gebhart/patrepeval huggingface dataset:
Lysosomal storage diseases and the heat shock response: convergences and therapeutic opportunities (2014)

Lysosomes play a vital role in the maintenance of cellular homeostasis through the recycling of cell constituents, a key metabolic function which is highly dependent on the correct function of the lysosomal hydrolases and membrane proteins, as well as correct membrane lipid stoichiometry and composition. The critical role of lysosomal functionality is evident from the severity of the diseases in which the primary lesion is a genetically defined loss-of-function of lysosomal hydrolases or membrane proteins. This group of diseases, known as lysosomal storage diseases (LSDs), number more than 50 and are associated with severe neurodegeneration, systemic disease, and early death, with only a handful of the diseases having a therapeutic option. Another key homeostatic system is the metabolic stress response or heat shock response (HSR), which is induced in response to a number of physiological and pathological stresses, such as protein misfolding and aggregation, endoplasmic reticulum stress, oxidative stress, nutrient deprivation, elevated temperature, viral infections, and various acute traumas. Importantly, the HSR and its cardinal members of the heat shock protein 70 family has been shown to protect against a number of degenerative diseases, including severe diseases of the nervous system. The cytoprotective actions of the HSR also include processes involving the lysosomal system, such as cell death, autophagy, and protection against lysosomal membrane permeabilization, and have shown promise in a number of LSDs. This review seeks to describe the emerging understanding of the interplay between these two essential metabolic systems, the lysosomes and the HSR, with a particular focus on their potential as a therapeutic target for LSDs.
Combination Chemotherapy With Mitoxantrone, Methotrexate, and Mitomycin (MMM Regimen) in Malignant Pleural Mesothelioma (2001)

The prognosis of malignant pleural mesothelioma is poor, with a median survival time from diagnosis of 7 to 17 months. At present there is no standardized treatment of this neoplasia. Between July 1995 and January 1999, 22 patients with malignant pleural mesothelioma were enrolled in our study. The characteristics of patients were: 16 men and 6 women; median age 61 years (range, 49-77 years); stage (according to Butchart): 8 patients stage I, 10 stage II, 2 stage III, and 2 stage IV; cytologic diagnosis in 5 cases and histologic diagnosis in 17 cases. The treatment consisted of mitoxantrone 10 mg/m2 intravenous (IV) or intrapleural (IPL), methotrexate 35 mg/m2 IV, and mitomycin 7 mg/m2 IV on day 1 and repeated every 3 weeks, with mitomycin in alternate cycles (MMM regimen). One complete response (4.5%) (42 months of duration) and 6 partial responses (27.3%) (5, 5, 7, 9, 14, and 19 months of duration) were achieved; the overall response rate (ORR) was 31.8% (95% CI, 12.4-51.3%); 7 patients were stable under this treatment (31.8%). According to the pathologic type, ORR for the only epithelial type was 39.9% (95% CI, 15.2-64.8%). Median time to progression was 6 months (range, 1-22). The overall median survival time was 13.5 months (range, 1-50); the median survival time of responders significantly differed from that of nonresponders (18.0 versus 8.5 months; p = 0.017). This treatment produced a considerable clinical benefit, with improvement of dyspnea (68.4%) and pain (33.3%); 15 of 19 patients (78.9%) with pleural effusion at the time of diagnosis showed an important reduction in pleural fluid during chemotherapy. Hematologic toxicity was the main side effect; World Health Organization grade III to IV of neutropenia, anemia, and thrombocytopenia were observed in 81.8%, 13.6%, and 22.7% of patients, respectively. From the data presented here, this regimen can be considered active in the treatment of malignant pleural mesothelioma.
Disseminated and sustained HIV infection in CD34 + cord blood cell-transplanted Rag2 −/− γ c −/− mice (2006)

Because of species selectivity, HIV research is largely restricted to in vitro or clinical studies, both limited in their ability to rapidly assess new strategies to fight the virus. To prospectively study some aspects of HIV in vivo, immunodeficient mice, transplanted with either human peripheral blood leukocytes or human fetal tissues, have been developed. Although these are susceptible to HIV infection, xenoreactivity, and short infection spans, resource and ethical constraints, as well as biased HIV coreceptor tropic strain infection, pose substantial problems in their use. Rag2(-/-)gamma(c)(-/-) mice, transplanted as newborns with human CD34(+) cells, were recently shown to develop human B, T, and dendritic cells, constituting lymphoid organs in situ. Here we tested these mice as a model system for HIV-1 infection. HIV RNA levels peaked to up to 2 x 10(6) copies per milliliter of plasma early after infection, and viremia was observed for up to 190 days, the longest time followed. A marked relative CD4(+) T cell depletion in peripheral blood occurred in CXCR4-tropic strain-infected mice, whereas this was less pronounced in CCR5-tropic strain-infected animals. Thymus infection was almost exclusively observed in CXCR4-tropic strain-infected mice, whereas spleen and lymph node HIV infection occurred irrespective of coreceptor selectivity, consistent with respective coreceptor expression on human CD4(+) T cells. Thus, this straightforward to generate and cost-effective in vivo model closely resembles HIV infection in man and therefore should be valuable to study virus-induced pathology and to rapidly evaluate new approaches aiming to prevent or treat HIV infection.
Clobazam as an adjunctive therapy in treating seizures associated with Lennox&ndash;Gastaut syndrome (2011)

Lennox-Gastaut syndrome (LGS) is a devastating childhood epilepsy syndrome characterized by the occurrence of multiple types of seizures and cognitive decline. Most children suffer from frequent seizures that are refractory to current medical management. Recent clinical trials have suggested that addition of clobazam may improve the clinical outcome for some LGS patients. Although clobazam has been available for over five decades, it has only recently been approved by the US Food and Drug Administration for this indication. As a 1,5-benzodiazepine, clobazam is structurally related to the widely used 1,4-benzodiazepines, which include diazepam. Clobazam has been shown to modulate GABAergic neurotransmission by positive allosteric modulation of GABA(A) receptors, and to increase expression of transporters for both GABA and glutamate. The active metabolite n-desmethylclobazam (norclobazam) also modulates GABA(A) receptors, and the relative importance of these two compounds in the clinical effectiveness of clobazam remains an open question. Clinical trials involving clobazam as an addon therapy in a variety of pediatric epilepsy populations have found a significant improvement in seizure control. In patients with LGS, clobazam may have greatest efficacy for drop seizures. Longstanding clinical experience suggests that clobazam is a safe and well tolerated antiepileptic drug with infrequent and mild adverse effects. These results suggest that adjunctive treatment with clobazam may be a reasonable option for LGS patients, particularly those who are treatment-resistant.
Molecular remission and response patterns in patients with mutant-IDH2 acute myeloid leukemia treated with enasidenib (2018)

Approximately 8% to 19% of patients with acute myeloid leukemia (AML) have isocitrate dehydrogenase-2 (<i>IDH2</i>) mutations, which occur at active site arginine residues R140 and R172. <i>IDH2</i> mutations produce an oncometabolite, 2-hydroxyglutarate (2-HG), which leads to DNA and histone hypermethylation and impaired hematopoietic differentiation. Enasidenib is an oral inhibitor of mutant-IDH2 proteins. This first-in-human phase 1/2 study evaluated enasidenib doses of 50 to 650 mg/d, administered in continuous 28-day cycles, in patients with mutant-<i>IDH2</i> hematologic malignancies. Overall, 214 of 345 patients (62%) with relapsed or refractory (R/R) AML received enasidenib, 100 mg/d. Median age was 68 years. Forty-two patients (19.6%) attained complete remission (CR), 19 patients (10.3%) proceeded to an allogeneic bone marrow transplant, and the overall response rate was 38.8% (95% confidence interval [CI], 32.2-45.7). Median overall survival was 8.8 months (95% CI, 7.7-9.6). Response and survival were comparable among patients with <i>IDH2</i>-R140 or <i>IDH2</i>-R172 mutations. Response rates were similar among patients who, at study entry, were in relapse (37.7%) or were refractory to intensive (37.5%) or nonintensive (43.2%) therapies. Sixty-six (43.1%) red blood cell transfusion-dependent and 53 (40.2%) platelet transfusion-dependent patients achieved transfusion independence. The magnitude of 2-HG reduction on study was associated with CR in <i>IDH2</i>-R172 patients. Clearance of mutant-<i>IDH2</i> clones was also associated with achievement of CR. Among all 345 patients, the most common grade 3 or 4 treatment-related adverse events were hyperbilirubinemia (10%), thrombocytopenia (7%), and IDH differentiation syndrome (6%). Enasidenib was well tolerated and induced molecular remissions and hematologic responses in patients with AML for whom prior treatments had failed. The study is registered at www.clinicaltrials.gov as #NCT01915498.
Evidence of genetic heterogeneity in Romano-Ward long QT syndrome. Analysis of 23 families. (1994)

In the 23 families with LQTS analyzed for linkage to the H-ras-1 locus on chromosome 11p15.5, 15 of 23 families had LOD scores consistent with linkage. The remaining 8 of 23 families had negative LOD scores, 4 of which were definitively excluded from linkage. Thus, genetic heterogeneity is definitively (P < .001) demonstrated for this disorder.
Tumor-reactive T-cells accumulate in lung cancer tissues but fail to respond due to tumor cell-derived factor. (1992)

The purpose of this study was to elucidate a possible immune response to tumor cells mediated by tumor-infiltrating lymphocytes (TIL) in lung cancer. In flow cytometry, the majority of T-cells of TIL were CD45RA-, CD45RO+, and CDw29high, and expressed HLA-DR. The expression of interleukin 2 receptor beta chain increased in both CD4+ and CD8+ TIL compared with both types of T-cells in peripheral blood. These results indicate that the major population of TIL is activated memory T-cells. The TIL preparation, which was usually contaminated with 5 to 10% tumor cells, did not exhibit any response in autologous mixed lymphocyte-tumor culture even in the presence of interleukin 2 (IL-2) in all five cases tested. Although purified T-cells from TIL showed the positive response in only 1 of 10 cases tested without addition of IL-2, it occurred in 7 of 10 cases in the addition of a low concentration of IL-2. The IL-2-dependent response to irradiated autologous tumor cells was suppressed when nonirradiated autologous tumor cells were added to the culture. Culture supernatants of four lung cancer cell lines and freshly prepared lung cancer cells obtained from 6 cases exhibited suppressive activity against anti-CD3 antibody-induced mitogenesis of peripheral blood mononuclear cells from healthy donors. We suggest that, taken together, (a) the major population of TIL in lung cancer are activated memory T-cells, and they include tumor-reactive ones, and that (b) the function of the TIL is impaired by unavailability of IL-2 and/or by suppression due to lung cancer cell-derived factor(s).
Recruitment of the transcriptional machinery through GAL11P: structure and interactions of the GAL4 dimerization domain (2001)

The GAL4 dimerization domain (GAL4-dd) is a powerful transcriptional activator when tethered to DNA in a cell bearing a mutant of the GAL11 protein, named GAL11P. GAL11P (like GAL11) is a component of the RNA-polymerase II holoenzyme. Nuclear magnetic resonance (NMR) studies of GAL4-dd revealed an elongated dimer structure with C(2) symmetry containing three helices that mediate dimerization via coiled-coil contacts. The two loops between the three coiled coils form mobile bulges causing a variation of twist angles between the helix pairs. Chemical shift perturbation analysis mapped the GAL11P-binding site to the C-terminal helix alpha3 and the loop between alpha1 and alpha2. One GAL11P monomer binds to one GAL4-dd dimer rendering the dimer asymmetric and implying an extreme negative cooperativity mechanism. Alanine-scanning mutagenesis of GAL4-dd showed that the NMR-derived GAL11P-binding face is crucial for the novel transcriptional activating function of the GAL4-dd on GAL11P interaction. The binding of GAL4 to GAL11P, although an artificial interaction, represents a unique structural motif for an activating region capable of binding to a single target to effect gene expression.
Coming to Grips with Notch (2001)

Notch proteins are highly conserved transmembrane receptors that are involved in cell fate regulation in invertebrates ([1][1]). While Notch receptors are initially synthesized as single polypeptide chains proteolytic processing results in the formation of a heterodimeric receptor in which the
Chloroplast‐derived enzyme cocktails hydrolyse lignocellulosic biomass and release fermentable sugars (2010)

It is widely recognized that biofuel production from lignocellulosic materials is limited by inadequate technology to efficiently and economically release fermentable sugars from the complex multi-polymeric raw materials. Therefore, endoglucanases, exoglucanase, pectate lyases, cutinase, swollenin, xylanase, acetyl xylan esterase, beta glucosidase and lipase genes from bacteria or fungi were expressed in Escherichia coli or tobacco chloroplasts. A PCR-based method was used to clone genes without introns from Trichoderma reesei genomic DNA. Homoplasmic transplastomic lines showed normal phenotype and were fertile. Based on observed expression levels, up to 49, 64 and 10, 751 million units of pectate lyases or endoglucanase can be produced annually, per acre of tobacco. Plant production cost of endoglucanase is 3100-fold, and pectate lyase is 1057 or 1480-fold lower than the same recombinant enzymes sold commercially, produced via fermentation. Chloroplast-derived enzymes had higher temperature stability and wider pH optima than enzymes expressed in E. coli. Plant crude-extracts showed higher enzyme activity than E. coli with increasing protein concentration, demonstrating their direct utility without purification. Addition of E. coli extracts to the chloroplast-derived enzymes significantly decreased their activity. Chloroplast-derived crude-extract enzyme cocktails yielded more (up to 3625%) glucose from filter paper, pine wood or citrus peel than commercial cocktails. Furthermore, pectate lyase transplastomic plants showed enhanced resistance to Erwina soft rot. This is the first report of using plant-derived enzyme cocktails for production of fermentable sugars from lignocellulosic biomass. Limitations of higher cost and lower production capacity of fermentation systems are addressed by chloroplast-derived enzyme cocktails.
Synthesis, Characterization, and Photochemical/Photophysical Properties of Ruthenium(II) Complexes with Hexadentate Bipyridine and Phenanthroline Ligands (1998)

Three hexadentate, podand-type, polypyridyl ligands, (5-bpy-2C)(3)Bz, (4-bpy-2C-Ph)(3)Et, and (4-phen-2C-Ph)(3)Et, and their Ru(II) and Fe(II) complexes have been prepared. Reaction of these ligands with Fe(II) produces only the monometallic hemicage species, while monometallic, bimetallic, and polymetallic Ru(II) complexes are formed. These species are separable by column chromatography, and NMR and ESI mass spectrometry demonstrate that with each ligand the first band to elute corresponds to the monometallic species, [RuL](2+). The ESI mass spectra show peaks for [RuL](2+) and [RuL](PF(6))(+) with expected m/z values and isotope peak spacings. (1)H NMR spectroscopy shows that [Ru(5-bpy-2C)(3)Bz](2+) is trigonally symmetric and contains a rigid methylene bridge between the capping group and the bipyridines. The excited-state lifetimes and emission quantum yields for the hemicage complexes, [Ru(5-bpy-2C)(3)Bz](2+), [Ru(4-bpy-2C-Ph)(3)Et](2+), and [Ru(4-phen-2C-Ph)(3)Et](2+), are significantly enhanced (tau = 2800, 1470, and 3860 ns, and Phi(em) = 0.271, 0.104, 0.202, respectively) relative to the model compounds and to the polymetallic complexes with the same ligand. An Arrhenius fit of temperature-dependent lifetime data for [Ru(5-bpy-2C)(3)Bz](2+) indicates a high activation energy for crossover to the dd state (DeltaE = 4960 cm(-)(1)) as well as the existence of an additional pathway for deactivation via a "4th MLCT" state. Only after extensive photolysis of [Ru(5-bpy-2C)(3)Bz](2+) is any decrease in emission intensity observed; this is accompanied by the formation of a bimetallic photoproduct, [Ru(2)L(2)](4+), with a quantum yield of 7.4 x 10(-)(6). Quenching studies with a variety of quenchers show that the useful excited-state redox and energy-transfer properties characteristic of Ru(II) polypyridyls are retained, but with improved photoinertness and photophysical properties arising from the rigidity of the hemicage complex.
Allosteric modulation of α7 nicotinic receptors selectively depolarizes hippocampal interneurons, enhancing spontaneous GABAergic transmission (2008)

The role of postsynaptic nicotinic receptors for acetylcholine (nAChRs) in mediating fast neurotransmission processes in the CNS is controversial. Here we have studied the modulation of synaptic transmission by an agonist (choline) and an allosteric modulator (5-OH-indole) of alpha7 nAChRs in rat hippocampal neuronal cultures. Choline evoked a fast inactivating inward current, causing neuron depolarization and action potential discharge, thereby enhancing the spontaneous postsynaptic current activity (sPSCs). This effect was markedly enhanced when both choline and 5-OH-indole were applied together and was blocked by the selective alpha7 nAChR antagonist methyllycaconitine. This choline action was suppressed by the GABA(A) receptor antagonist bicuculline, while the glutamatergic receptor antagonist kynurenic acid had no effect. Frequency, but not amplitude or area, of both excitatory and inhibitory miniature postsynaptic currents (mEPSCs and mIPSCs) were drastically reduced when Ca(2+) influx was blocked by Cd(2+). Additionally, nAChR activation did not modify the mIPSCs. These data suggest that Ca(2+) influx through the highly Ca(2+)-permeablealpha7 nAChRs was insufficient to directly activate neurotransmitter release, suggesting that a tight colocalization of this receptor with secretory hot spots is unlikely. In a few cases, the activation of alpha7 AChRs led to a suppression of spontaneous synaptic transmission. This effect may be related to the potentiation of GABAergic interneurons that inhibit the spontaneous activity of neurons making synapses with the cell under study. We suggest that GABA release is modulated by alpha7 nAChRs. Thus, selective allosteric modulators of alpha7 nAChRs could have potential therapeutic applications in brain disorders such as epilepsy and schizophrenia and in alterations of cognition and sensory processing.
An ambient light adaptive subretinal stimulator (2009)

This paper presents a subretinal stimulator which is able to automatically adapt to varying ambient light levels. Stimulation timing and intensity are controlled using an input amplifier with an offset current cancellation circuitry to eliminate offset current imposed on the pixel amplifier for accurate stimulation control and optimized power consumption. In order to enable the chip to operate over a wide range of luminance conditions without manual tuning, automatic ambient light adaptation is required. Comparing the local photosensor output with a global luminance reference signal forms the basis of the adaptation mechanism. Global brightness information is obtained by logarithmic conversion of the summed photocurrents to generate a global luminance reference voltage. The chip has been realized in Austria Micro Systems 0.35 mum CMOS Opto technology.
[Formation of free radicals and DNA breaks after pulsed laser irradiation of DNA complexes with intercalating dyes]. (1990)

Destruction of lambda phage DNA is studied under nanosecond pulse laser irradiation (lambda = 355 nm) of DNA-dye complexes in solution at 77K (dye--acridine orange, 8-methoxypsoralen, ethidium bromide). Free radicals induced by laser radiation are found to participate in DNA sugar-phosphate chain scission. It was observed that the quantity of DNA double-strand breaks correlated with that of the free radicals and that of oxygen influenced DNA laser destruction.
QSARs and activity predicting models for competitive inhibitors of adenosine deaminase (2007)

Combinations of multiple linear regressions, genetic algorithms and artificial neural networks were utilized to develop models for seeking quantitative structure-activity relationships that correlate structural descriptors and inhibition activity of adenosine deaminase competitive inhibitors. Many quantitative descriptors were generated to express the physicochemical properties of 70 compounds with optimized structures in aqueous solution. Multiple linear regressions were used to linearly select different subsets of descriptors and develop linear models for prediction of log(k(i)). The best subset then fed artificial neural networks to develop nonlinear predictors. A committee of six hybrid models - that included genetic algorithm routines together with neural networks - was also utilized to nonlinearly select most efficient subsets of descriptors in a cross-validation procedure for nonlinear log(k(i)) prediction. The best prediction model was found to be an 8-3-1 artificial neural network which was fed by the most frequently selected descriptors among these subsets. This prediction model resulted in train set root mean sum square error (RMSE) of 0.84 log(k(i)) and prediction set RMSE of 0.85 log(k(i)) (both equivalent of 0.10 in normal range of log(k(i))) and correlation coefficient (r(2)) of 0.91.
The origin and function of platelet glycosyltransferases (2012)

Platelets are megakaryocyte subfragments that participate in hemostatic and host defense reactions and deliver pro- and antiangiogenic factors throughout the vascular system. Although they are anucleated cells that lack a complex secretory apparatus with distinct Golgi/endoplasmic reticulum compartments, past studies have shown that platelets have glycosyltransferase activities. In the present study, we show that members of 3 distinct glycosyltransferase families are found within and on the surface of platelets. Immunocytology and flow cytometry results indicated that megakaryocytes package these Golgi-derived glycosyltransferases into vesicles that are sent via proplatelets to nascent platelets, where they accumulate. These glycosyltransferases are active, and intact platelets glycosylate large exogenous substrates. Furthermore, we show that activation of platelets results in the release of soluble glycosyltransferase activities and that platelets contain sufficient levels of sugar nucleotides for detection of glycosylation of exogenously added substrates. Therefore, the results of the present study show that blood platelets are a rich source of both glycosyltransferases and donor sugar substrates that can be released to function in the extracellular space. This platelet-glycosylation machinery offers a pathway to a simple glycoengineering strategy improving storage of platelets and may serve hitherto unknown biologic functions.