gebhart/patrepeval huggingface dataset:
Molecular Insight into the Ligand–IgG Interactions for 4-Mercaptoethyl-pyridine Based Hydrophobic Charge-Induction Chromatography (2012)

Hydrophobic charge-induction chromatography (HCIC) with 4-mercaptoethyl-pyridine (MEP) as the ligand is a novel technology for antibody purification. In the present work, the molecular simulation methods were used to investigate the interactions between MEP ligand and Fc fragment of IgG (Fc-A). Six ligands with different structures of spacer arm were studied with molecular docking and dynamics simulation at neutral and acidic pH. The binding modes and the interaction energies were analyzed. The results indicated that all ligands tested could bind into the selected pocket on the C(H2) domain of Fc-A at neutral pH. The pyridine ring on the top of MEP ligands acts as a major role to provide the hydrophobic association and hydrogen bond for the ligand-IgG binding; meanwhile, the sulfone group on the spacer arm might form the additional hydrogen bond and enhance the binding of ligand onto the surface of IgG. The replacements of thioether sulfur atom on the spacer arm with either nitrogen or oxygen atom seem to have little influence on the binding. The influences of pH on the ligand-IgG interactions were also studied with the molecular dynamics simulation. It was found that MEP ligands would departed from the surface of Fc-A at low pH due to the electrostatic repulsion. The ligands with a sulfone group on the spacer arm would weaken the electrostatic repulsion and need more acidic conditions for the departing of ligand. The molecular simulation results were in agreement with some experimental observations, which would be useful to elucidate the molecular mechanism of HCIC and design a novel ligand to improve the efficiency of antibody separation.
4. Umbilical cord blood transplantation after a non-myeloablative therapy in high risk adults and adolescents (2005)

Bone marrow transplantation (BMT) in adults is associated with a high risk of graft-versus-host disease (GVHD), opportunistic infection and regimen related toxicity. For these reason, umbilical cord blood (UCB) after a non myeloablative preparative regimen has been explored. The underlying hypothesis is that umbilical cord blood T cells will be sufficiently alloreactive to effect engraftment in the non myeloablative setting. Fifty-one adults with advanced hematologic malignancies [median age 49 years (range 19-60)], ineligible for myeloablative conditioning by virtue of advanced age (73%), extensive prior therapy (42%) or serious co-morbidities/poor fitness (31%) received UCB transplantation (UCBT) after cyclophosphamide 50 mg/kg, fludarabine 200 mg/m2, and 200 cGy TBI. Immunosuppression was with cyclosporine-A to at least day 100 and mycophenolate mofetil to day 30. Patients with no combination chemotherapy in the 6 months prior to transplant also received ATG during conditioning. Approximately 1/4 received single and 3/4 received double UCB grafts. Units were predominantly 1-2 antigen HLA mismatched with the recipient. The incidence of sustained neutrophil engraftment of donor origin was 89% (95% CI, 81-97) at a median of 8 days (range 5-32). Stratified into those with and without chemotherapy in the prior 4 months, the cumulative incidence of sustained donor engraftment was 98% (95% CI: 94-100) and 64% (95% CI, 39-89) (p = 0.03). The incidence of platelet recovery (50,000/μL) was 68% (95% CI, 53-83). The incidences of grade II-IV and grade III-IV acute GVHD were 63% (95% CI: 49-73) and 25% (95% CI: 14-36) at day 100, and chronic GVHD was 28% (95% CI: 16-40) at 1 year. TRM was 19% (95% CI: 9-29) at day 180. Regression of relapsed or persistent disease has been seen in patients with myelodysplasia and intermediate and low grade lymphoid malignancies. The probability of overall survival at 1 year is 44% (95% CI: 30-58). Notably, only fitness and not age was associated with poor outcome. These data suggest that the regimen is well tolerated and sufficient for engraftment particularly in patients with chemotherapy in the preceding 4 months. This approach extends access to transplant to many adults who would otherwise be ineligible based on lack of donor and/or inability to tolerate high-dose conditioning.
Postischemic forearm skin reactive hyperemia is related to cardovascular risk factors in a healthy female population (2002)

This study shows that in a very low CV risk female population, a significant correlation can be observed between the weight of CV risks and the impairment of postischemic forearm SRH. Thus, skin laser Doppler flowmetry may represent a valuable, simple and non-invasive tool to assess and monitor microvascular function in future prospective observational and interventional studies.
Development of low-CO 2 -emission vehicles and utilization of local renewable energy for the vitalization of rural areas in Japan (2013)

Most of Japan's energy supply depends on imports from foreign countries, making the independence ratio of energy in Japan very low. The Fukushima nuclear power plant accident triggered by the Great East Japan Earthquake and Tsunami led to a mass shutdown of all the nuclear plants in Japan, a stoppage that is still in effect. In this paper, we review the energy supply situation and some social problems faced by rural areas in Japan. Given that lifestyles in rural Japan are reliant on automobiles, there is significant demand for the establishment of a sustainable mobility society. Furthermore, Japan is now entering an aging society ahead of other countries. In order to enhance the vitalization of rural areas and accelerate the establishment of sustainable society, our project developed low-CO2-emission vehicles (i.e., a single-driver EV [micro-EV] and a low-speed E-bus) for elderly people and tourists through the cooperation of regional industries, a local university, and a city office. This paper also reports some trial test results on renewable energy utilization as the driving energy supply for these low-emission vehicles.
ASME Evaluation on Grid Mobile E-Commerce Process (2012)

With the development of E-commerce, more scholars have paid attention to research on Mobile E-commerce and mostly focus on the optimization and evaluation of existing process. This paper researches the evaluation of Mobile E-commerce process with a method called ASME. Based on combing and analyzing current mobile business process and utilizing the grid management theory, mobile business process based on grid are constructed. Firstly, the existing process, namely Non-grid Mobile E-commerce, and the Grid Mobile E-commerce process are ordered. Secondly, the evaluation system with ASME is formed. Thirdly, the benefits of the Grid Mobile E-commerce process are presented. This paper provides a new way to evaluate Mobile E-commerce.
Comparison of MEMS accelerometers and geophones at Spring Coulee, Alberta (2008)

Geophone and MEMS accelerometer data from a field experiment at Spring Coulee, Alberta are compared in the acceleration domain. At receiver stations where coupling and noise are not a problem, measurements from both sensor types are found to be very similar. Several different analyses of signal-to-noise ratio indicate a small advantage for geophones at low and medium frequencies, at later arrival times and longer offsets. Accelerometers appear to have a small advantage at higher frequencies, shorter arrival times and shorter offsets.
Hypermedia, multimedia and hypertext: definitions and overview (1993)

In this paper I will discuss definitions of hypermedia, multimedia and hypertext. Hypertext is the grouping of relevant information in the form of nodes. These nodes are then connected together through links. In the case of hypertext the nodes contain text or graphics. Multimedia is the combining of different media types for example sound, animation, text, graphics and video for the presentation of information by making use of computers. Hypermedia can be viewed as an extension of hypertext and multimedia. It is based on the concept of hypertext that uses nodes and links in the structuring of information in the system. In this case the nodes consist of all the different data types that are mentioned in the multimedia definition above. The ‘node‐and‐link’ concept is used in organisation of the information in hypermedia systems. The ‘book’ metaphor is an example of the way these systems are implemented. This concept is explained and a few advantages and disadvantages of making use of hypermedia systems are discussed. A new approach for the development of hypermedia systems, namely the knowledge‐based approach is now looked into. Joel Peing‐Ling Loo proposed this approach because he thought that it is the most effective way for handling this kind of technology. A semantic‐based hypermedia model is developed in this approach to formulate solutions for the restrictions in presenting information authoring, maintenance and retrieval. The knowledge‐based presentation of information includes the use of conventional data structures. These data structures make use of frames (objects), slots and the inheritance theory that is also used in expert systems. Relations develop between the different objects as these objects are included in the database. Relations can also exist between frames by means of attributes that belong to the frames.
Poor Reproducibility of IGF-I and IGF Binding Protein-3 Generation Test in Children with Short Stature and Normal Coding Region of the GH Receptor Gene (2002)

The IGF-I generation test has been proposed to select patients with GH insensitivity. Studies have shown that children with idiopathic short stature and GH deficiency, who were expected to be sensitive to GH, presented absent IGF-I and IGF binding protein (IGFBP)-3 responses and/or discordant results at IGF-I and IGFBP-3 generation test for unknown reasons. To assess the reproducibility of the generation test, we studied a group of 12 prepubertal children with short stature and normal GH secretion in whom defects in coding region of GH receptor gene were ruled out. All patients underwent the test twice. Discordant responses between the first and second test were found in five and six patients for IGF-I and IGFBP-3, respectively. When the results of the generation tests were compared, one notices that IGF-I generation has more concordant positive results than IGFBP-3. In eight generation tests that showed discordant results between IGF-I and IGFBP-3, seven presented a positive IGF-I with a negative IGFBP-3 response. Taking both tests into account, all children presented a normal IGF-I generation. Our findings showed that IGF-I and IGFBP-3 generation test was not reproducible in children that should have responded to GH stimulation. We suggest that, when IGF-I and IGFBP-3 levels fail to respond in the generation test, another test should be performed to confirm GH insensitivity.
Characterization of a Dinuclear MnVO Complex and Its Efficient Evolution of O2in the Presence of Water (2003)

Ein hochvalentes MnVO-Porphyrin-Dimer wurde durch Persäure-Oxidation eines MnIII-Dimers unter basischen Bedingungen bei Raumtemperatur hergestellt (siehe Bild; mCPBA=m-Chlorperbenzoesäure). Die Zugabe einer Säure zu der Lösung des MnVO-Komplexes führt zur quantitativen Freisetzung von Disauerstoff. Wasser und/oder Hydroxidionen sind hier die Quellen sowohl für den Oxoliganden als auch für den freigesetzten Sauerstoff.
Hypoglycemic effect of herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) (2010)

Herbicide 2,4-dichlorophenoxyacetic acid (2,4-D), a synthetic auxin which promotes uncontrolled plant growth is widely used. The aim of our study was to investigate, using an experimental model, the effect of herbicide 2,4-D on liver function tests, enzyme a amylase and glucose blood level. BALB/C mice were treated i.p. with the herbicide (30 mg/ kg 2,4-D) for four consecutive days. Twenty-four hours after the last injection, the treated and the control animals were weighed and sacrificed for biochemical analysis: haematocrit, glucose blood level, serum activities of enzymes alanine aminotransferase, aspartate aminotransferase, gamma glutamyl transferase, and a amylase, as well as liver reduced glutathione. Herbicide 2,4-D significantly decreased glucose blood level in mice. There were no changes in liver function tests or activity of enzyme a amylase. In this study on mice we confirmed the results obtained in the previous study, which showed a hypoglycemic effect of herbicide 2,4-D on agricultural workers. To elucidate the mechanism of this effect, a further research is needed.
A Method of Limited Replication for the Efficient In Vivo Delivery of Adenovirus to Cancer Cells (1998)

Replication-deficient viral vectors are currently being used in gene transfer strategies to treat cancer cells. Unfortunately, viruses are limited in their ability to diffuse through tissue. This makes it virtually impossible to infect the majority of tumor cells in vivo and results in inadequate gene transfer. This problem can be addressed by allowing limited viral replication. Limited viral replication facilitates greater penetration of virions into tissue and can improve gene transfer. We have developed a strategy of limited viral replication using AdRSVlaclys, a chemically modified E1-deleted adenovirus, to codeliver an exogenous plasmid encoding the adenovirus E1 region. This system allows one round of viral replication. We examined the effect of this limited adenovirus replication in vitro and in vivo. In culture, codelivery of virus and pE1 resulted in a large increase in infected cells when compared with control cells exposed to virus and pUC19. In experiments on nude mice bearing HeLa ascites tumors, intraperitoneal injection of AdRSVlaclys/pE1 resulted in a significantly higher percentage of infected HeLa cells as compared with the PBS controls (p < 0.05) or the AdRSVlaclys/pUC19 controls (p < 0.01). These data demonstrate that the transcomplementation of replication-deficient adenovirus with exogenous E1 DNA leads to limited replication, and this controlled replication enhances gene transfer efficiency of adenovirus in vivo.
Estimation of hormone receptor status in fine‐needle aspirates and paraffin‐embedded sections from breast cancer using the novel rabbit monoclonal antibodies SP1 and SP2 (2003)

We describe a method of immunocytochemical assessment of estrogen receptor (ER) status on alcohol-fixed smears obtained by fine-needle aspiration (FNA) from breast cancer patients, using a commercially available rabbit monoclonal antibody anti-ER (SP1) without any antigen retrieval. A series of 40 aspirates were analyzed and the results of ER status were compared with the respective formalin-fixed tissue using the same procedure and with assessment by the classical method using the mouse monoclonal antibody 6F11 (anti-ER) with antigen retrieval on paraffin sections. Twenty-four out of the 40 cases examined were positive at least by two methods and 16 were negative for all three determinations. The results obtained in the ER immunocytochemical assay on aspirates and paraffin sections using the antibody SP1 and those obtained on paraffin sections using the antibody 6F11 were quite similar. In one case the material was insufficient to interpret the reaction in the cytological specimen and only one case, with focal positivity reaction on paraffin sections, was negative in the cytological specimen. The intensity of nuclei staining in cytological smears of breast cancer cells was stronger than that observed by traditional methods. We also assessed progesterone receptor (PR) status on 40 paraffin-sections from breast cancer patients, using a commercially available rabbit monoclonal antibody anti-PR (SP2), with the same characteristics described for anti-ER (SP1). The results were compared with assessment by the classic method with mouse monoclonal antibody 1A6 (PR) on paraffin sections and total agreement was observed. Of the 40 cases examined, 18 were positive and 22 were negative for the two determinations. We conclude that the application of the ER method on alcohol-fixed smears/paraffin sections with the rabbit monoclonal antibody SP1, and the PR method on paraffin sections with the rabbit monoclonal antibody SP2, provide several advantages, such as high sensitivity and specificity of the reaction, stronger immunostaining, shorter procedures times, and avoidance of antigenic retrieval methods.
Self-perpetuating epigenetic pili switches in bacteria (2002)

Bacteria have developed an epigenetic phase variation mechanism to control cell surface pili-adhesin complexes between heritable expression (phase ON) and nonexpression (phase OFF) states. In the pyelonephritis-associated pili (pap) system, global regulators [catabolite gene activator protein (CAP), leucine-responsive regulatory protein (Lrp), DNA adenine methylase (Dam)] and local regulators (PapI and PapB) control phase switching. Lrp binds cooperatively to three pap DNA binding sites, sites 1-3, proximal to the papBA pilin promoter in phase OFF cells, whereas Lrp is bound to sites 4-6 distal to papBA in phase ON cells. Two Dam methylation targets, GATC(prox) and GATC(dist), are located in Lrp binding sites 2 and 5, respectively. In phase OFF cells, binding of Lrp at sites 1-3 inhibits methylation of GATC(prox), forming the phase OFF DNA methylation pattern (GATC(dist) methylated, GATC(prox) nonmethylated). Binding of Lrp at sites 1-3 blocks pap pili transcription and reduces the affinity of Lrp for sites 4-6. Together with methylation of GATC(dist), which inhibits Lrp binding at sites 4-6, the phase OFF state is maintained. We hypothesize that transition to the phase ON state requires DNA replication to dissociate Lrp and generate a hemimethyated GATC(dist) site. PapI and methylation of GATC(prox) act together to increase the affinity of Lrp for sites 4-6. Binding of Lrp at the distal sites protects GATC(dist) from methylation, forming the phase ON methylation pattern (GATC(dist) nonmethyated, GATC(prox) methylated). Lrp binding at sites 4-6 together with cAMP-CAP binding 215.5 bp upstream of the papBA transcription start, is required for activation of pilin transcription. The first gene product of the papBA transcript, PapB, helps maintain the switch in the ON state by activating papI transcription, which in turn maintains Lrp binding at sites 4-6.
RID: radio interference detection in wireless sensor networks (2005)

In wireless sensor networks, many protocols assume that if node A is able to interfere with node B's packet reception, node B is within node A's communication range. It is also assumed that if node B is within node A's communication range, node A is able to interfere with node B's packet reception from any transmitter. While these assumptions may be useful in protocol design, they are not valid, according to the real experiments we conducted in MICA2 platform. For a strong link that has a high packet delivery ratio, the interference range is observed smaller than the communication range, while for a weak link that has a low packet delivery ratio, the interference range is larger than the communication range. So using communication range information alone is not enough to design real collision-free media access control protocols. This paper presents a radio interference detection protocol (RID) and its variation (RID-B) to detect run-time radio interference relations among nodes. The interference detection results are used to design real collision-free TDMA protocols. With extensive simulations in GlomoSim, and with sensor network application scenarios, we observe that the TDMA which uses the interference detection results has 100% packet delivery ratio, while the traditional TDMA has packet loss up to 60%, in heavy load. In addition to the scheduling-based TDMA protocols, we also explore the application of interference detection on contention-based MAC protocols.
Inflammation and Potential Anti-Inflammatory Approaches in Stroke (2003)

Ischemic stroke develops when a major brain artery, most commonly the middle cerebral artery, is obstructed by an embolus or thrombosis and, consequently, blood flow in a restricted area of the brain is severely reduced. Even though animal research conducted on acute ischemic injury has revealed several pathophysiological cascades, which contribute to the enlargement of brain infarction, no major breakthroughs in developing clinically relevant stroke therapy have been achieved. There are several reasons for failed translation of successful basic research approaches into effective treatment modalities for stroke in humans (1). One important factor is that the animal models do not reflect well enough the ischemic damage in both permanent (no reperfusion) and transient (with reperfusion) ischemia in aged female and male victims, which may suffer from other age-related diseases, such as hypertension, diabetes, and Alzheimer’s disease (2). Another, even a more valid, fact is that the therapeutic time window for treating human stroke is delayed beyond the hours after the insult and, therefore, the pathophysiological events targeted pharmacologically need to occur several hours or days later (2). For these reasons, targeting mechanisms such as various glutamate receptors and calcium channels may not be considered for treatment of most of the stroke patients.
Ingredients from integral valorization of Isabel grape to formulate goat yogurt with stimulatory effects on probiotics and beneficial impacts on human colonic microbiota in vitro (2022)

Isabel grape (IG) products have high contents of phenolic compounds and fiber recognized for their positive impacts on microorganisms associated with health benefits to host. This study evaluated the effects of goat yogurts formulated with ingredients from IG integral valorization on the growth and metabolism of different probiotic strains, as well as on the population of selected bacterial groups and metabolic activity of human colonic microbiota in vitro. Goat yogurts with IG ingredients (IGI) stimulated the growth of tested Lactobacillus and Bifidobacterium probiotic strains during a 48-h cultivation, as well as decreased the pH values and enhanced the organic acid production. Goat yogurts with IGI increased the population of Lactobacillus spp. and Bifidobacterium spp. during a 24-h in vitro colonic fermentation. A stable Firmicutes:Bacteroidetes ratio close to 1 was found in media with goat yogurt formulations during the colonic fermentation, being similar to the effect caused by fructooligosaccharides. Goat yogurt formulations with IGI caused increased production of short-chain fatty acids and sugar consumption during colonic fermentation. Goat yogurts with IGI should be a valuable strategy for development of novel added-value foods with beneficial effects on gut microbiota and human health.