gebhart/patrepeval huggingface dataset:
Approaches to eliminating cycles in the UMLS Metathesaurus: naïve vs. formal. (2005)

Applications exploiting the hierarchical relations recorded in the Unified Medical Language System (UMLS) Metathesaurus suffer from the presence of inconsistencies in these relations. A formal approach to identifying and eliminating circular hierarchical relations has been proposed in previous work, leading to the creation of a directed acyclic Metathesaurus graph. However, this approach is at best semi-automatic and its implementation is far from trivial. A simpler, alternative approach consists in avoiding loops while traversing the Metathesaurus graph by preventing nodes from being visited twice. Our objective is to evaluate the benefit of the formal approach to eliminating cycles over a naïve approach to avoiding them. To this end, we compared the size and semantic coherence of sets of descendants obtained by both approaches. 12% of the concepts with descendants exhibit some differences. The formal approach significantly reduces the number of descendants in these cases. The benefits in terms of semantic coherence are more subtle.
Modeling and Prediction of the Internet End-to-end Delay using Recurrent Neural Networks (2009)

This paper focuses on modeling and predicting the Internet end-to-end (e2e) delay multi-step ahead using Recurrent Neural Networks (RNNs). In this work, Round- Trip Time (RTT) is used as the basic metric to forecast the Internet e2e delay. A method for delay prediction model is developed using RNNs, able to model nonlinear systems. By observing the delay between two Internet nodes, RTT data has been collected as a time series during several days. Then this discrete-time series data has been organized into two parts, the first one is used as a training/learning set of the RNN, whereas the rest of data is used for the testing/evaluation of the RNN performance. To achieve this purpose, a learning phase has been performed to provide a mathematical characterization of RTT during one or several reference days. The test phase consists of iteratively forecasting RTT acquired during the test day. Simulation results illustrate that the suggested model is adaptive and it tracks RTT dynamics rapidly and accurately, even for long time ahead prediction.
Numerical solution of large scale Lyapunov equations using Krylov subspace methods (2005)

The authors consider several methods for calculating low rank approximate solutions to large scale Lyapunov equations of the form AP+PA'+BB'=0. The interest in this problem stems from model reduction where the task is to approximate high-dimensional models by ones of lower order. The two recently developed Krylov subspace methods exploited are the Arnoldi method and the generalized minimum residual method (GMRES). Exact expressions for the approximation errors incurred are derived in both cases. The numerical solution of the low-dimensional linear matrix equation arising from the GMRES method is discussed, and an algorithm for its solution is proposed. Problems are considered in which B has more than one column with the use of block Krylov schemes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Non-Ulcer Dyspepsia: Potential Causes and Pathophysiology (1988)

Dyspepsia, defined as chronic or recurrent upper abdominal pain or nausea, is a common occurrence. Dyspepsia without an ulcer (non-ulcer dyspepsia) is diagnosed in patients at least twice as often as peptic ulceration. Diseases that may present with similar symptoms include gastroesophageal reflux, biliary tract disease, chronic pancreatitis, and irritable bowel syndrome. A careful history and physical examination, supplemented by selected tests, usually lead to a correct diagnosis. The pathogenesis of non-ulcer dyspepsia remains unknown. Gastric acid secretion, duodenogastric reflux, psychological factors, environmental exposures, and heredity probably do not play a major role. Some patients may have motility disturbances, but whether these disturbances cause dyspepsia is unknown. Campylobacter pylori infection and associated gastritis are common in non-ulcer dyspepsia, but their etiologic role is controversial, as is the importance of chronic duodenitis. By recognizing the heterogeneity of patients who present with non-ulcer dyspepsia, more rational management may be possible. Although an empiric trial of antacids or H2 blockers has been recommended to treat dyspepsia, most controlled trials show that although these substances reduce severity of symptoms, they are no more effective than placebos in non-ulcer dyspepsia.
Model for scheduling multi-skilled personnel at the Department of Clinical Neurophysiology (2012)

This study is performed at the Department of Clinical Neurophysiology in Enschede. It is a self-operating department within Medisch Spectrum Twente where the functioning of the central and peripheral nervous system is examined by lab assistants. Within the department there is a need for improving the process of creating the personnel schedule, since the schedule is currently made manually by a lab assistant, which is time-consuming and complex.
The purpose of this study is to investigate whether it is possible to find a simple, clear and quick way to create a personnel planning. With the method found, a decision support model (also called personnel planning tool) is designed to help the planner creating a schedule. The planning tool should provide the planner with a weekly schedule in which the tasks in specific examination rooms are assigned to an available employee with the right skills. The input parameters are employees, examination rooms, shifts and skills. Output variables are an automatic generated week schedule, and an overview of the over- and under capacity.
First, the problems at the department are indicated by a context analysis. Relevant for the planning tool are the big differences in the skills levels and the unclear digital system in which the planning currently is made. Other problems, more relevant to patient appointment scheduling, are identified as well.
Second, a literature study is conducted to find an appropriate method to solve the problem. The goal is to assign an employee that is available during a shift and has the right skill to perform the examination to every examination room where examinations are scheduled. We find that integer linear programming is a suitable method to solve the problem. The method can solve optimization problems by using an objective, decision variables and constraints. The objective is to minimize the unfulfilled positions in examination rooms and to minimize the number of employees that are more than two times per week in the same examination room, in order to obtain a schedule in which employees are assigned to needed examination rooms and that it offers variation to the employees. The modeling environment AIMMS 3.12 is used to implement the model.
The conclusion is that the new planning tool can make a week schedule in a matter of seconds, when using standard input data of the department. Changes, like sudden absence of an employee, can be easily processed in the model after which the model provides the planner with a new day and/or week schedule.
It is recommended to improve the model and investigate whether the decision support model can be extended for the use at other departments in the hospital with comparable scheduling problems. Furthermore, it is advised to print out the schedules for the employees, to ensure that they do not have to log onto the computer when they want to see to which rooms they have to go.
Damn good statistics (2008)

If teachers are looking for a student-centred approach to learning, but cannot find raw data that engages students they can try using the latest internationally focused Census at School online survey. The next Census at School survey from the Australian Bureau of Statistics (ABS) is taking this data-rich resource to a new level with the introduction of several exciting initiatives in 2008. The 2008 version builds on the capacity of Census at School to provide students with the opportunity to use real, raw data in their analyses, and on the engagement enabled by the fact that the data relate to them. Students complete an online questionnaire about themselves to build an Australian-wide database from which random samples of real data can be generated. The student-centred approach to learning means students are able to pose their own questions about what interests them, utilizing the Census at School database as the source of their investigations. Essentially students turn data into information that makes sense, allowing them to build a picture of the world around them. Students effectively simulate the statistical collection process by placing themselves in the role of statistician; but the real benefits of the project lie in the multitude of cross- curricula analysis opportunities available for students, ranging from Years 5 to 12. Census at School allows students to model the census process, which is an important aspect of statistical literacy, to understand the problems of data collection, before they analyse the data. To participate, schools need to complete a registration form. Teachers can then create an online account and access numbers for students to complete the online questionnaire. The 2008 data will be available in July. [Author abstract, ed]
A New Technique in Sand Control Using Liner Vibration with Gravel Packing (1984)

Abstract Vibration of the liner in shop tests and field gravel completions illustrates the substantial difference achieved in compaction of the gravel. The standard gravel pack results in cubic packing' of the gravel whereas the liner vibration technique results in hexagonal packing. This achieves a denser more stable pack with an average 15% to 25% more gravel in the same volume. Vibration eliminates the fluid placement to the formation to achieve compaction with viscous aqueous polymer completion fluids. Also, this method of vibration has eliminated liner washing which stops the comingling of the formation with the gravel. Liner vibration is now being used extensively in development wells and also for completions in injection, steam and gas storage wells.
Effects of Distraction on Pain, Fear, and Distress During Venous Port Access and Venipuncture in Children and Adolescents With Cancer (2006)

This study evaluates the effect of self-selected distracters (ie, bubbles, I Spy: Super Challenger book, music table, virtual reality glasses, or handheld video games) on pain, fear, and distress in 50 children and adolescents with cancer, ages 5 to 18, with port access or venipuncture. Using an intervention-comparison group design, participants were randomized to the comparison group (n = 28) to receive standard care or intervention group (n = 22) to receive distraction plus standard care. All participants rated their pain and fear, parents rated participant fear, and the nurse rated participant fear and distress at 3 points in time: before, during, and after port access or venipuncture. Results show that self-reported pain and fear were significantly correlated (P = .01) within treatment groups but not significantly different between groups. Intervention participants demonstrated significantly less fear (P <.001) and distress (P = .03) as rated by the nurse and approached significantly less fear (P = .07) as rated by the parent. All intervention parents said the needlestick was better because of the distracter. The authors conclude that distraction has the potential to reduce fear and distress during port access and venipuncture.
Chronically denervated rat schwann cells respond to GGF in vitro (1998)

C-erbB receptor/neuregulin signalling plays a significant role in Schwann cell function. In vivo, Schwann cells up-regulate expression of c-erbB receptors in the first month after injury, but receptor expression is down-regulated with time to levels that are not detectable immunohistochemically. The inability of chronically denervated Schwann cells to respond adequately to signals derived from regenerating axons may be one reason why delayed repair of an injured peripheral nerve frequently fails. We have examined the effects of GGF on denervated Schwann cells in vitro. A modified delayed dissociation technique was used to obtain adult rat Schwann cells from the distal stumps of transected sciatic nerves which had been acutely (7 days) or chronically (2-6 month) denervated. We found that in vitro denervated Schwann cells invariably expressed p75NTR and c-erbB receptors. There was a progressive decrease in total cell yield and the percentage of cells with Schwann cell phenotype (p75NTR and/S-100 or/laminin or /GFAP or/c-erbB positive); proliferation rate; migratory potential; and expression of the cell adhesion molecules N-CAM and N-cadherin, with increasing time of denervation. Addition of GGF2 had a significant stimulatory effect upon Schwann cell proliferation and migration, and an increased proportion of Schwann cells expressed N-CAM and N-cadherin, suggesting that these responses were mediated via GGF/c-erbB signalling. Our results support the view that it may be possible to manipulate chronically denervated Schwann cells so that they become more responsive to signals derived from regrowing axons.
An Improved Naïve Bayesian Classifier Technique Coupled With a Novel Input Solution Method (2001)

Data mining is the study of how to determine underlying pat- terns in the data to help make optimal decisions on computers when the database involved is voluminous, hard to characterize accurately, and con- stantly changing. It deploys techniques based on machine learning, along- side the conventional methods. More importantly, these techniques can gen- erate decision or prediction models, based on the actual historical data. Therefore, they represent true evidence-based decision support. Rainfall prediction is a good problem to solve by these data mining techniques. This paper proposes an improved Naive Bayes classifier (INCB) technique and explores the use of genetic algorithms (GAs) for selection of a subset of input features in classification problems. It then carries out a comparison with several other techniques. It sets a comparison of the following algorithms, namely: 1) genetic algorithm with average classification or general classi- fication (GA-AC, GA-C) ,2 )C4.5 with pruning, and 3) INBC with relative frequency or initial probability density (INBC-RF, INBC-IPD) on the real meteorological data in Hong Kong. Two simple schemes are proposed to construct a suitable data set for improving the performance. Scheme I uses all basic input parameters for rainfall prediction. Scheme II uses the op- timal subset of input variables which are selected by a GA. The results show that among the methods we compared, INBC achieved about 90% accuracy rate on the rain/no-rain (Rain) classification problems. This method also at- tained reasonable performance on rainfall prediction with three-level depth (Depth3) and five-level depth (Depth5), which are around 65%-70%. Index Terms—Data mining, genetic algorithm (GA), improved Naive Bayes classification (INCB), rainfall prediction.
Antimicrobial activity of frankincense of Boswellia serrata (2014)

Plant antimicrobials tender prospective agent to deal with the hazard of biological warfare (Gibbons, 2008). Consideration to the sighting of novel plant antimicrobials must be paid in this new era of chemotherapeutic healing of infection by using plant-derived principles and on discovery of new antiinfective agents (Cowan, 1999). Herbal preparations can supplement other systems of medicine for the treatment of diseases caused by bacteria (Archana and Abraham, 2011). In fact, efforts are going on to identify and isolate secondary metabolites from plants as prospective modulators of bacterial resistance (Stavri et al., 2007). Taxonomic status of Boswellia serrata
Extraction, purification, and partial characterization of bovine parathyroid secretory protein. (1981)

Parathyroid secretory protein (PSP) was purified from extracts of bovine parathyroid glands using radioactive PSP as a marker during purification. The labeled preparation was obtained by gel filtration of medium resulting from incubation of parathyroid glands with radioactive amino acids for 4 h. Alkaline extraction, ammonium sulfate precipitation, ion-exchange chromatography on DEAE-cellulose, and gel filtration over Bio-Gel A 1.5 M and A 5 M resulted in a homogeneous product. Purified PSP monomer had a Mr = 67,000, was highly acidic on gel electrophoresis, and contained over 35% glutamic and aspartic acid residues. Approximately 18% of the protein consisted of carbohydrate residues. The homogeneity of the final product was established by polyacrylamide and sodium dodecyl sulfate (SDS) gel electrophoresis and the identification of a single NH2-terminal leucine. A radioimmunoassay for PSP was developed to identify the protein in tissue extracts and in incubation medium. Purification of PSP should be useful in defining further its biochemistry, biologic function, and control of secretion.
Distilling the underlying dimensions of tactile melodies (2003)

We created 59 tactile melodies by transforming pieces of music from the auditory domain to the vibrotactile domain. Sixteen observers judged these tactile melodies on a set of 16 characteristics such as 'melodious', 'bombastic', and 'alarming'. By using advanced multivariate statistical methods, we distilled two main underlying dimensions of the tactile melodies. We interpreted these dimensions as intrusiveness and tempo. The results are important to understand the perception of tactile melodies and to support the creation of better distinguishable and recognizable tactile signals for single point tactile displays such as in mobile phones and computer mice.
The detection of human papillomavirus DNA in skin tags (1998)

Human papillomavirus (HPV) is associated with benign cutaneous or mucosal lesions and with malignant tumours, but none of the HPV types has so far been related to skin tags. Skin biopsy specimens from 49 Caucasian patients suffering from the presence of multiple soft fibromas were analysed by means of dot blot hybridization and by polymerase chain reaction assays aimed at detecting all known HPV types. The results revealed the presence of HPV DNA type 6/11 in 88% of the skin tags examined. This result supports the hypothesis that HPV plays a part in the progression of cutaneous soft fibromas, as previously reported for laryngeal papillomas.
Sequence analysis and regulation of the<i>htr</i>A gene of<i>Escherichin coli:</i>a σ<sup>32</sup>-independent mechanism of heat-inducible transcription (1988)

Previous work has established that the E. coli htrA gene product is essential for bacterial survival at temperatures above 42 degrees. We have sequenced the htrA gene region and found an open reading frame (ORF) coding for a protein of 491 amino acids with a calculated molecular weight of 51,163 daltons. This molecular weight corresponds well with that seen following electrophoresis on SDS-polyacrylamide gels. This protein has an amino-terminal sequence typical for a leader peptide and undergoes post-translational modification by cleavage of an amino-terminal portion. The insertional mutations which affect the function of the htrA gene map inside this ORF. The levels of htrA mRNA increase rapidly and transiently upon heat shock in a manner independent of the rpoH gene, which encodes the sigma 32 RNA polymerase subunit and is known to regulate transcription of typical heat shock genes. Using S1 mapping and RNA primer extension, we have identified the htrA promoter and found that it is similar to the P3 promoter of the rpoH gene. The P3 promoter is especially active at high temperatures and is recognized by a recently identified transcriptional factor, sigma E.
Growth Suppression by an E2F-Binding-Defective Retinoblastoma Protein (RB): Contribution from the RB C Pocket (1998)

Growth suppression by the retinoblastoma protein (RB) is dependent on its ability to form complexes with transcription regulators. At least three distinct protein-binding activities have been identified in RB: the large A/B pocket binds E2F, the A/B pocket binds the LXCXE peptide motif, and the C pocket binds the nuclear c-Abl tyrosine kinase. Substitution of Trp for Arg 661 in the B region of RB (mutant 661) inactivates both E2F and LXCXE binding. The tumor suppression function of mutant 661 is not abolished, because this allele predisposes its carriers to retinoblastoma development with a low penetrance. In cell-based assays, 661 is shown to inhibit G1/S progression. This low-penetrance mutant also induces terminal growth arrest with reduced but detectable activity. We have constructed mutations that disrupt C pocket activity. When overproduced, the RB C-terminal fragment did not induce terminal growth arrest but could inhibit G1/S progression, and this activity was abolished by the C-pocket mutations. In full-length RB, the C-pocket mutations reduced but did not abolish RB function. Interestingly, combination of the C-pocket and 661 mutations completely abolished RB's ability to cause an increase in the percentage of cells in G1 and to induce terminal growth arrest. These results suggest that the A/B or C region can induce a prolongation of G1 through mechanisms that are independent of each other. In contrast, long-term growth arrest requires combined activities from both regions of RB. In addition, E2F and LXCXE binding are not the only mechanisms through which RB inhibits cell growth. The C pocket also contributes to RB-mediated growth suppression.
Analytical description for the diffusion and recombination of point defects in silicon (1989)

A simplified analysis is given of point-defect diffusion in the presence of traps which saturate on recombination. Examples of this phenomenon are self-interstitial diffusion and gettering in Czochralski silicon, and coupled interstitial-vacancy diffusion in perfect crystalline silicon. When recombination is diffusion limited, a simple diffusion equation is obtained, with an effective diffusivity D̃ which is an analytical function of the point-defect and trap concentrations. The physical meaning of this function is described.
Residual Undifferentiated Cells During Differentiation of Induced Pluripotent Stem Cells In Vitro and In Vivo (2011)

Induced pluripotent stem (iPS) cells are a potential cell source for regenerative medicine. However, the tumorigenicity of iPS cells is a big concern for clinical application. In addition to the genetic manipulation of the reprogramming process and the greater risk of tumor formation, it is unclear whether iPS cells with normal development potential are still tumorigenic. Here, we investigated 3 mouse iPS cell lines, including one line that is able to generate full-term mice via tetraploid blastocyst complementation. We found that a small number of undifferentiated iPS cells could be steadily isolated and expanded after long-term differentiation of cells in vitro or in vivo. The residual undifferentiated iPS cells could be expanded and redifferentiated, and undifferentiated pluripotent stem cells could again be isolated after further rounds of differentiation, suggesting that residual undifferentiated iPS cells could not be eliminated by extended cell differentiation. The residual undifferentiated cells could form teratomas in vivo, indicating that they are a potential tumorigenic risk during transplantation. These findings prompt us to reconsider the strategies for solving the tumorigenic problem of iPS cells, not only focusing on improving the reprogramming process.