as affecting airway patency as a result of their antagonism against β2-adrenergic receptors within airway muscles. New molecules with a better respiratory tolerability were subsequently designed in order to overcome the narrow therapeutic window of first-generation β-adrenergic receptor antagonists. Nebivolol is a third-generation β-adrenergic receptor antagonist with high β1-selective adrenergic receptor antagonism and vasodilating properties that induces a substantial decrease of arterial pressure in hypertensive subjects while preserving their left ventricular function. Respiratory effects of nebivolol have been investigated in animal models, in healthy volunteers and in clinical trials carried out on patients suffering from bronchial asthma and chronic obstructive pulmonary disease (COPD). In contrast to older compounds, nebivolol, which modulates the endogenous production of nitric oxide and affects oxidative cascade, proved clinically well tolerated in terms of respiratory outcomes in this type of subject. Moreover, due to the substantial dissociation between its cardiac and pulmonary activity, nebivolol confirmed a very good safety profile when regularly administered to hypertensive subjects with obstructive respiratory comorbidities.
Homoclinic tangles-classification and applications

Here we develop the topological approximation method which gives a new description of the mixing and transport processes in chaotic two-dimensional time-periodic Hamiltonian flows. It is based upon the structure of the homoclinic tangle, and supplies a detailed solution to a transport problem for this class of systems, the characteristics of which are typical to chaotic, yet not ergodic dynamical systems. These characteristics suggest some new criteria for quantifying transport and mixing-hence chaos-in such systems. The results depend on several parameters, which are found by perturbation analysis in the near integrable case, and numerically otherwise. The strength of the method is demonstrated on a simple model. We construct a bifurcation diagram describing the changes in the homoclinic tangle as the physical parameters are varied. From this diagram we find special regions in the parameter space in which we approximate the escape rates from the vicinity of the homoclinic tangle, finding nontrivial self-similar solutions as the forcing magnitude tends to zero. We compare the theoretical predictions with brute force calculations of the escape rates, and obtain satisfactory agreement.
Exploring similarity between academic paper and patent based on Latent Semantic Analysis and Vector Space Model

With the development of network technology, the storage format of science and technology literature changes from paper to electronic version, and its size also is increasing. The academic papers and patents are important science and technology literature. To a certain extent, they represent the highest level of academic research and technical innovation. In this paper, we perform a study to measure the semantic similarity between academic papers and patents. The paper argues it's important to get similarity between single paper and single patent. To find linkage between them, four semantic similarity measurements are compared: Latent Semantic Analysis (LSA) based on words, LSA based on terms, Vector Space Model (VSM) based on words, VSM based on terms. A case study is conducted in the area of optical sensors. And result shows that the measurement method of terms based VSM is the best to find the similarity between single paper and single patent.
Cerebral Flow Velocities During Daily Activities Depend on Blood Pressure in Patients With Chronic Ischemic Infarctions

Background and Purpose— Target blood pressure (BP) values for optimal cerebral perfusion after an ischemic stroke are still debated. We sought to examine the relationship between BP and cerebral blood flow velocities (BFVs) during daily activities. Methods— We studied 43 patients with chronic large vessel ischemic infarctions in the middle cerebral artery territory (aged 64.2±8.94 years; at 6.1±4.9 years after stroke) and 67 age-matched control subjects. BFVs in middle cerebral arteries were measured during supine baseline, sitting, standing, and tilt. A regression analysis and a dynamic phase analysis were used to quantify the BP–BFV relationship. Results— The mean arterial pressure was similar between the groups (89±15 mm Hg). Baseline BFVs were lower by approximately 30% in the patients with stroke compared with the control subjects (P=0.0001). BFV declined further with postural changes and remained lower in the stroke group during sitting (P=0.003), standing (P=0.003), and tilt (P=0.002) as compared with the control group. Average BFVs on the stroke side were positively correlated with BP during baseline (R=0.54, P=0.0022, the slope 0.46 cm/s/mm Hg) and tilt (R=0.52, P=0.0028, the slope 0.40 cm/s/mm Hg). Regression analysis suggested that BFV may increase approximately 30% to 50% at mean BP >100 mm Hg. Orthostatic hypotension during the first minute of tilt or standing was independently associated with lower BFV on the stroke side (P=0.0008). Baseline BP–BFV phase shift derived from the phase analysis was smaller on the stroke side (P=0.0006). Conclusion— We found that BFVs are lower in patients with stroke and daily activities such as standing could induce hypoperfusion. BFVs increase with mean arterial pressure >100 mm Hg. Dependency of BFV on arterial pressure may have implications for BP management after stroke. Further prospective investigations are needed to determine the impact of these findings on functional recovery and strategies to improve perfusion pressure during daily activities after ischemic stroke.
The application of the large particles method of numerical modeling of the process of carbonic nanostructures synthesis in plasma

The article deals with the numerical solution of the mathematical model of the particles motion and interaction in multicomponent plasma by the example of electric arc synthesis of carbon nanostructures. The high order of the particles and the number of their interactions requires a significant input of machine resources and time for calculations. Application of the large particles method makes it possible to reduce the amount of computation and the requirements for hardware resources without affecting the accuracy of numerical calculations. The use of technology of GPGPU parallel computing using the Nvidia CUDA technology allows organizing all General purpose computation on the basis of the graphical processor graphics card. The comparative analysis of different approaches to parallelization of computations to speed up calculations with the choice of the algorithm in which to calculate the accuracy of the solution shared memory is used. Numerical study of the influence of particles density in the macro particle on the motion parameters and the total number of particle collisions in the plasma for different modes of synthesis has been carried out. The rational range of the coherence coefficient of particle in the macro particle is computed.
Effects of land-use change on the carbon balance of 1 st generation biofuels : 3 An analysis for the European Union combining spatial modeling and LCA 4 5 Authors : 6

22 Biofuels are considered as an important option for the mitigation of climate change. 23 However, the negative impact of land-use change (LUC) on soil and vegetation carbon pools 24 may jeopardize the potentially achievable savings of greenhouse gas (GHG) emissions. In this 25 study the impact of GHG emissions from LUC on the overall GHG performance of 1 generation 26 biofuels was analyzed for the European Union (EU). The scenario-based analysis was done by 27 coupling a spatial land-use model to a Life Cycle Assessment (LCA) of biofuels. The biofuel 28 demand in the scenarios was derived from figures for the transport sector of the EU-27 Member 29 States. The calculation of GHG emissions was performed with a Geographic Information System. 30 Finally, these results were integrated into the LCA approach of the EU Renewable Energy 31 Directive (RED). Without taking LUC into account, the average GHG emission saving compared 32 to fossil fuel use amounts to ~50%. In this case the mandatory 35% emission saving target laid 33 down in the RED would be fulfilled. If LUC is considered, this target is reached under none of the 34 *Manuscript Click here to view linked References
Towards a secure controller platform for openflow applications

The OpenFlow (OF) paradigm embraces third-party development efforts, and therefore suffers from potential trust issue on OF applications (apps). The abuse of such trust could lead to various types of attacks impacting the entire network. In this paper, we propose PermOF, a fine-grained permission system, as the first line of defense, in order to apply minimum privilege on apps. We summarize a set of 18 permissions to be enforced at the API entry of the controller. To accommodate the isolation requirements, we propose a customized isolation mechanism, which achieves comprehensive resource isolation and access control.