gebhart/patrepeval huggingface dataset:
Optimization of pattern matching algorithm for memory based architecture (2007)

Due to the advantages of easy re-configurability and scalability, the memory-based string matching architecture is widely adopted by network intrusion detection systems (NIDS). In order to accommodate the increasing number of attack patterns and meet the throughput requirement of networks, a successful NIDS system must have a memory-efficient pattern-matching algorithm and hardware design. In this paper, we propose a memory-efficient pattern-matching algorithm which can significantly reduce the memory requirement. For total Snort string patterns, the new algorithm achieves 29% of memory reduction compared with the traditional Aho-Corasick algorithm [5]. Moreover, since our approach is orthogonal to other memory reduction approaches, we can obtain substantial gain even after applying the existing state-of-the-art algorithms. For example, after applying the bit-split algorithm [9], we can still gain an additional 22% of memory reduction.
Needle versus Tube Thoracostomy in a Swine Model of Traumatic Tension Hemopneumothorax (2009)

In this animal model, needle thoracostomy using a 14-gauge or Cook catheter was as successful as chest tube thoracostomy for relieving tension hemopneumothorax.
Data Intensive Computing for Bioinformatics (2013)

Data intensive computing, cloud computing, and multicore computing are converging as frontiers to address massive data problems with hybrid programming models and/or runtimes including MapReduce, MPI, and parallel threading on multicore platforms. A major challenge is to utilize these technologies and large-scale computing resources effectively to advance fundamental science discoveries such as those in Life Sciences. The recently developed next-generation sequencers have enabled large-scale genome sequencing in areas such as environmental sample sequencing leading to metagenomic studies of collections of genes. Metagenomic research is just one of the areas that present a significant computational challenge because of the amount and complexity of data to be processed. This chapter discusses the use of innovative data-mining algorithms and new programming models for several Life Sciences applications. The authors particularly focus on methods that are applicable to large data sets coming from high throughput devices of steadily increasing power. They show results for both clustering and dimension reduction algorithms, and the use of MapReduce on modest size problems. They identify two key areas where further research is essential, and propose to develop new O(NlogN) complexity algorithms suitable for the analysis of millions of sequences. They suggest Iterative MapReduce as a promising programming model combining the best features of MapReduce with those of high performance environments such as MPI.
Cytogenetic Abnormalities Associated with Endocrine Neoplasia (1997)

During the past decade, cytogenetic studies of solid human neoplasms have come of age. Although technically more difficult and often ambiguous in comparison with cytogenetic studies of leukemias and lymphomas (1) cytogenetic studies of many solid tumors have yielded valuable insights into tumor pathogenesis and prognosis. In addition, in the last decade we have seen increasing application of molecular genetic techniques to the study of cancer, which has contributed greatly to our understanding of mechanisms controlling cell growth. Specific genetic alterations responsible for the pathogenesis of a number of neoplasms have been identified.
A linear recursive bad data identification method with real-time application to power system state estimation (1992)

A fast and efficient algorithm, the recursive measurement error estimation identification (RMEEI) method, for bad data (BD) analysis is further developed. By using a set of linear recursive formulas, state variables, residuals, and their variances are updated after the removal of a measurement from a suspected data set to the remaining data set, or in the reverse direction. Neither a re-estimation nor a residual sensitivity matrix are needed in the identification process, which increases the computational speed greatly. Digital tests have been done to compare the RMEEI method with other conventional BD identification methods in terms of identification performance and computational speed. The real-time operational experience of the RMEEI method in the northeast China power system is outlined.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Computational Prediction of Protein Secondary Structure from Sequence (2016)

Secondary structure of proteins refers to local and repetitive conformations, such as α-helices and β-strands, which occur in protein structures. Computational prediction of secondary structure from protein sequences has a long history with three generations of predictive methods. This unit summarizes several recent third-generation predictors. We discuss their inputs and outputs, availability, and predictive performance and explain how to perform and interpret their predictions. We cover methods for the prediction of the 3-class secondary structure states (helix, strand, and coil) as well as the 8-class secondary structure states. Recent empirical assessments and our small-scale analysis reveal that these predictions are characterized by high levels of accuracy, between 70% and 80%. We emphasize that modern predictors are available to end users in the form of convenient-to-use Web servers and stand-alone software. © 2016 by John Wiley & Sons, Inc.
Human skin color is influenced by an intergenic DNA polymorphism regulating transcription of the nearby BNC2 pigmentation gene (2014)

Single nucleotide polymorphisms (SNPs) found to be statistically significant when associated with human diseases, and other phenotypes are most often located in non-coding regions of the genome. One example is rs10765819 located in the first intron of the BNC2 gene previously associated with (saturation of) human skin color. Here, we demonstrate that a nearby intergenic SNP (rs12350739) in high linkage disequilibrium with rs10756819 is likely the causal DNA variant for the observed BNC2 skin color association. The highly conserved region surrounding rs12350739 functions as an enhancer element regulating BNC2 transcription in human melanocytes, while the activity of this enhancer element depends on the allelic status of rs12350739. When the rs12350739-AA allele is present, the chromatin at the region surrounding rs12350739 is inaccessible and the enhancer element is only slightly active, resulting in low expression of BNC2, corresponding with light skin pigmentation. When the rs12350739-GG allele is present however, the chromatin at the region surrounding rs12350739 is more accessible and the enhancer is active, resulting in a higher expression of BNC2, corresponding with dark skin pigmentation. Overall, we demonstrate the identification of the functional DNA variant that explains the BNC2 skin color association signal, providing another important step towards further understanding human pigmentation genetics beyond statistical association. We thus deliver a clear example of how an intergenic non-coding DNA variant modulates the regulatory potential of the enhancer element it is located within, which in turn results in allele-dependent differential gene expression affecting variation in common human traits.
A Glimmer of Hope: A Proposal to Keep the Indian Child Welfare Act of 1978 Intact (1997)

THE ICWA INTACT 3Georgia and Ohio had already been farming for many years and owned property!Even though Congress hoped the Indian Removal Act would relieve tensions between settlers and the tribes, this Act alone could not solve the problems
A Study of Handwritten Characters by Shape Descriptors: Doping Using the Freeman Code (2012)

In this paper, we present the role of shape descriptors in the off-line recognition process of handwritten isolated Arabic and Latin characters. We will give some statistical and structural shape descriptors and mention their performance. Then we will present an hybrid approach that uses structural shapes' descriptors from a different angle in order to improve the recognition's results from a statistical descriptor. We will therefore introduce the concept of doping aiming to raise the recognition rate.
Subcutaneous Low Molecular Weight Heparin for Management of Anticoagulation in Infants on Excor Ventricular Assist Device (2006)

Anticoagulation in infants and children on a ventricular assist device presents particular challenges. Unfractionated heparin has poor bioavailability; it can be difficult to achieve a stable anticoagulant effect; and, in the long-term, there is a risk of osteopenia. Long-term warfarin can be difficult to manage in infants on formula milk with vitamin K supplementation. We review our recent experience with subcutaneous low molecular weight heparin. Two patients received a left ventricular assist device (Excor, Berlin Heart AG) as a bridge to transplantation. Initial anticoagulation consisted of unfractionated heparin infusion beginning 6 hours after implantation to maintain an activated partial thromboplastin time of 70 seconds, checked every 4 to 6 hours. Platelet count (aim >80,000/microl) and thromboelastography were assessed daily. Antithrombin required substitution to maintain levels >70 IU/dl. To optimize anticoagulation, both infants were switched to subcutaneous low molecular weight heparin twice daily aiming for an anti-Xa activity between 0.5 and 1.0 IU/ml. Aspirin was added on day 4, checking platelet aggregation every 2 to 4 days, aiming at arachidonic acid stimulated aggregation 10% to 30% of baseline, collagen 100% of baseline. Dipyridamole was added once stability was reached if platelets count exceeded 150,000/microl. There were no clinical thromboembolic or bleeding events. Both patients had successful transplantation.
[PET in clinical work. A refined instrument for imaging]. (1995)

Positron emission tomography (PET) enables in vivo studies to be performed in patients to investigate the binding or metabolism of biologically/functionally active substances labelled with short-lived positron-emitting radionuclides. The procedure has been used for discriminative analysis of physiology and function, both normal and pathological. The range of clinical applications includes studies of cerebral ischaemia and heart diseases, tumor diagnosis and treatment follow-up, presurgical work-up in cases of epilepsy, and characterization and treatment follow-up in cases of dementia. The clinical uses of PET are outlined in a review of the last three years' experience at the PET centre at Uppsala University.
OnTheTipsofOne' sToes: Self-localizatio n ina Dynamic Environment (2005)

unige.it Abstract -Thispaperdeals withtheself-localizatio n ofan autonomous mobilerobotwithin a dynamic environment. Theconcept ofdynamic environments is extended along thevertical direction: this paper assumes thataboveourheads exists afree zonewherealsohighly dynamicenvironments becomealmoststatic. The localization process, ifmanaged intothefree zone, does notsuffer fromfeature occlusions andotherrelated issues. Thefeature matching process iscarried outusing a typical Split & Mergealgorithm whichsupplies an Extended KalmanFilter withobservations usedto perform position tracking.
Optimized Clamp Deployment with Simulation and Characterization in Full-Chip ESD (Electro-Static-Discharge) Design (2006)

DOE (design of experiment) with simulation approach is presented that allow early visibility, guidance, and analysis of clamp placement in early design stage (power template design) on a chip level complexity. ESD robustness of product is largely attributed to the degree of correct implementation of ESD design rules in a highly complex design. Correct clamp placements is one of the most difficult and less guidance. Therefore, a 'reliable' & 'comprehensive' ESD clamp placement analysis is urgently needed. This simulation would deliver a preliminary guidance of clamp placement. It provides the information of where the most probable clamp placement is in the particular power template design. Since it takes into consideration the ESD ohm rules requirements during the construction of ohm sector, it would have a very high confident level that the design would not encounter much issue in the ESD resistance checkout later. Apart from the ESD design rules checkout, we also couple with TLP (transient line pulse) testing which has proven this approach could deliver a promising ESD protection robustness. We can characterize, co-relate, and compare our simulation with the Si data from various design perspectives. All in all, the real strength of this simulation is the ability to provide earlier design guidance & optimization options starting from the product concept phase (power template design stage), which allows to align ESD with all design issues on a cost and time efficient way. Without the simulation, designer would need to manually calculate the resistance , rely on past experience and some assumption with nil data support which is tedious & error prone for complex design nowadays. This allows ESD design rules compliance in the early design stage, thus enhancing the approach of "correct-by-construction" on ESD design.
Tissue Distribution and Variant Characterization of Human Herpesvirus (HHV)–6: Increased Prevalence of HHV‐6A in Patients with Multiple Sclerosis (2000)

Human herpesvirus (HHV)-6 has been associated with the pathogenesis of multiple sclerosis (MS) on the basis of serologic, molecular, and histopathologic studies. This study sought to determine the distribution of HHV-6 in different MS body fluids, including serum, saliva, urine, and peripheral blood lymphocytes. The study results extend the observation of an increased frequency of HHV-6 DNA in serum of patients with MS to the unique detection of viral sequences in urine of a subset of patients with MS. Moreover, the HHV-6 identified in these cell-free compartments was predominantly the HHV-6A variant, which has been reported to be neurotropic. These results support the hypothesis that HHV-6 may contribute to the MS disease process.
Ito cell expression of a nuclear retinoic acid receptor (1992)

Although it has been suggested that retinoids regulate Ito cell proliferation and collagen synthesis, little is known about the ability of Ito cells to respond to retinoids in vivo. Because retinoids may mediate their molecular effects through nuclear receptors, Ito cells were examined for the presence of one of these receptors, nuclear retinoic acid receptor-beta. The modulation of nuclear retinoic acid receptor-beta expression was also studied during cell culture and hepatic fibrogenesis. Northern hybridization analysis revealed that Ito cells freshly isolated from normal rat liver contained nuclear retinoic acid receptor-beta messenger RNA at levels significantly higher than those found in other hepatic cell types. Ito cells also contained messenger RNA for two other nuclear retinoic acid receptors, nuclear retinoic acid receptor-alpha and nuclear retinoic acid receptor-gamma. Using an antibody to human nuclear retinoic acid receptor-beta, the nuclear presence of this receptor was demonstrated in normal Ito cells. In contrast, Ito cells cultured for at least 7 days had no detectable messenger RNA or nuclear staining for nuclear retinoic acid receptor-beta despite a 20 +/- 5-fold increase in the messenger RNA level of another retinoid binding protein, cellular retinol binding protein. Analysis of Ito cells isolated from rats with carbon tetrachloride-induced hepatic fibrosis revealed an 81% +/- 3% decrease in nuclear retinoic acid receptor-beta messenger RNA levels in these cells when compared with normal Ito cells. No difference in the messenger RNA levels of cellular retinol binding protein was found in Ito cells isolated from either normal or fibrotic liver.(ABSTRACT TRUNCATED AT 250 WORDS)
Single muscle fibre analysis of carnosine and associated metabolites in Korean breath hold divers (AMA). (2007)

Intermittent hypoxia and cold water immersion during breath-hold diving may result in adaptations to facilitate muscle activity in these conditions. Previous work has highlighted increased carnosine (Carn) concentrations and enzyme activity in marine mammals exposed to hypoxic conditions. The aim of this study was to assess the adaptive responses in breath-hold divers. Divers (n=9, 54±11y; 59±12kg) were biopsied from the v.Lateralis. Single muscle fibres were dissected and characterised as type I (T1) and II (TII). Characterised fibres were subsequently analyzed for Carn, taurine (Tau) (mmol.kg−1 dm), citrate synthase (CS) and phosphorylase (Phos) (μmol.g−1.min−1@ 25oC). Carn concentrations were higher in TI fibres (20.0±13.4) than TI (10.9±10.3) with Tau showing the opposite distribution (TI 16.3±12.1; TII 20.4±16.9). CS activities were higher in TI (39.9±11.1) than TII (30.2±12.4) fibres with Phos showing the opposite (TI 24.4±7.3;TII 39.8±10.7). CONCLUSIONS: Intermittent hypoxia experienced by divers in this study maybe insufficient to cause tissue de-oxygenation to the extent to increase intracellular Carn in single muscle fibres compared to previously published values for untrained subjects.
Modeling the Invasion of Community‐Acquired Methicillin‐Resistant Staphylococcus aureus into Hospitals (2009)

Improving compliance with hand hygiene and screening for and decolonization of CA-MRSA carriers are effective strategies. However, hand hygiene has the greatest return of benefits and, if compliance is optimized, other strategies may have minimal added benefit.
The effect of antibiotics on bone healing: current evidence (2011)

The available experimental data and clinical evidence are rather limited to allow safe conclusions. In vitro studies indicate that high doses administered after systemic administration have little or no direct effect on bone cells. Further studies are desirable to define the effect of higher or prolonged concentrations on bone biology and especially that of high concentrations released by locally implanted antibiotic-delivery systems, that is, bone cement, spacers and beads.
Assessment of masticatory function in patients with non‐sagittal occlusal discrepancies (2014)

Non-sagittal occlusal discrepancies such as posterior cross-bite and anterior openbite are common types of malocclusion, but studies on masticatory function related to those malocclusions have been scarce. The aim of this study was to quantify the masticatory performance in patients with non-sagittal discrepancies compared to those with normal occlusion, using both objective and subjective measures. Maximum bite force and contact area using Dental Prescale(®) system as a static objective assessment, Mixing Ability Index (MAI) as a dynamic objective evaluation and food intake ability (FIA) as a subjective assessment were analysed from 21 people in normal occlusion (Group N) and 64 patients with posterior cross-bite (Group C), anterior openbite (Group O) or both (Group B). The differences of the maximum bite force, the contact area, the MAI and the FIA were compared, and their correlations were figured out. The non-sagittal malocclusion groups showed lower values in the maximum bite force, the contact area, the MAI and the FIA compared to those in the normal group (P < 0·0001). Compared to Group N, Groups C, O and B showed 61·5%, 42·1% and 40·1% of the maximum bite force, and 84%, 84% and 76% of hard food FIA, respectively. However, there were no significant differences among Groups C, O and B. The MAI showed higher correlation with the FIA (r = 0·38, P < 0·01), than with the maximum bite force and the contact area (both r = 0·24, P < 0·5). These results revealed that masticatory function in patients with non-sagittal discrepancies is significantly reduced both objectively and subjectively.
Oral type II collagen treatment in early rheumatoid arthritis. A double‐blind, placebo‐controlled, randomized trial (1996)

Only a minority of patients responded to treatment with oral type II collagen. These results justify further efforts to identify which patients will have good response to such therapy.
Nanoscale hyperspectral imaging of tilted cholesteric liquid crystal structures (2019)

Ongoing research on chiral liquid crystals takes advantage of the peculiar behavior of twisted structures subject to curvature. We demonstrate the fine tunability of the characteristics of the bandgap of a cholesteric structure in which the orientation of the helix axis spatially changes. To date, the spectral resolution of the order of 6 nm, herein reached by hyperspectral imaging, has not been solved in tilted helices. A correlation between spectral shifts and spatial twists is thus made possible.
Protein crystallization at the Laboratory of Molecular Biology: robotics, procedures and developments (2008)

Protein crystals grown by the cubic phase method diffract well and have been useful in determining high-resolution structures of several membrane proteins.The lipidic cubic phase methodology employed produces crystallization experiments that pose additional challenges to inspection.A versatile microscope platform, with automated x-y stage and various illumination and imaging options, has been developed with specific application to protein crystal detection.The DETECT-X microscope is a fully automated protein crystallization imaging instrument that operates in polarization, oblique angle and trans-illumination and UV-epi illumination fluorescence mode.Protein crystallization trials in traditional crystallization trays can be imaged in a fully automatic fashion.In its unique birefringence imaging mode the DETECT-X microscope produces false-color coded images of crystalline matter depicting the orientation of the slow optical axis of protein crystals and their orientation independent birefringence.Images that demonstrate the unique protein crystal imaging capabilities of the DETECT-X microscope are presented.The combination of the different observation modes allows the imaging of protein crystals that have strong contrast with respect to their facets as well as the interior body of the crystal.Colorless, transparent protein crystals appear colored.This enhanced contrast, along with UV epifluorescence, allows researchers to (i) see protein crystals through a layer of precipitate, (ii) discern between amorphous precipitate and non-facetted sphaerulites or precrystalline matter, (iii) identify crystal twins, and (iv) distinguish between protein and salt crystals.
Supplementary Table 3 from <i>STAT3</i> Antisense Oligonucleotide Remodels the Suppressive Tumor Microenvironment to Enhance Immune Activation in Combination with Anti–PD-L1 (2023)

&lt;p&gt;Gene expression signatures used in Figure 1&lt;/p&gt;
Factors Associated with Dietary Adherence in Celiac Disease: A Nationwide Study (2012)

Good dietary adherence can be achieved also in patients diagnosed and followed in primary health care. In a country with a high prevalence and good general knowledge of celiac disease, only age at diagnosis and age at present would appear to be major determinants for adherence.
Prospective Trial of Cisplatin, Adriamycin, and Dacarbazine in Metastatic Mixed Mesodermal Sarcomas of the Uterus and Ovary (1991)

Twenty-four patients with advanced or recurrent uterine (13) and ovarian (11) mixed mesodermal sarcomas received a combination of cisplatin. Adriamycin and dacarbazine (PAD) as initial therapy after surgical debulking. Of the 13 patients with metastatic uterine sarcoma, six (46.1%) remained without evidence of disease (NED) from 8 to 36 months from the start of PAD. The estimated 1-, 2-, and 3-year survivals for these patients were 68%, 68%, and 51%, respectively. Of the 11 ovarian sarcoma patients, five (45.4%) were NED at 5, 7, 32, 56, and 59 months from the start of PAD. The estimated 1-, 2-, and 3-year survivals for these patients were 70%, 35%, and 35%, respectively. The PAD regimen is an active regimen in patients with metastatic uterine and ovarian mixed mesodermal sarcomas and progression-free survival may be improved by maximum debulking surgery prior to the initiation of PAD chemotherapy.