gebhart/patrepeval huggingface dataset:
Whole-Genome Shotgun Optical Mapping of Deinococcus radiodurans (1999)

A whole-genome restriction map of Deinococcus radiodurans, a radiation-resistant bacterium able to survive up to 15,000 grays of ionizing radiation, was constructed without using DNA libraries, the polymerase chain reaction, or electrophoresis. Very large, randomly sheared, genomic DNA fragments were used to construct maps from individual DNA molecules that were assembled into two circular overlapping maps (2.6 and 0.415 megabases), without gaps. A third smaller chromosome (176 kilobases) was identified and characterized. Aberrant nonlinear DNA structures that may define chromosome structure and organization, as well as intermediates in DNA repair, were directly visualized by optical mapping techniques after gamma irradiation.
Pre-clinical evaluation of small molecule LOXL2 inhibitors in breast cancer (2017)

Lysyl Oxidase-like 2 (LOXL2), a member of the lysyl oxidase family of amine oxidases is known to be important in normal tissue development and homeostasis, as well as the onset and progression of solid tumors. Here we tested the anti-tumor properties of two generations of novel small molecule LOXL2 inhibitor in the MDA-MB-231 human model of breast cancer. We confirmed a functional role for LOXL2 activity in the progression of primary breast cancer. Inhibition of LOXL2 activity inhibited the growth of primary tumors and reduced primary tumor angiogenesis. Dual inhibition of LOXL2 and LOX showed a greater effect and also led to a lower overall metastatic burden in the lung and liver. Our data provides the first evidence to support a role for LOXL2 specific small molecule inhibitors as a potential therapy in breast cancer.
High-Intensity Electromagnetic Stimulation can Reduce Spasticity in Post-Stroke Patients (2018)

Background: Level of spasticity in post-stroke patients allows for the predictability of the patient’s level of recovery. The study aimed to assess the anti-spastic effect of high-intensity electromagnetic field stimulation in post-stroke condition. Methods: 30 post-stroke patients, randomized into two groups participated. The treatment group (TG) was delivered ten therapies to spastic muscles with high-intensity electromagnetic stimulation. The control group (CG) was delivered ten electrotherapy sessions in the spastic muscle area combined with kinesiotherapy. Modified Ashworth Scale (MAS) was used as a primary outcome measure to evaluate the level of spasticity. Secondary outcome measure, Barthel Index of Activities of Daily Living (ADL) was used to evaluate the patient’s quality of life. Results were obtained pre-treatment, post-treatment and after 1-month follow-up was completed. Results: During the 1-month follow-up, TG improved results up to 66% decreasing spasticity from 2.33±0.90 in the beginning to 0.87±0.64 points on the MAS. The CG, during the 1-month follow-up, improved up to 31% decreasing spasticity from 2.13±0.74 in the beginning to 1.47±0.74 points on the MAS. According to Barthel Index, 81% level of improvement was observed in TG during 1-month follow-up vs. 72% level of improvement observed for the CG in a 1-month follow-up. Conclusion: The evaluation showed greater spasticity reduction in TG - 66% vs. 31% in the CG after the 1-month follow-up visit. Results suggest that high-intensity electromagnetic stimulation is an effective extracorporeal physical modality for spasticity management in post-stroke patients.
Classifying Dialogue Acts in One-on-One Live Chats (2010)

We explore the task of automatically classifying dialogue acts in 1-on-1 online chat forums, an increasingly popular means of providing customer service. In particular, we investigate the effectiveness of various features and machine learners for this task. While a simple bag-of-words approach provides a solid baseline, we find that adding information from dialogue structure and inter-utterance dependency provides some increase in performance; learners that account for sequential dependencies (CRFs) show the best performance. We report our results from testing using a corpus of chat dialogues derived from online shopping customer-feedback data. 1
DNA ploidy, proliferation, and neu-oncogene protein overexpression in breast carcinoma. (1992)

DNA content, proliferative activity (Ki-67 immuno-staining and S-phase fraction by flow cytometry), and neu-oncogene overexpression were studied in 135 patients with invasive breast carcinoma. Image analysis and flow cytometry of fresh tumors showed good correlation between the two methods and yielded 39% diploid tumors and 61% aneuploid tumors. Aneuploidy, including tetraploidy, was significantly related to the loss of estrogen (p = 0.0002) and progesterone (p = 0.03) receptors, high histologic (p = 0.014) and nuclear (p less than 0.0001) grades, and mitotic rate (p = 0.0001). Immunohistochemical evaluation of proliferation by staining with Ki-67 monoclonal antibody and of neu-oncogene protein overexpression was performed in fresh frozen tissue from 83 tumors. The Ki-67 score, quantitated by the CAS-200 image analyzer, correlated only moderately with S-phase fraction obtained by flow cytometry by linear regression analysis (r = 0.39, p less than 0.001). However, both of these proliferation markers correlated strongly with the mitotic rate (p less than 0.0001). Aneuploid and tetraploid tumors demonstrated higher Ki-67 scores and S-phase fractions than diploid tumors. Neu-oncogene protein overexpression was seen in 24 tumors (29%) overall and was much higher in aneuploid tumors (38%) and tetraploid tumors (50%) than in diploid tumors (7%). However, the concentration of neu-oncogene protein positive tumors in the tetraploid region reported by others was not observed. Neu-oncogene protein overexpression was also associated with higher Ki-67 scores (p = 0.016) and S-phase fractions (p = 0.037).(ABSTRACT TRUNCATED AT 250 WORDS)
Association of a protein with membrane vesicles at the collisional limit: studies with blood coagulation factor Va light chain also suggest major differences between small and large unilamellar vesicles (1987)

Vesicle size can be a very sensitive modulator of protein-membrane association. In addition, reactions at the collisional limit may be characteristic of many types of protein-membrane or protein-receptor interactions. To probe these effects quantitatively, we analyzed the association of blood clotting factor Va light chain (Va-LC) with phospholipid vesicles of 15-150-nm radius. The number of protein binding sites per vesicle was approximately proportional to vesicle surface area. Association rates approached the collisional limit, and the activation energy for the association reaction was 4.5 +/- 0.5 kcal/mol. In agreement with diffusional theory for this type of interaction at the collisional limit, the observed association rate constant for filling all sites was approximately proportional to the inverse of vesicle radius. This general property has important implications for many systems such as blood coagulation including possible slower association rates and higher Km values for reactions involving whole cells relative to those obtained for phospholipid vesicles. Dissociation rate constants for reactions that are near the collisional limit should also be proportional to the inverse of vesicle size if diffusional parameters are the only factors influencing dissociation. However, Va-LC bound to small unilamellar vesicles (SUVs, less than or equal to 15-nm radius) gave slower dissociation rates than Va-LC bound to large unilamellar vesicles (LUVs, greater than or equal to 35-nm radius). This indicated a change in KI, the intrinsic protein-phospholipid affinity constant for LUVs vs SUVs. The cumulative effect of association and dissociation rates resulted in higher affinity of Va-LC for SUVs than LUVs under equilibrium conditions. The latter was corroborated by competition binding studies. Furthermore, the temperature dependence of both rate constants indicated an entirely entropy-driven binding to LUVs but a largely enthalpy-driven binding to SUVs. Interactions which are largely entropic are thought to be ionic in nature. The differences observed between binding to LUVs and SUVs may reflect thermodynamic differences between these types of phospholipid structures.
Genomic and non-genomic actions of glucocorticoids in asthma (2010)

Glucocorticoids are the mainstay of asthma therapy. They are primarily used to suppress airway inflammation, which is the central pathological change in asthmatic patients' airways. This is achieved by many different mechanisms. The classical mechanism is by suppression of the genetic transcription of many inflammatory cytokines that are key in asthma pathophysiology (transrepression). On the other hand, the transcription of certain inhibitory cytokines is activated by glucocorticoids (transactivation), a mechanism that also mediates many of the adverse effects of glucocorticoids. The onset of action through these mechanisms is often delayed (4-24 hours). Other mechanisms mediated through non-genomic pathways are increasingly appreciated. These are delivered in part by binding of glucocorticoids to nonclassical membrane-bound glucocorticoid receptors or by potentiating the α1-adrenergic action on the bronchial arterial smooth muscles, in addition to other mechanisms. These effects are characterized by their rapid onset and short duration of action. Understanding these different mechanisms will help in the development of new and better drugs to treat this common disease and to develop new improved strategies in our approach to its management. Here, the genomic and non-genomic mechanisms of actions of glucocorticoids in asthma are briefly reviewed, with special emphasis on the current updates of the non-genomic mechanisms.
Human CD4+ T cells stimulated by conserved adenovirus 5 hexon peptides recognize cells infected with different species of human adenovirus (2006)

The immune response against human adenovirus (HAdV) has gained interest because of the application of HAdV-based vectors in gene therapy and the high incidence of infections in pediatric recipients of allogeneic stem cell grafts. Because antiviral medication is frequently ineffective, the option of adoptive transfer of HAdV-specific donor-derived T cells in these immunocompromised patients is investigated. To generate good manufacturing practice-compatible reagents, a panel of 63 long, overlapping, peptides of the hexon protein was screened for recognition by T cells. Five conserved peptides of 30 amino acids were identified that were recognized by the majority of adult donors. CD4+ T cells from long-term cultures of PBMC, stimulated with this set of five peptides, recognized cells infected with HAdV serotypes belonging to different species. These data demonstrate that adult human T cells preferentially recognize conserved sequences of amino acid residues from a structural protein of HAdV. In the context of gene therapy, this observation may limit the beneficial effect of switching to HAdV-based vectors derived from less common serotypes of HAdV in an attempt to circumvent pre-existing immunity. However, this cross-reactivity benefits the application of HAdV-specific T cells for adoptive immunotherapy in immunocompromised transplant recipients.
A Phase I Dose Escalation Study with Anti-CD44v6 Bivatuzumab Mertansine in Patients with Incurable Squamous Cell Carcinoma of the Head and Neck or Esophagus (2006)

The main toxicity of bivatuzumab mertansine was directed against the skin, most probably due to CD44v6 expression in this tissue. The majority of skin reactions was reversible; however, one fatal drug-related adverse event had occurred. Clinical development was discontinued before reaching maximum tolerated dose.
Mast cells: novel clinical perspectives from recent insights (2009)

Abstract: Mast cells are still generally viewed as mediators of type I allergic or pseudoallergic reactions. Research over the past 10 years revealed that our view was too small and that mast cells are of key importance in innate immunity and also types II, III and IV adaptive immune reactions. Understanding their role in modulating and amplifying of inflammatory responses provides important insights into the pathogenesis of skin diseases such as psoriasis, atopic dermatitis, bullous pemphigoid or the control of infections. This helps us to understand the course of these diseases, their trigger mechanisms, and, the new role of agents, which can modulate the function of mast cells. These insights will help to develop new therapeutic approaches.
IN VITRO GERMINATION AND POLLEN TUBE GROWTH OF MAIZE (ZEA MAYS L.) POLLEN.: I. CALCIUM AND BORON EFFECTS (1967)

Pollen grains from the single cross hybrid Wf9 × H55 were cultured on an artificial medium containing 15% sucrose and 0.6% bacto-agar supplemented with all possible combinations of three concentrations (0.00, 0.03, and 0.06%) of calcium nitrate and three concentrations (0.00, 0.01, and 0.02%) of boric acid. The combination containing 0.03% calcium nitrate and 0.01% boric acid produced the highest germination (47.9%) and the longest tube length (405 μ). The addition of either calcium nitrate or boric acid alone decreased the germination percentage and pollen tube length. The percentage of grains producing more than one pollen tube was reduced by the addition of calcium nitrate or boric acid singly or in combination. The significance of these results in relation to pollen physiology was discussed.
A Case Series of Epilepsy-derived Memory Impairment Resembling Alzheimer Disease (2009)

We report 4 cases of epilepsy-derived progressive memory disturbances that clinically resembled Alzheimer disease. The patients were 3 women and 1 man, aged 56 to 79 years. The greatest disturbance was in recent memory. The patients' remote memory and orientation were relatively intact. Mental dullness and a decline in daily activities were also observed. No overt seizures were observed in any of the patients. Electroencephalography (EEG) revealed spikes in the left temporal region in 3 patients and in the left central region in the other patient. Single photon emission computed tomography or positron emission tomography revealed focal areas of hypofunction in the frontal, parietal, and parietotemporal regions. Performance of activities and memory improved rapidly in all patients after treatment with carbamazepine; the improvement was maintained after more than a year. It might be speculated that epileptic discharges caused dysfunction in the temporal lobe and the remote cortex through the neocortical and mesiotemporal network. EEG would be useful to rule out the possibility of a reversible condition in patients with cognitive disturbance. Moreover, investigation of this epilepsy-related condition with the combination of EEG and neurofunctional imaging might provide clues to clarify the pathophysiology of Alzheimer disease.
Sulfated disaccharide with greater inhibitory potency for L-selectin than sialyl Lewis x (1995)

The selectins are a family of three adhesion molecules (L-, P-, and E-) that direct the interaction of circulating leukocytes with endothelial cells during the first step in recruitment to tissue sites. Their involvement in inflammatory disease makes the selectins attractive targets for anti-inflammatory therapy. The sialyl Lewis x tetrasaccharide binds weakly to all three selectins and has demonstrated anti-inflammatory activity in vivo. However, the synthetic difficulties inherent to sialylated and fucosylated oligosaccharides motivate the search for alternative antagonists. Here we demonstrate that information gained from the biochemical analysis of a physiological selectin ligand can provide new leads for small molecule design. Previous structural analysis of the oligosaccharide chains on GlyCAM-1, an endothelial-derived ligand for L-selectin, revealed two novel structures: 6'-sulfo sialyl Lewis x and 6-sulfo sialyl Lewis x. The sulfate esters on these structures are thought to be essential for high-affinity binding to L-selectin. By incorporating sulfate esters on the analogous positions of the disaccharide lactose, we generated a simple small molecule (lactose 6',6-disulfate) with greater inhibitory potency for L-selectin than sialyl Lewis x.
Metabolism of high density lipoprotein subfractions and constituents in Tangier disease following the infusion of high density lipoproteins. (1981)

The metabolism of apolipoproteins A-I and A-II, as well as other high density lipoprotein (HDL) constituents, was studied in patients with homozygous familial HDL deficiency (Tangier disease) prior to and after plasma exchange or HDL infusion. Mean plasma apoA-I, apoA-II, and HDL cholesterol values in homozygotes (n = 2) were 2.0 mg/dl, 2.7 mg/dl, and 1.5 mg/dl, respectively, and in a normal control subject were 125.1 mg/dl, 23.0 mg/dl, and 53.0 mg/dl, respectively. Based on radioiodinated apoA-I and apoA-II kinetic studies in the baseline state, synthesis rates for apoA-I and apoA-II in mg/kg/day were 3.81 and 1.61, respectively, in one homozygote (patient B) and 11.82 and 1.99, respectively, in the normal subject. ApoA-I and apoA-II plasma residence times in days were 0.22 and 0.81, respectively, in the homozygote, and 4.04 and 4.44, respectively, in the normal subject. These data indicate that this homozygote had both a moderate decrease in the synthetic rates of apoA-I and apoA-II, as well as a marked decrease in the plasma residence times of these two apolipoproteins. In one homozygote (patient A) following a complete plasma exchange during cardiopulmonary bypass, plasma HDL cholesterol, apoA-I, and apoA-II levels were very similar to pre-exchange values within 64 hr after exchange. A second homozygote (patient B) received HDL intravenously as well as 125I-labeled apoA-I and 131I-labeled apoA-II. Following infusion, the residence time in days for HDL subfractions, HDL2b, HDL2a, and HDL3 were 0.1, 0.8, and 2.7, respectively. HDL protein and phospholipid both had a monoexponential decay, with residence times of 0.7 days, while HDL triglyceride disappeared monoexponentially with a residence time of 0.5 days. HDL cholesterol had a biexponential decay, with the residence time of the slow component being 0.7 days. Plasma and HDL apoA-I decayed down to baseline values significantly faster than did plasma and HDL apoA-II. ApoA-II specific radioactivity decreased throughout the course of the infusion study in both plasma and HDL, while apoA-I specific radioactivity decreased slightly, then rose, and subsequently declined in both plasma and HDL. The data indicate that the rapid and altered catabolism of apoA-I and apoA-II in Tangier homozygotes persists despite major increases in the plasma pool size of these proteins. In addition, following HDL infusion, HDL2b and HDL2a disappeared at a faster rate than HDL3, HDL cholesterol and triglyceride were catabolized at a faster rate than HDL protein and phospholipid, and apoA-I disappeared more rapidly than apoA-II. These observations may have important implications with regard to the catabolism of HDL subfractions and constituents in normal man.
The evaluation of gallbladder function by quantitative radionuclide cholescintigraphy in patients with noninsulin-dependent diabetes mellitus (1993)

Twenty-nine patients (24 males, 5 females; aged 62.8 +/- 10.1 years) with noninsulin-dependent diabetes mellitus (NIDDM) without gallstones and impaired liver function were included in our study. The patients were categorized by blood sugar control and disease duration. Twelve normal controls (10 males, 2 females; aged 62.8 +/- 12.4 years) were also studied for comparison. The gallbladder filling fraction (FF) and ejection fraction (EF) were calculated following the method of Krishnamurthy et al. The results showed no significant difference (P > 0.5) between (1) NIDDM and normal controls in FF (69.1 +/- 29.4 versus 67.5 +/- 24.0%) and EF (45.0 +/- 23.5 versus 54.8 +/- 10.0%) by a t-test, (2) good and poor blood sugar control in FF (64.9 +/- 30.9 versus 73.7 +/- 26.4%) and EF (42.0 +/- 25.4 versus 54.8 +/- 10.0%) by a Mann-Whitney U test, (3) long and short disease durations in FF (70.9 +/- 29.7 versus 67.9 +/- 28.7%) and EF (37.9 +/- 20.7 versus 50.0 +/- 24.1%) by a Mann-Whitney U test. In conclusion, the results challenge some previous reports and warrant further research.
Dielectric Method for Prediction of Porosity of Saturated Soil (1991)

The electromagnetic theory of Maxwell‐Fricke for the electrical conduction through heterogeneous media is extended to develop a theoretical relationship for fluid‐saturated porous media, accounting for the orientation of particles, the porosity and the dielectric constants of the pore fluid, the solid phase and the mixture. Based on this relationship, it is shown that a knowledge of the dielectric constants of saturated soils in the horizontal and vertical directions at high frequencies around 50 MHz provides the necessary data for the evaluation of the porosity for most soils when the dielectric constants of the particle and the solution are known. The method provides a rapid means for laboratory evaluation of the porosity of any saturated soil. It may also be adopted to in situ evaluations of the porosity of any saturated soil.
A formal model for virtual machine introspection (2009)

Virtual machine introspection (VMI) describes the method of monitoring and analyzing the state of a virtual machine from the hypervisor level. In this paper, we present a formal discussion of the development of VMI-based security applications. We begin by identifying three major challenges that all VMI-based security applications must overcome. The main contribution of our work is the definition of a formal model for describing VMI techniques. This model is broken down in such a way that allows for thorough discussion of any VMI approach with regard to each of the three challenges. Then, we specify three design patterns for interpreting state information using our model. We argue that these patterns are complete, that is, they cover all possible methods for state interpretation. The properties of all patterns are thoroughly discussed so that the pros and cons of their application may be fully understood. Finally, we describe and discuss an ideal VMI-based intrusion detection system using our model and begin to detail the practical implications in building such a system.
Leunig's Ducks and Drakes (2006)

The article explores the style of leftist cartoonist Michael Leunig. He regularly contributes to Australia's left-wing newspaper The Age.