gebhart/patrepeval huggingface dataset:
Room temperature SiO2∕SiO2 covalent bonding (2006)

Room temperature covalent bonds between bonded silicon oxide layers can be realized by forming surface and subsurface absorption layers followed by terminating outmost bonding surfaces with desired bonding groups prior to bonding. For example, by introducing fluorine into bonding oxide layers and NH2 groups onto surfaces of bonding oxide layers before bonding, bonding energy equivalent to silicon fracture energy (2500mJ∕m2) has been realized at room temperature after storage in air. Fluorine incorporation causes Si–O–Si ring breaking leading to fluorinated oxide formation with lower density, thus facilitating a higher diffusion rate of polymerization by-products and enhanced moisture absorptivity. Results indicate that by-products of the polymerization reaction between NH2 groups on mating surfaces appear to be more easily diffused and dispersed away from the bonding interface by the low density fluorinated oxide than are polymerization by-products of OH groups. This enhanced by-product removal results in covalent bonding at room temperature.
Gradual Reduction of Endotracheal Tube Diameter during Mechanical Ventilation via Different Humidification Devices (1996)

During prolonged mechanical ventilation, significant alterations in inner ETT configuration occur frequently and are influenced by the type of humidification device used. In vivo monitoring of ETT mechanical properties might be clinically useful.
Human Cathepsin V Functional Expression, Tissue Distribution, Electrostatic Surface Potential, Enzymatic Characterization, and Chromosomal Localization (1999)

Cathepsin V, a thymus and testis-specific human cysteine protease, was expressed in Pichia pastoris, and its physicokinetic properties were determined. Recombinant procathepsin V is autocatalytically activated at acidic pH and is effectively inhibited by various cysteine protease class-specific inhibitors. The S2P2 subsite specificity of cathepsin V was found to be intermediate between those of cathepsins S and L. The substrate binding pocket, S2, accepted both aromatic and nonaromatic hydrophobic residues, whereas cathepsins L and S preferred either an aromatic or nonaromatic hydrophobic residue, respectively. In contrast to cathepsin L, but similar to cathepsin S, cathepsin V exhibited only a very weak collagenolytic activity. Furthermore, cathepsin V was determined to be significantly more stable at mildly acidic and neutral pH than cathepsin L, but distinctly less stable than cathepsin S. A homology structure model of cathepsin V revealed completely different electrostatic potentials on the molecular surface when compared with human cathepsin L. The model-based electrostatic potential of human cathepsin V was neutral to weakly positive at and in the vicinity of the active site cleft, whereas that of cathepsin L was negative over extended regions of the surface. Surprisingly, the electrostatic potential of the human cathepsin V model structure resembled that of the model structure of mouse cathepsin L. These differences in the electrostatic potential at the molecular surfaces provide a reactivity determinant that may be the source of differences in substrate selectivity and pH stability. Cathepsin V was mapped to the chromosomal region 9q22.2, a site adjacent to the cathepsin L locus. The high sequence identity and the overlapping chromosomal gene loci suggest that both proteases evolved from an ancestral cathepsin L-like precursor by gene duplication.
Comparison of a fungal (family I) and bacterial (family II) cellulose-binding domain (1995)

A family II cellulose-binding domain (CBD) of an exoglucanase/xylanase (Cex) from the bacterium Cellulomonas fimi was replaced with the family I CBD of cellobiohydrolase I (CbhI) from the fungus Trichoderma reesei. Expression of the hybrid gene in Escherichia coli yielded up to 50 mg of the hybrid protein, CexCBDCbhI, per liter of culture supernatant. The hybrid was purified to homogeneity by affinity chromatography on cellulose. The relative association constants (Kr) for the binding of Cex, CexCBDCbhI, the catalytic domain of Cex (p33), and CbhI to bacterial microcrystalline cellulose (BMCC) were 14.9, 7.8, 0.8, and 10.6 liters g-1, respectively. Cex and CexCBDCbhI had similar substrate specificities and similar activities on crystalline and amorphous cellulose. Both released predominantly cellobiose and cellotriose from amorphous cellulose. CexCBDCbhI was two to three times less active than Cex on BMCC, but significantly more active than Cex on soluble cellulose and on xylan. Unlike Cex, the hybrid protein neither bound to alpha-chitin nor released small particles from dewaxed cotton fibers.
Case‐Control Study of Risk Factors for Human Infection with a New Zoonotic Paramyxovirus, Nipah Virus, during a 1998–1999 Outbreak of Severe Encephalitis in Malaysia (2000)

An outbreak of encephalitis affecting 265 patients (105 fatally) occurred during 1998-1999 in Malaysia and was linked to a new paramyxovirus, Nipah, that infected pigs, humans, dogs, and cats. Most patients were pig farmers. Clinically undetected Nipah infection was noted in 10 (6%) of 166 community-farm controls (persons from farms without reported encephalitis patients) and 20 (11%) of 178 case-farm controls (persons from farms with encephalitis patients). Case patients (persons with Nipah infection) were more likely than community-farm controls to report increased numbers of sick/dying pigs on the farm (59% vs. 24%, P=.001) and were more likely than case-farm controls to perform activities requiring direct contact with pigs (86% vs. 50%, P=.005). Only 8% of case patients reported no contact with pigs. The outbreak stopped after pigs in the affected areas were slaughtered and buried. Direct, close contact with pigs was the primary source of human Nipah infection, but other sources, such as infected dogs and cats, cannot be excluded.
The effects of force-feeding on enzymes of the liver, kidney, pancreas and digestive tract of chicks (1974)

1. Force-feeding of young chicks for 15 d increased kidney arginase ( EC 3·5·3·1) activity threefold. Fasting for 30 h decreased this activity by 50%. 2. Liver xanthine dehydrogenase was slightly increased after force-feeding and decreased following fasting. 3. The specific activities of two pentose-phosphate-cycle enzymes were not significantly affected by force-feeding, but glucose-6-phosphate dehydrogenase ( EC 1.1.1.49) decreased following fasting. 4. The over-all secretion of digestive enzymes increased parallel to the increase in food consumption. Therefore, despite an increased absolute weight of the pancreas and intestinal chyme, specific activities were the same in the force-fed and ad lib .-fed groups, except for a higher activity in intestinal amylase. 5. Fasting did not affect the pancreatic enzymic activities.
Developmental and Age‐Related Changes in Rat Brain Glycosaminoglycans (1988)

The quantities of each major class of glycosaminoglycan were determined in rat cerebrum from postnatal day 5 to 30 months of age. Chondroitin sulphate, dermatan sulphate, heparan sulphate, heparin, and hyaluronate were found, but no keratan sulphate was detected. Large and rapid changes in glycosaminoglycan content were observed during the period of brain maturation, and thereafter relatively steady levels were maintained until after the age of 12 months. The most remarkable change in the aged rat cerebrum was the ratio by weight of hyaluronate to chondroitin sulphate, which was approximately 1:1 from postnatal day 10 to 18 months but increased to 2.6:1 by the age of 30 months. In immature rats, the proportion of nonsulphated and 6-sulphated disaccharides derived from chondroitinase AC digests of brain glycosaminoglycans was much greater than in adults. In mature rats, chondroitin sulphate was composed almost entirely of 4-sulphated disaccharide subunits. The possibility that these changes could affect the permeability properties of the cerebral extracellular space and ionic equilibria in the brain is discussed.
A call for clinically driven experimental design in assessing neuroprotection in experimental Parkinsonism (2006)

Parkinson's disease is a progressive neurodegenerative disorder. At present, only symptomatic treatments are of proven efficacy, whereas strategies that slow or stop the neurodegenerative process are currently not available. The selection of interesting drug candidates or surgical strategies should be based on the soundest clinically driven preclinical validation. My goal here is not to discuss the relative merits of the available models, but to simply raise the issue of the experimental design that has led to the demonstration of efficacy of given compounds in these models. As some compounds previously shown to be active in classic experimental designs fail when tested in clinically relevant experimental designs, I emphasize the need for progressive screening methods and for the use of different animal species before entering into the clinic.
The first integrase inhibitor. (1996)

Clinical trials of an HIV integrase inhibitor, Aronex Pharmaceuticals' AR-177, are in progress at San Francisco General Hospital. AR-177 appears to keep integrase, the HIV enzyme, from binding to newly processed DNA. The drug is an oligonucleotide, unique to other oligonucleotides in that AR-177 folds upon itself to form a stable structure less prone to destruction in the blood. Use of AR-177 blocks viral replication by keeping the viral DNA from being integrated into the cell's DNA. High-dose studies will soon be evaluated, including the pharmacokinetics, safety, and antiviral effect of multiple dosing. AR-177 is currently an injectable, however, rodent studies are suggesting the drug has some oral bioavailability.
Rapid Development of Drug-Resistant Mutants of Poliovirus (1961)

Guanidine hydrochloride is a potent inhibitor of poliovirus synthesis in cell culture. However, the viral progeny which do grow in the presence of guani-dine may become approximately 10,000 times more resistant to the drug. The phenomenon of drug resistance poses yet another problem in the search for a satisfactory viral chemotherapeutic agent.
RIPK1 and NF-κB signaling in dying cells determines cross-priming of CD8 + T cells (2015)

Dying cells initiate adaptive immunity by providing both antigens and inflammatory stimuli for dendritic cells, which in turn activate CD8(+) T cells through a process called antigen cross-priming. To define how different forms of programmed cell death influence immunity, we established models of necroptosis and apoptosis, in which dying cells are generated by receptor-interacting protein kinase-3 and caspase-8 dimerization, respectively. We found that the release of inflammatory mediators, such as damage-associated molecular patterns, by dying cells was not sufficient for CD8(+) T cell cross-priming. Instead, robust cross-priming required receptor-interacting protein kinase-1 (RIPK1) signaling and nuclear factor κB (NF-κB)-induced transcription within dying cells. Decoupling NF-κB signaling from necroptosis or inflammatory apoptosis reduced priming efficiency and tumor immunity. Our results reveal that coordinated inflammatory and cell death signaling pathways within dying cells orchestrate adaptive immunity.
Multimode squeezing properties of a confocal optical parametric oscillator: Beyond the thin-crystal approximation (2005)

Up to now, transverse quantum effects (usually labeled as ``quantum imaging'' effects) which are generated by nonlinear devices inserted in resonant optical cavities have been calculated using the ``thin-crystal approximation,'' i.e., taking into account the effect of diffraction only inside the empty part of the cavity, and neglecting its effect in the nonlinear propagation inside the nonlinear crystal. We introduce in the present paper a theoretical method which is not restricted by this approximation. It allows us in particular to treat configurations closer to the actual experimental ones, where the crystal length is comparable to the Rayleigh length of the cavity mode. We use this method in the case of the confocal optical parametric oscillator, where the thin-crystal approximation predicts perfect squeezing on any area of the transverse plane, whatever its size and shape. We find that there exists in this case a ``coherence length'' which gives the minimum size of a detector on which perfect squeezing can be observed, and which gives therefore a limit to the improvement of optical resolution that can be obtained using such devices.
Acid-Catalyzed Synthesis of Bicyclo[3.n.1]alkenediones (2011)

An acid-catalyzed Dieckmann-type reaction has been developed to access functionalized bicyclo[3.2.1]alkenediones. This methodology has been successfully extended to more substituted and larger ring homologues, providing a new and efficient route to the core of numerous attractive natural products and their analogues.
B1‐based specific energy absorption rate determination for nonquadrature radiofrequency excitation (2012)

The current gold standard to estimate local and global specific energy absorption rate for MRI involves numerically modeling the patient and the transmit radiofrequency coil. Recently, a patient-individual method was presented, which estimated specific energy absorption rate from individually measured B(1) maps. This method, however, was restricted to quadrature volume coils due to difficulties distinguishing phase contributions from radiofrequency transmission and reception. In this study, a method separating these two phase contributions by comparing the electric conductivity reconstructed from different transmit channels of a parallel radiofrequency transmission system is presented. This enables specific energy absorption rate estimation not only for quadrature excitation but also for the nonquadrature excitation of the single elements of the transmit array. Though the contributions of the different phases are known, unknown magnetic field components and tissue boundary artifacts limit the technique. Nevertheless, the high agreement between simulated and experimental results found in this study is promising. B(1)-based specific energy absorption rate determination might become possible for arbitrary radiofrequency excitation on a patient-individual basis.
Trastuzumab for treatment of refractory/relapsed HER2-positive adult B-ALL: results of a phase 2 GRAALL study (2012)

The aim of this phase 2 study was to evaluate the efficacy and safety of trastuzumab, a humanized monoclonal antibody targeted against the human epidermal growth factor receptor 2 (HER2), for adult patients with relapsed/refractory HER2-positive B-ALL. Fifteen patients, with a median age of 62 years, received trastuzumab according to the schedule approved for breast cancer patients (ie, 4 mg/kg intravenous loading dose followed by 2 mg/kg weekly). The overall response rate was 13% with 2 patients achieving partial response and partial remission cytolytic response, respectively. Two other patients were documented with blast clearance. Only 1 reversible grade 3 cardiac toxic event occurred. This phase 2 study showed that trastuzumab monotherapy can allow for some responses in a very high-risk refractory/relapsed HER2-positive adult B-ALL population. Combination of trastuzumab with chemotherapy or other therapeutic monoclonal antibodies should be tested in the future.
Synthesis and Characterization of Oligo(poly(ethylene glycol) fumarate) Macromer (2001)

A novel oligomer based on alternating fumaric acid and poly(ethylene glycol) (PEG) units was synthesized and characterized. End group analysis by nuclear magnetic resonance (NMR) spectroscopy showed that the oligo (PEG fumarate) (OPF) had end PEG chains and multiple fumarate groups along its macromolecular chain. According to thermal characterization by differential scanning calorimetry (DSC), the crystallinity of OPF was found to be lower than PEG. The molecular weight and the degree of oligomerization of OPF determined by gel permeation chromatography (GPC) revealed that the conversion of OPF was substantially affected by the steric factors associated with large PEG chains. OPF was cross-linked using radical polymerization in the presence of either a chemical initiator or photoinitiator. As the OPF cross-linked, the unsaturated fumarate bonds disappeared and the PEG proton peak broadened in the NMR spectra. The cross-linked OPF gel showed swelling behavior that was dependent on the molecular weight of PEG. This novel cross-linkable PEG macromer is the first macromer with unsaturated double bonds along its macromolecular chain that allows for the preparation of hydrogels with tailored structure and properties.
Stomach regulates energy balance via acylated ghrelin and desacyl ghrelin (2004)

Background/Aims: The gastric peptide ghrelin, an endogenous ligand for growth-hormone secretagogue receptor, has two major molecular forms: acylated ghrelin and desacyl ghrelin. Acylated ghrelin induces a positive energy balance, while desacyl ghrelin has been reported to be devoid of any endocrine activities. The authors examined the effects of desacyl ghrelin on energy balance. Methods: The authors measured food intake, gastric emptying, c-Fos expression in the hypothalamus, and gene expression of hypothalamic neuropeptides in mice after administration of desacyl ghrelin. To explore the effects of long term overexpression of desacyl ghrelin, transgenic mice that overexpressed desacyl ghrelin were created. Results: Administration of desacyl ghrelin decreased food intake and gastric emptying rate through an action on the paraventricular nucleus and the arcuate nucleus in the hypothalamus. Gene expression of anorexigenic cocaine and amphetamine regulated transcript and urocortin in the hypothalamus was increased by desacyl ghrelin. Desacyl ghrelin overexpressing mice exhibited a decrease in body weight, food intake, and fat pad mass weight accompanied by moderately decreased linear growth. Gastric emptying was also decreased in desacyl ghrelin overexpressing mice. Conclusions: These findings indicate that in contrast to acylated ghrelin, desacyl ghrelin induces a negative energy balance by decreasing food intake and delaying gastric emptying. The effect is mediated via the hypothalamus. Although derived from the same precursor, the inverse effects of these two peptides suggest that the stomach might be involved as an endocrine organ in the regulation of the energy balance.
Shedding of tumor necrosis factor receptors by activated human neutrophils. (1990)

The capacity of human neutrophils (PMN) to bind tumor necrosis factor (TNF) was rapidly lost when the cells were incubated in suspension with agents that can stimulate their migratory and secretory responses. Both physiological (poly)peptides (FMLP, C5a, CSF-GM) and pharmacologic agonists (PMN, calcium ionophore A23187) induced the loss of TNF receptors (TNF-R) from the cell surface. Half-maximal loss in TNF-R ensued after only approximately 2 min with 10(-7) M FMLP at 37 degrees C, and required only 10(-9) M FMLP during a 30-min exposure. However, there were no such changes even with prolonged exposure of PMN to FMLP at 4 degrees or 16 degrees C. Scatchard analysis revealed loss of TNF-binding sites without change in their affinity (Kd approximately 0.4 nM) as measured at incompletely modulating concentrations of FMLP, C5a, PMA, or A23187. The binding of anti-TNF-R mAbs to PMN decreased in parallel, providing independent evidence for the loss of TNF-R from the cell surface. At the same time, soluble TNF-R appeared in the medium of stimulated PMN. This inference was based on the PMN- and FMLP-dependent generation of a nonsedimentable activity that could inhibit the binding of TNF to fresh human PMN or to mouse macrophages, and the ability of mAbs specific for human TNF-R to abolish inhibition by PMN-conditioned medium of binding of TNF to mouse macrophages. Soluble TNF-R activity was associated with a protein of Mr approximately 28,000 by ligand blot analysis of cell-free supernatants of FMLP-treated PMN. Thus, some portion of the FMLP-induced loss of TNF-R from human PMN is due to shedding of TNF-R. Shedding was unaffected by inhibitors of serine and thiol proteases and could not be induced with phosphatidylinositol-specific phospholipase C. Loss of TNF-R from PMN first stimulated by other agents may decrease their responsiveness to TNF. TNF-R shed by PMN may be one source of the TNF-binding proteins found in body fluids, and may blunt the actions of the cytokine on other cells.
A Meta-Analysis of the Impact of Anaerobic Soil Disinfestation on Pest Suppression and Yield of Horticultural Crops (2016)

Anaerobic soil disinfestation (ASD) is a proven but relatively new strategy to control soil borne pests of horticultural crops through anaerobic decomposition of organic soil amendments. The ASD technique has primarily been used to control soil borne pathogens; however, this technique has also shown potential to control plant parasitic nematodes and weeds. ASD can utilize a broad range of carbon (C) amendments and optimization may improve efficacy across environments. In this context, a meta-analysis using a random-effects model was conducted to determine effect sizes of the ASD effect on soil borne pathogens (533 studies), plant parasitic nematodes (91 studies), and weeds (88 studies) compared with unamended controls. Yield response to ASD was evaluated (123 studies) compared to unamended and fumigated controls. We also examined moderator variables for environmental conditions and amendments to explore the impact of these moderators on ASD effectiveness on pests and yield. Across all pathogen types with the exception of Sclerotinia spp., ASD studies show suppression of bacterial, oomycete and fungal pathogens (59 to 94%). Pathogen suppression was effective under all environmental conditions (50 to 94%) and amendment types (53 to 97%), except when amendments were applied at rates less than 0.3 kg m(-2). The ASD effect ranged from 15 to 56% for nematode suppression and 32 to 81% for weed suppression, but these differences were not significant. Significant nematode moderators included study type, soil type, sampling depth, incubation period, and use of mixed amendments. Weed suppression due to ASD showed significant heterogeneity for all environmental conditions, confirming that these studies do not share a common effect size. Total crop yield was not reduced by ASD when compared to a fumigant control and yield was significantly higher (30%) compared to an unamended control, suggesting ASD as a feasible option to maintain yield without chemical soil fumigants. We conclude ASD is effective against soil borne pathogens and while not conclusive due to a limited number of studies, we expect the same for nematodes and weeds given observed effect sizes. Findings should assist researchers in exploring ASD efficacy in particular environmental conditions and allow for development of standard treatment protocols.