gebhart/patrepeval huggingface dataset:
In situ co-crystallisation as a tool for low-temperature crystal engineeringElectronic supplementary information (ESI) available: details of the in situ melting point determinations and a plot of the variation in crystal density and melting point for 1–10. See http://www.rsc.org/suppdata/cc/b2/b208904a/ (2002)

Synthesis and single-crystal X-ray diffraction of a series of low-melting co-crystals of pyrazine and n-alkyl carboxylic acids demonstrates in situ co-crystallisation as a versatile tool for low-temperature crystal engineering.
Discovery of 4-(4-(2-((5-Hydroxy-1,2,3,4-tetrahydronaphthalen-2-yl)(propyl)amino)ethyl)piperazin-1-yl)quinolin-8-ol and Its Analogues as Highly Potent Dopamine D2/D3 Agonists and as Iron Chelator: In Vivo Activity Indicates Potential Application in Symptomatic and Neuroprotective Therapy for Parkinson’s Disease (2010)

The role of iron in the pathogenesis of Parkinson's disease (PD) has been implicated strongly because of generation of oxidative stress leading to dopamine cell death. In our overall goal to develop bifunctional/multifunctional drugs, we designed dopamine D2/D3 agonist molecules with a capacity to bind to iron. Binding assays were carried out with HEK-293 cells expressing either D2 or D3 receptor with tritiated spiperone to evaluate inhibition constants (K(i)). Functional activity of selected compounds was carried out with GTPgammaS binding assay. SAR results identified compounds (+)-19a and (-)-19b as two potent agonists for both D2 and D3 receptors (EC(50) (GTPgammaS); D2 = 4.51 and 1.69 nM and D3 = 1.58 and 0.74 nM for (-)-19b and (+)-19a, respectively). In vitro complexation studies with 19b demonstrated efficient chelation with iron. Furthermore, the deoxyribose assay with 19b demonstrated potent antioxidant activity. In PD animal model study, (-)-19b exhibited potent in vivo activity in reversing locomotor activity in reserpinized rats and also in producing potent rotational activity in 6-OHDA lesioned rats. This reports initial development of unique lead molecules that might find potential use in symptomatic and neuroprotective treatment of PD.
The protein product of the c-cbl protooncogene is the 120-kDa tyrosine-phosphorylated protein in Jurkat cells activated via the T cell antigen receptor. (1994)

Tyrosine phosphorylation of multiple cellular proteins is a critical event in T cell receptor (TCR)-mediated activation. This pathway has also been implicated in cellular transformation in multiple systems. The viral oncogene v-cbl is the transforming gene of a murine retrovirus that induces pre-B cell lymphomas and myelogenous leukemias. The product of its cellular homolog, p120cbl, is a 120-kDa cytoplasmic protein that is non-transforming when overexpressed. Here we show that the 120-kDa protein tyrosine phosphorylated in Jurkat T cells upon TCR engagement is p120cbl. Following stimulation through the TCR, this tyrosine phosphorylation is rapid and reversible. Tyrosine-phosphorylated p120cbl binds to glutathione S-transferase fusion proteins generated from SH2 domains of the Fyn, Lck, and Blk protein tyrosine kinases, GTPase-activating protein and phospholipase C gamma. The p120cbl from unactivated and activated cells also binds to full-length glutathione S-transferase-Grb2 and the Grb2 N-terminal SH3 domain, but not to the Grb2 C-terminal SH3 domain. Additionally, p120cbl binds to SH3 domains of Fyn and Lck, but not Blk. These data expand our knowledge of protein tyrosine kinase signaling pathways in T cells by identifying a prominent tyrosine kinase substrate. This protein, the product of the cellular homolog of a transforming oncogene, can interact with several known signaling molecules.
Cyclooxygenase-2 Inhibitors in Tumorigenesis (Part II) (1998)

The rate-limiting step in arachidonate metabolism is mediated by enzymes known as cyclooxygenases (COXs). These enzymes catalyze the biosynthesis of prostaglandin H 2 , the precursor of molecules such as prostaglandins, prostacyclin, and thromboxanes. The COX enzyme family consists of the classical COX-1 enzyme, which is constitutively expressed in many tissues, and a second isozyme, i.e., COX-2, which is induced by various stimuli, such as mitogens and cytokines, and is involved in many inflammatory reactions. Because nonsteroidal anti-inflammatory drugs (NSAIDs) inhibit both COX-1 and COX-2, these drugs also cause unwanted side effects, exemplified by gastrointestinal bleeding. Accumulating evidence indicates that NSAIDs can reduce the incidence of colorectal cancers in human and experimental animals and can reduce the number and size of polyps in patients with familial adenomatous polyposis. This Part II (of a two-part review) focuses on the growing clinical and experimental evidence that NSAIDS and COX-2 inhibitors can influence the risk of colon (and possibly of other) cancers.
The P gene product of hepatitis B virus is required as a structural component for genomic RNA encapsidation (1990)

Encapsidation of the pregenomic RNA into nucleocapsids is a selective process which depends on specific RNA-protein interactions. The signal involved in the packaging of the hepatitis B virus (HBV) RNA pregenome was recently defined as a short sequence located near the 5' end of that molecule (Junker-Niepmann et al., EMBO J., in press), but it remained an open question which viral proteins are required. Using a genetic approach, we analyzed whether proteins derived from the HBV P gene play an important role in pregenome encapsidation. The results obtained with point mutations, deletions, and insertions scattered throughout the P gene clearly demonstrate that (i) a P gene product containing all functional domains is required both for the encapsidation of HBV pregenomic RNA and for packaging of nonviral RNAs fused to the HBV encapsidation signal, (ii) known enzymatic activities are not involved in the packaging reaction, suggesting that P protein is required as a structural component, and (iii) P protein acts primarily in cis, i.e., pregenomic RNAs from which P protein is synthesized are preferentially encapsidated.
Mucin biosynthesis: upregulation of core 2 β1,6N-acetylglucosaminyltransferase by retinoic acid and Th2 cytokines in a human airway epithelial cell line (2004)

Vitamin A and the T helper 2 cytokines IL-4 and IL-13 play important roles in the induction of mucin gene expression and mucus hypersecretion. However, the effects of these agents on enzymes responsible for mucin glycosylation have received little attention. Here, we report the upregulation of core 2 beta1,6 N-acetylglucosaminyltransferase (C2GnT) activity both by all-trans retinoic acid (RA) and by IL-4 and IL-13 in the H292 airway epithelial cell line. Northern blotting analysis showed that the M isoform of C2GnT, which is expressed in mucus-secreting tissues and can form all mucin glycan beta1,6-branched structures, including core 2, core 4, and blood group I antigen, was upregulated by both RA and IL-4/13. The L isoform, which forms only the core 2 structure, was moderately upregulated by IL-4/13 but not by RA. Enhancement of the M isoform of C2GnT by RA was abolished by an inhibitor of RA receptor alpha, implicating RA receptor alpha in the effect of RA. Likewise, an inhibitor of the Janus kinase 3 pathway blocked the enhancing effects of IL-4/13 on the L and M isoforms of C2GnT, suggesting a role of this pathway in the upregulation of these two C2GnTs by these cytokines. Taken together, the results suggest that IL-4/13 T helper 2 cytokines and RA can alter the activity of enzymes that synthesize branching mucin carbohydrate structure in airway epithelial cells, potentially leading to altered mucin carbohydrate structure and properties.
Induction of apoptosis (programmed cell death) in human leukemic HL-60 cells by inhibition of RNA or protein synthesis. (1990)

Apoptosis is regarded as a suicidal cell response since the dying cell appears to be an active participant. Previous studies have shown that apoptosis of various murine cell types, induced by a variety of stimuli, required RNA and/or protein synthesis. However, when human promyelocytic leukemia HL-60 cells were induced to undergo apoptosis by treatment with the calcium ionophore A23187 or microtubule-disrupting agents, in the presence of inhibitors of macromolecular synthesis, apoptosis of these cells was neither abrogated nor delayed. Furthermore, the presence of either cycloheximide, an inhibitor of protein synthesis, or actinomycin D, an RNA synthesis inhibitor, alone was found to induce large scale apoptosis of these cells. Apoptosis in these cells was characterized by cell and chromatin condensation followed by nuclear and DNA fragmentation. In common with many other studies, this DNA fragmentation was found to have an approximately 200-bp multiple pattern, which is consistent with the activation of an endogenous endonuclease which cleaves at internucleosomal sites. Calcium-dependent endonuclease activity of this type was also detected in the isolated nuclei of untreated HL-60 cells. The morphologic and biochemical changes characteristic of apoptosis were found to precede cell death, as measured by trypan blue uptake and were completely distinct from death caused by toxic stimuli such as azide, ethanol, or heat treatment. Similar experiments with six other human cell lines confirmed that this phenomenon was not peculiar to the HL-60 cell line. These results suggest that certain dividing cell populations do not require RNA or protein synthesis to undergo apoptosis and further, that continuous transcription and translation of some regulatory protein(s) may be required to maintain control over the apoptotic "machinery" of such cells.
Rapid pulmonary delivery of inhaled tobramycin for Pseudomonas infection in cystic fibrosis: A pilot project (2008)

It is possible to deliver an equivalent amount of tobramycin in a shorter period of time with the new vibrating membrane system and a more concentrated formulation. These data will allow the design of a comparison in patients with CF.
TERT Promoter Mutations in Familial and Sporadic Melanoma (2013)

Cutaneous melanoma occurs in both familial and sporadic forms. We investigated a melanoma-prone family through linkage analysis and high-throughput sequencing and identified a disease-segregating germline mutation in the promoter of the telomerase reverse transcriptase (TERT) gene, which encodes the catalytic subunit of telomerase. The mutation creates a new binding motif for Ets transcription factors and ternary complex factors (TCFs) near the transcription start and, in reporter gene assays, caused up to twofold increase in transcription. We then screened the TERT promoter in sporadic melanoma and observed recurrent ultraviolet signature somatic mutations in 125 of 168 (74%) of human cell lines derived from metastatic melanomas, 45 of 53 corresponding metastatic tumor tissues (85%), and 25 of 77 (33%) primary melanomas. The majority of those mutations occurred at two positions in the TERT promoter and also generated binding motifs for Ets/TCF transcription factors.
Proanthocyanidin Synthesis and Expression of Genes Encoding Leucoanthocyanidin Reductase and Anthocyanidin Reductase in Developing Grape Berries and Grapevine Leaves (2005)

Proanthocyanidins (PAs), also called condensed tannins, can protect plants against herbivores and are important quality components of many fruits. Two enzymes, leucoanthocyanidin reductase (LAR) and anthocyanidin reductase (ANR), can produce the flavan-3-ol monomers required for formation of PA polymers. We isolated and functionally characterized genes encoding both enzymes from grapevine (Vitis vinifera L. cv Shiraz). ANR was encoded by a single gene, but we found two highly related genes encoding LAR. We measured PA content and expression of genes encoding ANR, LAR, and leucoanthocyanidin dioxygenase in grape berries during development and in grapevine leaves, which accumulated PA throughout leaf expansion. Grape flowers had high levels of PA, and accumulation continued in skin and seeds from fruit set until the onset of ripening. VvANR was expressed throughout early flower and berry development, with expression increasing after fertilization. It was expressed in berry skin and seeds until the onset of ripening, and in expanding leaves. The genes encoding LAR were expressed in developing fruit, particularly in seeds, but had low expression in leaves. The two LAR genes had different patterns of expression in skin and seeds. During grape ripening, PA levels decreased in both skin and seeds, and expression of genes encoding ANR and LAR were no longer detected. The results indicate that PA accumulation occurs early in grape development and is completed when ripening starts. Both ANR and LAR contribute to PA synthesis in fruit, and the tissue and temporal-specific regulation of the genes encoding ANR and LAR determines PA accumulation and composition during grape berry development.
Inhibition of Triglyceride Synthesis as a Treatment Strategy for Obesity (2004)

Because the ability to make triglycerides is essential for the accumulation of adipose tissue, inhibition of triglyceride synthesis may ameliorate obesity and its related medical consequences. Acyl coenzyme A (CoA):diacylglycerol acyltransferase 1 (DGAT1) is 1 of 2 DGAT enzymes that catalyze the final reaction in the known pathways of mammalian triglyceride synthesis. Mice lacking DGAT1 are resistant to obesity and have increased sensitivity to insulin and leptin. DGAT1-deficient mice are also resistant to diet-induced hepatic steatosis. The effects of DGAT1 deficiency on energy and glucose metabolism result in part from the altered secretion of adipocyte-derived factors. Although complete DGAT1 deficiency causes alopecia and impairs development of the mammary gland, these abnormalities are not observed in mice with partial DGAT1 deficiency. These findings suggest that pharmacological inhibition of DGAT1 may be a feasible therapeutic strategy for human obesity and type 2 diabetes.
Anti-T cell immunotoxins containing pokeweed anti-viral protein: potential purging agents for human autologous bone marrow transplantation. (1985)

The ex vivo anti-leukemic efficacy and stem cell toxicity of two different T cell directed immunotoxins containing pokeweed antiviral protein (PAP) were studied by clonal assays. 5E9-11-PAP, an immunotoxin directed against human transferrin receptors, elicited a maximum leukemic cell kill of 3.9 logs. However, it was also toxic against normal pluripotent stem cells, and therefore is not a clinically useful purgative reagent. PAP conjugated to 3-A1, a monoclonal antibody directed against CD7 (T, p41), was more effective against leukemic T cells than 5E9-11-PAP and eliminated a maximum of 4.8 log of cells. 3A1-PAP was only slightly toxic to pluripotent stem cells: 13% of CFU-GEMM were lost after treatment with 3000 ng of 3A1-PAP/ml, a concentration that eliminated 99.96% of contaminating leukemic T cells from a 200-fold excess of normal bone marrow. Cryopreservation of treated cells by conventional methods did not affect the extreme selectivity and potency of 3A1-PAP. Incubation of 3A1-PAP with peripheral blood mononuclear cells resulted in the complete inhibition of phytohemagglutinin-induced mitogenic response, illustrating the possibility of using this immunotoxin as a potent anti-T cell reagent for prophylaxis against graft vs host disease in allogeneic BMT as well.
Emerging treatment options for type 2 diabetes (2010)

Type 2 diabetes mellitus (T2DM) is rapidly increasing in prevalence and is a major public health problem. It is a progressive disease which commonly requires multiple pharmacotherapy. Current options for treatment may have undesirable side effects (particularly weight gain and hypoglycaemia) and contraindications, and little effect on disease progression. Incretin based therapy is one of several newer therapies to improve glycaemia and is available in two different forms, dipeptidyl peptidase-4 (DPP-4) inhibitors and glucagon-like peptide-1 (GLP-1) agonists. Use of these agents results in a 'glucose-dependant' increase in insulin secretion and glucagon suppression resulting in improved glycaemia with low incidence of hypoglycaemia. DPP-4 inhibitors are oral drugs which are weight neutral, while GLP-1 agonists are injected subcutaneously and help promote weight loss while improving glycaemia. GLP-1 agonists have also been shown to increase beta cell mass in rat models. Bariatric surgery is another option for the obese patient with T2DM, with blood glucose normalizing in over half of the patients following surgery. Other therapies in development for the treatment of T2DM include sodium-glucose transporter 2 (SGLT-2) inhibitors, glucagon receptor antagonists, glucokinase activators and sirtuins. In this article, we will review the various existing and emerging treatment options for T2DM.
Waveform Modeling and Generation Using Hierarchical Recurrent Neural Networks for Speech Bandwidth Extension (2018)

This paper presents a waveform modeling and generation method using hierarchical recurrent neural networks (HRNN) for speech bandwidth extension (BWE). Different from conventional BWE methods that predict spectral parameters for reconstructing wideband speech waveforms, this BWE method models and predicts waveform samples directly without using vocoders. Inspired by SampleRNN, which is an unconditional neural audio generator, the HRNN model represents the distribution of each wideband or high-frequency waveform sample conditioned on the input narrowband waveform samples using a neural network composed of long short-term memory (LSTM) layers and feed-forward layers. The LSTM layers form a hierarchical structure and each layer operates at a specific temporal resolution to efficiently capture long-span dependencies between temporal sequences. Furthermore, additional conditions, such as the bottleneck features derived from narrowband speech using a deep neural network based state classifier, are employed as auxiliary input to further improve the quality of generated wideband speech. The experimental results of comparing several waveform modeling methods show that the HRNN-based method can achieve better speech quality and run-time efficiency than the dilated convolutional neural network based method and the plain sample-level recurrent neural network based method. Our proposed method also outperforms the conventional vocoder-based BWE method using LSTM-RNNs in terms of the subjective quality of the reconstructed wideband speech.
Gene transfer into the mammalian kidney: direct retrovirus-transduction of regenerating tubular epithelial cells. (1994)

Gene transfer using retroviral vectors requires cell replication for insertion of the DNA provirus. Since the mitotic index of the mammalian kidney is very low, renal tubular cell replication was induced in adult rats as part of a regenerative response to the nephrotoxic injury induced by an intraperitoneal injection of folic acid. At 48 h, at the time of maximum 3H-thymidine incorporation, the left kidney was directly injected with a suspension of the Psi2 BAG retrovirus which transduces the beta-galactosidase gene. At 1-7 weeks after virus administration the left kidney was harvested. Using the polymerase chain reaction to amplify viral DNA, successful gene transfer was achieved in 8 of 15 kidneys. In 6 of 10 kidneys assessed histochemically positive staining for beta-galactosidase activity was detected in the cytoplasm of tubular epithelial cells. There was no evidence of gene expression in glomerular, vascular or endothelial cells. All analyses were negative in vehicle-injected kidneys and in the kidneys of animals which did not receive pretreatment with folic acid. These studies demonstrate the feasibility of gene transfer into the adult kidney provided that replication of specific cell types can be achieved.
Amplification of Ehrlichial DNA from Dogs 34 Months after Infection withEhrlichia canis (1998)

In order to determine whether dogs in the subclinical phase of canine monocytic ehrlichiosis (CME) are carriers of Ehrlichia canis and to determine the significance of persistent indirect immunofluorescent anti-E. canis antibody titers during this phase, PCR was performed with blood, bone marrow, and splenic aspirates collected 34 months postinoculation from six clinically healthy beagle dogs experimentally infected with E. canis. At least one of the three samples (spleen, bone marrow, and blood) from four of the six dogs was PCR positive. The spleens of all four of these dogs were PCR positive, and the bone marrow and blood of two of the four dogs were PCR positive. Indirect immunofluorescent-antibody titers increased progressively during the first 5 months postinfection, remained high for an additional period of more than 11 months, and declined thereafter, suggesting that the dogs were recovering from the disease. Five of the dogs remained seropositive 34 months postinfection. The data obtained in this study demonstrate for the first time that clinically healthy dogs in the subclinical phase of CME are carriers of the rickettsia. It was shown that dogs can harbor E. canis for years without developing the chronic clinical disease and that dogs can eliminate the parasite and recover from CME without medical treatment. Our findings suggest that the spleen is the organ most likely to harbor E. canis parasites during the subclinical phase and the last organ to accommodate the parasite before elimination. It was concluded that PCR of DNA extracted from splenic aspirates is a reliable method for determining the carrier state of CME.
Triterpene Saponins, Quaternary Ammonium Compounds, Phosphatidyl Cholines, and Amino Acids in the Pronotal and Elytral Secretions of Platyphora opima and Desmogramma subtropica (2000)

Secretions of the pronotal and elytral glands of adults of the chrysomelid beetle Platyphora opima from Panama have been shown to contain two oleanane triterpene saponins: the known 3-O-β-d-glucopyranosyl-(1→3)-β-d-glucuronopyranosyl-oleanolic acid-28-O-β-d-glucopyranoside and compound 1, whose structure was established as 3-O-β-d-glucopyranosyl-(1→3)-β-d-glucuronopyranosyl-29-hydroxyoleanolic acid-28-O-β-d-glucopyranoside by a combination of 1D and 2D NMR methods (COSY, HMQC, HMBC, and TOCSY) and FABMS. The secretions also contained N,N,N-trimethylcadaverine and its 1,2-dehydro derivative 3, as well as the nicotinamide derivative 4. Secretions of Desmogramma subtropica, also from Panama, contained as sole triterpene derivative 3-O-β-d-glucopyranosyl-(1→2)-β-d-glucuronopyranosyl-24-hydroxyoleanolic acid (2), together with glutamic acid, glutamine, pyroglutamic acid, and arginine. A mixture of phosphatidylcholines was also present in the secretions of both species.
TONAK: a distributed low-latency and scalable optical switch architecture (2013)

This paper proposes TONAK, an AWGR-based optical switch with distributed control plane. Simulations results for a 128-port switch show high throughput and low average packet latency for offered loads of up to 75%, while achieving an energy efficiency of ≈50pJ/bit.