gebhart/patrepeval huggingface dataset:
U-Shaped Dose-Responses in Biology, Toxicology, and Public Health (2001)

The occurrence of U-shaped dose-response relationships (often termed hormesis) has been documented in numerous biological, toxicological, and pharmacological investigations. Many of the endpoints studied are of considerable significance to public health (e.g. body weight, cholesterol levels, ethanol consumption, longevity, cancer incidence, etc). Despite the fact that U-shaped dose-responses are widely and independently observed, little attempt has been made to assess this phenomenon in an integrative manner. This review provides an overview of the historical foundations of hormesis and a discussion of its definition within a mechanistic framework. The occurrence, generalizability, and biological significance of U-shaped dose-response relationships along with the concept of biological optimality are addressed.
Hepatitis delta (δ) cDNA clones: Undetectable hybridization to nucleic acids from infectious non‐A, non‐B hepatitis materials and hepatitis B DNA (1987)

Hepatitis Delta (delta) cDNA clones were hybridized to RNA extracted from livers of chimpanzees infected with the blood-borne Non-A, Non-B hepatitis (NANBH) agent(s) and to total nucleic acids extracted from chimpanzee plasma containing a high titer of these NANBH agent(s). Since no hybridization was observed, the data suggests that the hepatitis Delta viral genome is not closely related to the genome(s) of the NANB agent(s). Our studies, in which the Hepatitis B virus genomic DNA was hybridized to hepatitis Delta cDNA clones, also confirm and extend previous studies [Hoyer et al, 1983], which report a lack of detectable homology between the hepatitis Delta genome and HBV DNA.
Inducible Caspase 9 Suicide Gene to Improve the Safety of Allodepleted T Cells after Haploidentical Stem Cell Transplantation (2007)

Addback of donor T cells following T cell-depleted stem cell transplantation (SCT) can accelerate immune reconstitution and be effective against relapsed malignancy. After haploidentical SCT, a high risk of graft-versus-host disease (GVHD) essentially precludes this option, unless the T cells are first depleted of alloreactive precursor cells. Even then, the risks of severe GVHD remain significant. To increase the safety of the approach and thereby permit administration of larger T cell doses, we used a suicide gene, inducible caspase 9 (iCasp9), to transduce allodepleted T cells, permitting their destruction should administration have adverse effects. We made a retroviral vector encoding iCasp9 and a selectable marker (truncated CD19). Even after allodepletion (using anti-CD25 immunotoxin), donor T cells could be efficiently transduced, expanded, and subsequently enriched by CD19 immunomagnetic selection to >90% purity. These engineered cells retained antiviral specificity and functionality, and contained a subset with regulatory phenotype and function. Activating iCasp9 with a small-molecule dimerizer rapidly produced >90% apoptosis. Although transgene expression was downregulated in quiescent T cells, iCasp9 remained an efficient suicide gene, as expression was rapidly upregulated in activated (alloreactive) T cells. We have demonstrated the clinical feasibility of this approach after haploidentical transplantation by scaling up production using clinical grade materials.
Improved Total Synthesis and Biological Evaluation of Potent Apratoxin S4 Based Anticancer Agents with Differential Stability and Further Enhanced Activity (2014)

Apratoxins are cytotoxic natural products originally isolated from marine cyanobacteria that act by preventing cotranslational translocation early in the secretory pathway to downregulate receptor levels and inhibit growth factor secretion, leading to potent antiproliferative activity. Through rational design and total synthesis of an apratoxin A/E hybrid, apratoxin S4 (1a), we have previously improved the antitumor activity and tolerability in vivo. Compound 1a and newly designed analogues apratoxins S7-S9 (1b-d), with various degrees of methylation at C34 (1b,c) or epimeric configuration at C30 (1d), were efficiently synthesized utilizing improved procedures. Optimizations have been applied to the synthesis of key intermediate aldehyde 7 and further include the application of Leighton's silanes and modifications of Kelly's methods to induce thiazoline ring formation in other crucial steps of the apratoxin synthesis. Apratoxin S9 (1d) exhibited increased activity with subnanomolar potency. Apratoxin S8 (1c) lacks the propensity to be deactivated by dehydration and showed efficacy in a human HCT116 xenograft mouse model.
Determination of the Escherichia coli S-Nitrosoglutathione Response Network Using Integrated Biochemical and Systems Analysis (2007)

During infection or denitrification, bacteria encounter reactive nitrogen species. Although the molecular targets of and defensive response against nitric oxide (NO) in Escherichia coli are well studied, the response elements specific to S-nitrosothiols are less clear. Previously, we employed an integrated systems biology approach to unravel the E. coli NO-response network. Here we use a similar approach to confirm that S-nitrosoglutathione (GSNO) primarily impacts the metabolic and regulatory programs of E. coli in minimal medium by reaction with homocysteine and cysteine and subsequent disruption of the methionine biosynthesis pathway. Targeting of homocysteine and cysteine results in altered regulatory activity of MetJ, MetR, and CysB, activation of the stringent response and growth inhibition. Deletion of metJ or supplementation with methionine strongly attenuated the effect of GSNO on growth and gene expression. Furthermore, GSNO inhibited the ArcAB two-component system. Consistent with the underlying nitrosative and thiol-oxidative chemistry, growth inhibition and the majority of the regulatory perturbations were dependent upon GSNO internalization by the Dpp dipeptide transporter. Contrastingly, perturbation of NsrR appeared to be a result of the submicromolar levels of NO released from GSNO and did not require GSNO internalization.
Use of Multiscreen plates for the preparation of bacterial DNA suitable for PCR. (1995)

A rapid and inexpensive method for isolating bacterial DNA for use in PCR is described. The method is based on the guanidinium thiocyanate (GuSCN)-lysis method of Boom et al. (J. Clin. Microbiol. 28:495-503, 1990) and enables a multiple of 96 samples to be prepared in only one hour. We use Multiscreen plates and a vacuum manifold from Millipore. Clinical samples are lysed and washed in the wells of a Multiscreen plate, and DNA is eluted in a standard microplate. Purified DNA was recovered with high yields (over 25%). The method allows multichannel or robotic pipetting for both the sample preparation as well as for the PCR step. The method has been applied successfully to detect pathogenic Streptococcus suis type 2 in nasal and tonsil swab specimens of pigs.
The Hemopexin-like C-terminal Domain of Membrane Type 1 Matrix Metalloproteinase Regulates Proteolysis of a Multifunctional Protein, gC1qR (2002)

Matrix metalloproteinases (MMPs) including membrane type 1 MMP (MT1-MMP) can degrade extracellular matrix and cell surface receptor molecules and have an essential function in malignancy. Recently, we established a functional link between MT1-MMP and the receptor of complement component 1q (gC1qR). The gC1qR is known as a compartment-specific regulator of diverse cellular and viral proteins. Once released by proliferating cells, soluble gC1qR may inhibit complement component 1q hemolytic activity and play important roles in vivo in assisting tumor cells to evade destruction by complement. Here, we report that gC1qR is susceptible to MT1-MMP proteolysis in vitro and in cell cultures. The major MT1-MMP cleavage site (Gly(79) down arrow Gln(80)) is localized within the structurally disordered loop connecting the beta(3) and the beta(4) strands of gC1qR. The recombinant MT1-MMP construct that included the catalytic domain but lacked the hemopexin-like domain lost the proteolytic capacity; however, it retained the ability to bind gC1qR. Inhibition of MT1-MMP activity by a hydroxamate inhibitor converted the protease into a cell surface receptor of gC1qR and promoted co-precipitation MT1-MMP with the soluble gC1qR protein. It is tempting to hypothesize that these novel mechanisms may play important roles in vivo and have to be taken into account in designing hydroxamate-based cancer therapy.
Laser additive manufacturing of metallic components: materials, processes and mechanisms (2012)

Unlike conventional materials removal methods, additive manufacturing (AM) is based on a novel materials incremental manufacturing philosophy. Additive manufacturing implies layer by layer shaping and consolidation of powder feedstock to arbitrary configurations, normally using a computer controlled laser. The current development focus of AM is to produce complex shaped functional metallic components, including metals, alloys and metal matrix composites (MMCs), to meet demanding requirements from aerospace, defence, automotive and biomedical industries. Laser sintering (LS), laser melting (LM) and laser metal deposition (LMD) are presently regarded as the three most versatile AM processes. Laser based AM processes generally have a complex non-equilibrium physical and chemical metallurgical nature, which is material and process dependent. The influence of material characteristics and processing conditions on metallurgical mechanisms and resultant microstructural and mechanical properties of AM processed components needs to be clarified. The present review initially defines LS/LM/LMD processes and operative consolidation mechanisms for metallic components. Powder materials used for AM, in the categories of pure metal powder, prealloyed powder and multicomponent metals/alloys/MMCs powder, and associated densification mechanisms during AM are addressed. An in depth review is then presented of material and process aspects of AM, including physical aspects of materials for AM and microstructural and mechanical properties of AM processed components. The overall objective is to establish a relationship between material, process, and metallurgical mechanism for laser based AM of metallic components.
In vitro accumulation of glucocerebroside in neuroblastoma cells: A model for study of Gaucher disease pathobiology (1996)

Gaucher disease is the most common lysosomal glycosphingolipid storage disease; decreased activity of glucosylceramide beta-glucosidase (GCase) results in the accumulation of glucocerebroside (GlcCer) in macrophage-derived cells. The most devastating types of Gaucher disease also involve neuronopathology, thought to be mediated by intracellular GlcCer accumulation in the brain. In this study, we developed an in vitro neuronal cell model for accumulation of endogenous GlcCer to enable studies on the cellular basis for the neuronopathology of this disease. A human neuroblastoma cell line (SH-SY5Y) was selected because it produced appreciable GCase. When these cells were treated with conduritol B epoxide (CBE), a competitive, irreversible inhibitor of this enzyme, GCase levels fell precipitously, while other lysosomal hydrolase levels were unaffected. Relative to untreated control cells, the CBE-treated cells accumulated higher levels of GlcCer, but not other related glycolipids, over time. Thus, this in vitro system displayed many essential biological parameters relevant for studies on cellular events responsible for the neurologic damage that occurs in some types of Gaucher disease. This model should also be useful in investigations of the normal role of sphingolipids in neuronal cell function.
Could drought constrain woody encroachers in savannas? (2020)

Droughts are expected to become more frequent and severe, due to climate change, with uncertain consequences for savanna vegetation. Drought-driven tree mortality has been observed in some savannas, but little is known about how tolerant savanna trees are to drought, or what determines differences among species in drought vulnerability. Here, we examine which characteristics best distinguished tree species that were most negatively affected by a recent drought in Kruger National Park, South Africa. Woody-encroaching, root-suckering species, which tended to have relatively low investments in non-structural carbohydrates, had the highest mortality rates. Of particular interest was Dichrostachys cinerea, a notable contributor to widespread woody encroachment across southern African savannas, which suffered high drought mortality. Using rainfall maps and vegetation survey data, we show that D. cinerea distributions in Kruger National Park are limited to areas with higher mean annual rainfall and lower past drought frequency, and stem densities are lower where droughts have occurred more frequently, suggesting that past droughts have had lasting impacts on the distribution and abundance of this species. Woody encroachers, such as D. cinerea, may face a trade off between traits promoting proliferation vs. drought tolerance, and more frequent and severe droughts could increasingly limit their spread.
Alpha-Synuclein Cell-to-Cell Transfer and Seeding in Grafted Dopaminergic Neurons In Vivo (2012)

Several people with Parkinson's disease have been treated with intrastriatal grafts of fetal dopaminergic neurons. Following autopsy, 10-22 years after surgery, some of the grafted neurons contained Lewy bodies similar to those observed in the host brain. Numerous studies have attempted to explain these findings in cell and animal models. In cell culture, α-synuclein has been found to transfer from one cell to another, via mechanisms that include exosomal transport and endocytosis, and in certain cases seed aggregation in the recipient cell. In animal models, transfer of α-synuclein from host brain cells to grafted neurons has been shown, but the reported frequency of the event has been relatively low and little is known about the underlying mechanisms as well as the fate of the transferred α-synuclein. We now demonstrate frequent transfer of α-synuclein from a rat brain engineered to overexpress human α-synuclein to grafted dopaminergic neurons. Further, we show that this model can be used to explore mechanisms underlying cell-to-cell transfer of α-synuclein. Thus, we present evidence both for the involvement of endocytosis in α-synuclein uptake in vivo, and for seeding of aggregation of endogenous α-synuclein in the recipient neuron by the transferred α-synuclein. Finally, we show that, at least in a subset of the studied cells, the transmitted α-synuclein is sensitive to proteinase K. Our new model system could be used to test compounds that inhibit cell-to-cell transfer of α-synuclein and therefore might retard progression of Parkinson neuropathology.
Stabilization of enzymes in ionic liquids via modification of enzyme charge (2013)

Due to the propensity of ionic liquids (ILs) to inactivate enzymes, the development of strategies to improve enzyme utility in these solvents is critical to fully exploit ILs for biocatalysis. We have developed a strategy to broadly improve enzyme utility in ILs based on elucidating the effect of charge modifications on the function of enzymes in IL environments. Results of stability studies in aqueous-IL mixtures indicated a clear connection between the ratio of enzyme-containing positive-to-negative sites and enzyme stability in ILs. Stability studies of the effect of [BMIM][Cl] and [EMIM][EtSO4 ] on chymotrypsin specifically found an optimum ratio of positively-charged amine-to-negatively-charged acid groups (0.39). At this ratio, the half-life of chymotrypsin was increased 1.6- and 4.3-fold relative to wild-type chymotrypsin in [BMIM][Cl] and [EMIM][EtSO4 ], respectively. The half-lives of lipase and papain were similarly increased as much as 4.0 and 2.4-fold, respectively, in [BMIM][Cl] by modifying the ratio of positive-to-negative sites of each enzyme. More generally, the results of stability studies found that modifications that reduce the ratio of enzyme-containing positive-to-negative sites improve enzyme stability in ILs. Understanding the impact of charge modification on enzyme stability in ILs may ultimately be exploited to rationally engineer enzymes for improved function in IL environments.
Rapid Destruction of Porcine Islets of Langerhans by Fresh Human Blood. (1998)

484 Previous studies, by us and others have demonstrated only minor effects of human complement active serum on porcine islets in vitro. In this study, adult porcine islets were exposed to fresh non-heparinized human blood in a device originally devised by us for studies on complement activation.Method: Adult porcine islets (API) were isolated, using standard procedures and cultured in RPMI containing 10% porcine serum for 1-4 days. One, 2, or 5 μl of API (1μl=1000 IEQ) suspended in 100 μl medium, was placed in a circular device consisting of a surface-heparinized cardiovascular plastic tube. Subsequently, 7 ml of non-heparinized fresh human blood was added and the device placed in an incubator at 37 °C and rocked back and forth for 5, 15, 30 or 60 minutes. Blood supplemented with 100 μl culture medium served as controls. Thrombocytes (TRC), differential leukocyte count, C3a, soluble Terminal Complement Complex (TCC), Thrombin-Anti-Thrombin(TAT) and insulin was measured. Results: Thetable below summarizes the findings after 60 minutes:When API were placed in the device, there was a rapid consumption of TRC during the first 5-15 minutes and an extensive, visible coagulation could be observed. In parallel, there was a significant increase in C3a, TCC and TAT compared to the controls. By 15-30 minutes there was a selective loss of neutrophils and monocytes with little or no effect on lymphocytes. The changes where equally pronounced whether 1, 2 or 5 μl of islets had been added. Islet cell destruction was manifest within 30 minutes, as evidenced by the release of large amounts of insulin. Conclusion: When mixed with fresh non-heparinized human blood adult porcine islets caused a marked activation of the complement and coagulation systems, and induced consumption of neutrophils and monocytes. During these events the islets were destroyed. The events mimic those seen in hyperacute xenograft rejection. These findings are in marked contrast to those seen in previous in vitro studies, with human serum and may have important implications for clinical islet xenotransplantation with regards to the protective measures required.
Role of Ca2+ in serum-stimulated Na+ influx in normal and transformed cells (1985)

Previous studies in human foreskin fibroblasts suggested that the mechanism by which serum stimulates Na+ influx is via a Ca2+-calmodulin-mediated event. In the present experiments in normal WI-38 cells (human lung fibroblasts), both the intracellular Ca2+ antagonist 8-(N,N-diethylamino)-octyl-3,4,5-trimethoxybenzoate (TMB-8) and the potent calmodulin antagonist trifluoperazine (TFP) blocked serum-stimulated Na+ influx [TMB-8 concentration causing half-maximal inhibition (Ki) = 15 microM and TFP Ki = 10 microM]. Similar results were obtained in Swiss 3T3 cells. In contrast, in transformed WI-38 or Swiss 3T3 cells neither TMB-8 nor TFP had any effect on serum-stimulated Na+ influx (TMB-8 Ki greater than 100 microM and TFP Ki greater than 100 microM). In addition, when 45Ca2+ efflux measurements were made on normal and transformed cells, serum stimulated significant 45Ca2+ efflux (P less than 0.05) from WI-38 and Swiss 3T3 cells, while having no effect on 45Ca2+ efflux from simian virus 40 (SV40)-WI-38 or SV40-Swiss 3T3 cells. However, an elevation of intracellular Ca2+ can stimulate Na+ influx, since it was found that A23187 mimicked the effects of serum in both normal and transformed cells. These results suggest that the Ca2+-calmodulin-mediated event, which is thought to be involved in serum-stimulated Na+ influx in normal cells, may be bypassed or overridden in transformed cells.
Toxicity on human hemopoietic progenitors of 2'-2'-difluoro-2'deoxycytidine (gemcitabine). (1998)

This study presents results on 2'-2'-difluoro-2'deoxycytidine's (dFdC: gemcitabine) in vitro toxicity on peripheral blood CFU-GM and BFU-E obtained from healthy volunteers. Peripheral blood mononucleated non-adherent cells were cultured according to standard methods with continuous exposure (13 days) to dFdC (4,40 and 400 pmol/L) or following 1 hour's, incubation with increasing drug concentrations (1, 10, 100 mumol/L). The results indicate that dFdC has a marked dose-dependent inhibitory effect on the in vitro growth of peripheral blood hemopoietic progenitors., No significant differences were observed for the growth inhibition induced on CFU-GM and BFU-E. Continuous exposure to dFdC gave an IC50 of 4 pmol/L for both CFU-GM and BFU-E. In four chemotherapy naive patients affected by tumors of different type treated with three standard courses of dFdC the variations in the peripheral blood of hemopoietic progenitor level were determined. Patterns of changes were different, but a marked and sustained decrease of both CFU-GM and BFU-E was observed in one case only. The contrast between the apparently rather mild clinical hemotoxicity of dFdC and its in vitro dramatically potent inhibitory activity on hemopoietic progenitors is discussed.
Development and Significance of the HIV-1 Reverse Transcriptase M184V Mutation During Combination Therapy With Lamivudine, Zidovudine, and Protease Inhibitors (1999)

To analyze the emergence and role of the lamivudine (3TC)-selected HIV-1 reverse transcriptase (RT) M184V mutation under triple therapy, we performed a retrospective study of 40 nucleoside RT inhibitor-pretreated and 16 drug-naive patients who were switched to combined treatment with zidovudine (ZDV) plus 3TC plus a protease inhibitor (PI). Plasma viral load and pol genotype were analyzed at baseline and after 24 and 48 weeks of combination therapy. Emergence of the M184V RT mutation at week 48 was detected in 3 of 16 (18.7%) initially drug-naive subjects as opposed to 21 of 40 (52.5%) ZDV-pretreated patients. Multivariate logistic analysis detected HIV-1 RNA load at week 24 as the best predictor of subsequent selection of the M184V mutant (p = .0121). Among ZDV-resistant study subjects at week 24 (n = 17), those with mutant RT M184V codon had a more favorable HIV-1 RNA slope than those with wild-type RT 184M codon (p = .0551). This trend was observed, although in a less evident manner, even in pretreated ZDV-sensitive patients. These findings suggest that development of the 3TC-resistance M184V mutation under triple therapy with 3TC, ZDV, and a PI may have unexpected beneficial effects in vivo in addition to those associated with resensitization of ZDV-resistant virus to ZDV.
Natural language query filtration in the Conceptual Query Language (2002)

Natural language (NL) interfaces for database query formulation have always been recognized as a much needed enhancement for end-users. Poor performances with earlier NL systems had led to a lull in research in this field. However, latter-day experiments and systems appear to be sufficiently more promising to warrant continued and further research in this area. This paper proposes an experimental query interface that filters NL query statements for search predicates that are derived from constructs on conceptual schemas, thereby avoiding the computational difficulty with full-fledged NL parsing. A prototype of the Conceptual Query Language (CQL) exists as a front-end to an Oracle relational DBMS.