gebhart/patrepeval huggingface dataset:
Developing Novel Strategies to Target B-Cell Malignancies (2013)

In the past several years we have seen the identification and validation of several key pathways that drive malignant B-cell development. In addition, the effect nonmalignant effector cells within the immune microenvironment have on tumor survival, proliferation, and possibly chemotherapy resistance is increasingly understood. Although there is still much to be learned, this improved understanding combined with rapid advances in medicinal chemistry focusing on structure-based drug design have resulted in a shift in the development of new agents away from traditional chemotherapy to more selective agents targeting key cellular pathways. Examples of “hot” new therapeutic targets include the B-cell receptor signaling pathway, PI3K/mTOR/AKT pathway, histone deacetylases (HDAC), regulators of apoptosis such as the BCL-2 family, the proteasome, and cell–cell interactions within the tumor environment. Many drugs that target specific agents in early clinical development have demonstrated activity in various subtypes of lymphoma and leukemia. Monoclonal and conjugated antibodies targeting cell surface proteins such as CD19, CD22, CD37, and different epitopes of CD20 have also shown promise in relapsed B-cell malignancies and are rapidly moving into efficacy studies. This review will focus on a few of the new nonantibody-based targeted agents in development, their respective pathways, and their activity in various B-cell malignancies.
Construction schedule simulation for improved project planning: activity criticality index assessment (2013)

The objective of this paper is to illustrate the application of construction schedule simulation during the planning phase of a construction project. Schedule simulations can be used to develop risk informed schedules that support improved contingency planning. This paper discusses the challenges underlying construction schedule simulation, and how they can be addressed by an interactive simulation platform such as the Interactive Construction Decision-Making Aid (ICDMA). Further, the paper uses ICDMA during the planning process, for a case study, to identify the activities in a project that are most likely to change criticality during the construction process. Current scheduling techniques such as the Critical Path Method (CPM) are capable of identifying critical activities, but they cannot be used to assess the likelihood of alternative critical paths emerging during construction due to unexpected disruptions in the as-planned schedule. The research illustrates the usefulness of construction simulation in supporting the scheduling process.
Low-Loss Analog and Digital Reflection-Type MEMS Phase Shifters With 1 : 3 Bandwidth (2004)

Broad-band analog and digital reflection-type phase shifters (RTPSs), showing constant phase shift over 1:3 bandwidth, have been developed using microelectromechanical systems (MEMS) technology. Two-unit RTPSs centered at two different frequencies have been cascaded to achieve flat phase responses over a wide frequency band. Each phase shifter uses air-gap overlay coplanar-waveguide couplers for low-loss 3-dB coupling and bridge-type MEMS capacitors for reflective terminations. The fabricated analog phase shifter shows the average insertion loss of 3.5 dB, and maximum phase error of /spl plusmn/4.9/spl deg/ from 15 to 45 GHz. The 2-bit digital RTPS shows reduced maximum phase error of /spl plusmn/2.8/spl deg/ together with a comparable insertion loss of 3.1 dB from 5 to 15 GHz. The details of the circuit design, analysis, and fabrication procedures are presented together with the measurement results. Compared with the similar constant phase shifters using semiconductor diodes and transistors, the micromachined RTPS of this study shows superior performance in terms of phase errors, insertion losses, and bandwidth.
Rosiglitazone and PPAR‐γ overexpression protect mitochondrial membrane potential and prevent apoptosis by upregulating anti‐apoptotic Bcl‐2 family proteins (2009)

To determine the involvement of peroxisome proliferator-activated receptor-gamma (PPAR-gamma) in cytoprotection, we subjected N2-A cells to oxygen-glucose deprivation followed by reoxygenation (H-R). Following H-R insults, H(2)O(2) production was increased while cell viability declined, which was accompanied by loss of mitochondrial membrane potential (MMP), cytochrome c release, caspases 9 and 3 activation, poly(ADP-ribose)polymerase (PARP) cleavage and apoptosis. Rosiglitazone up to 5 microM protected cell viability, normalized MMP, and prevented apoptotic signals. The protective effect of rosiglitazone was abrogated by GW9662, a PPAR-gamma antagonist, or a specific PPAR-gamma small interference RNA (siRNA) but not a control scRNA. PPAR-gamma overexpression alone was effective in maintaining MMP and preventing apoptosis and its protective effect was also abrogated by PPAR-gamma siRNA or GW9662. To elucidate the mechanism by which PPAR-gamma protects MMP and prevents apoptosis, we analyzed Bcl-2, Bcl-xl, and phosphorylated Bad (p-Bad). H-R suppressed them. Rosiglitazone or PPAR-gamma overexpression restored them via PPAR-gamma. Rosiglitazone or PPAR-gamma overexpression preserved phosphorylated Akt and 3-phosphoinositide-dependent kinase-1 (PDK-1) in a PPAR-gamma dependent manner. These results indicate that ligand-activated PPAR-gamma protects N2-A cells against H-R damage by enhancing Bcl-2/Bcl-xl and maintaining p-Bad via preservation of p-Akt.
Basic fibroblast growth factor stimulates endothelial regrowth and proliferation in denuded arteries. (1990)

A large percentage of vascular reconstructions, endarterectomies, and angioplasties fail postoperatively due to thrombosis and restenosis. Many of these failures are thought to result from an inability of the vascular endothelium to adequately regenerate and cover the denuded area. After balloon catheter denudation of the rat carotid artery, regrowth of endothelium ceases after approximately 6 wk, leaving a large area devoid of endothelium. Here we show that this cessation of reendothelialization can be overcome by the systemic administration of basic fibroblast growth factor (bFGF). Administration of 120 micrograms bFGF over an 8-h period caused a highly significant increase in the replication rate of endothelial cells at the leading edge of 38.5 vs. 2.1% in controls, and, when given over a longer period of time (12 micrograms daily for 12 d), resulted in a significant increase in the extent of endothelial outgrowth onto the denuded surface. Furthermore, total regrowth could be achieved within 10 wk after balloon catheter denudation when 12 micrograms bFGF was injected twice per week for a period of 8 wk. Endothelium in unmanipulated arteries responded to bFGF with a significant increase in replication, but no increase in endothelial cell density was observed in these arteries. These data demonstrate that bFGF can act as a potent mitogen for vascular endothelial cells in vivo, and add considerably to our understanding of the mechanism underlying endothelial repair after in vivo vascular injuries.
A unified SOC test approach based on test data compression and TAM design (2004)

Test access mechanism (TAM) optimization and test data compression lead to a reduction in test data volume and testing time for SOCs. In this paper, we integrate for the first time both these approaches into a single test methodology. We show, how an integrated test architecture based on TAMs and test data decoders can be designed. The proposed approach offers considerable savings in test resource requirements. Two case studies using the integrated test architecture are presented. Experimental results on rest data volume reduction, savings in test application time and the low test pin overheads for a benchmark SOC demonstrate the effectiveness of this approach.
Pharmacokinetic properties of current antiepileptic drugs: what improvements are needed? (2000)

The pharmacokinetics of antiepileptic drugs (AEDs) largely determine their ability to achieve and maintain concentrations that maximize their efficacy and safety. The term "pharmacokinetics" encompasses the quantitative assessment of changes of drug concentrations over time as a function of absorption, distribution, and elimination. Interaction among AEDs, and between AEDs and other classes of drugs, can result in undesirable drug levels. The pharmacokinetic properties of AEDs considered to be clinically most relevant include complete or constant bioavailability, availability of a parenteral formulation, elimination half-life or preparation suitable for once- or twice-daily dosing, linear elimination kinetics, no autoinduction of enzymatic biotransformation, and lack of pharmacokinetic interactions with other drugs. Both established AEDs (carbamazepine, phenytoin, valproate, phenobarbital, and primidone) and newer AEDs (oxcarbazepine, felbamate, gabapentin, lamotrigine, topiramate, tiagabine) are evaluated in terms of these properties. None of the currently marketed AEDs combines all of these desirable pharmacokinetic characteristics. However some of the newer AEDs have more favorable pharmacokinetic profiles. The main improvements needed are limited or no pharmacokinetic interactions, preparations suitable for once- or twice-daily administration, and availability of parenteral formulations.
Dealing with immunogenicity of biologicals: assessment and clinical relevance (2009)

Immunogenicity affects a significant number of patients treated with biologicals. Monitoring of drug levels as well as of antibodies against therapeutic antibodies may lead to more rational treatment strategies.
The Wnt/β-catenin pathway regulates Gli-mediatedMyf5expression during somitogenesis (2006)

Canonical Wnt/beta-catenin signaling regulates the activation of the myogenic determination gene Myf5 at the onset of myogenesis, but the underlying molecular mechanism is unknown. Here, we report that the Wnt signal is transduced in muscle progenitor cells by at least two Frizzled (Fz) receptors (Fz1 and/or Fz6), through the canonical beta-catenin pathway, in the epaxial domain of newly formed somites. We show that Myf5 activation is dramatically reduced by blocking the Wnt/beta-catenin pathway in somite progenitor cells, whereas expression of activated beta-catenin is sufficient to activate Myf5 in somites but not in the presomitic mesoderm. In addition, we identified Tcf/Lef sequences immediately 5' to the Myf5 early epaxial enhancer. These sites determine the correct spatiotemporal expression of Myf5 in the epaxial domain of the somite, mediating the synergistic action of the Wnt/beta-catenin and the Shh/Gli pathways. Taken together, these results demonstrate that Myf5 is a direct target of Wnt/beta-catenin, and that its full activation requires a cooperative interaction between the canonical Wnt and the Shh/Gli pathways in muscle progenitor cells.
Quinazoline antifolate thymidylate synthase inhibitors: difluoro-substituted benzene ring analogs (1992)

The synthesis of a series of new C2-methyl-N10-alkylquinazoline-based thymidylate synthase (TS) inhibitors containing difluroinated p-aminobenzoate rings is described. Derivatives of the N10-propargyl and N10-methylquinazoline antifolates were prepared with 2',3'-, 2',5'-, and 2',6'-difluoro substitution. The synthesis of the 2',5'-difluoro analogues involved oxidation of the difluoronitrotoluene to 2,5-difluoro-4-nitrobenzoic acid followed by glutamation, reduction, and alkylation (propargyl bromide or MeI) to the diethyl N-(4-(alkylamino)-2,5-difluorobenzoyl)-L-glutamates. For the synthesis of the 2',3'- and 2',6'-difluoro compounds a new route was devised starting from methyl 4-((tert-butoxycarbonyl)amino)-2,6-difluorobenzoate and its 2,3-substituted counterpart. Treatment with NaH and then an alkyl halide introduced the N10-substituent. The methyl ester was hydrolyzed and the resulting acid was condensed with diethyl L-glutamate. The secondary amine was liberated using CF3CO2H and coupled with 6-(bromo-methyl)-3,4-dihydro-2-methyl-4-oxoquinazoline to yield the antifolate diesters. Final deprotection with mild alkali completed the synthesis in each case. The target compounds were tested as inhibitors of partially purified L1210 TS and also examined for their inhibition of the growth of L1210 cells in culture. Compared to their nonfluorinated parent compounds all the difluoro analogues were poorer inhibitors of TS. The greatest loss of enzyme activity was seen in the N10-propargyl analogues which contained one of the fluorine atoms ortho to the amine substituent. This loss was less apparent in the N10-methyl derivatives. Despite this lower inhibition of TS the majority of new compounds have equivalent cytotoxicity to their nonfluorinated predecessors.
A Slicer-Mediated Mechanism for Repeat-Associated siRNA 5' End Formation in Drosophila (2007)

In Drosophila, repeat-associated small interfering RNAs (rasiRNAs) are produced in the germ line by a Dicer-independent pathway and function through the PIWI subfamily of Argonautes to ensure silencing of retrotransposons. We sequenced small RNAs associated with the PIWI subfamily member AGO3. Although other members of PIWI, Aubergine (Aub) and Piwi, associated with rasiRNAs derived mainly from the antisense strand of retrotransposons, AGO3-associated rasiRNAs arose mainly from the sense strand. Aub- and Piwi-associated rasiRNAs showed a strong preference for uracil at their 5' ends, and AGO3-associated rasiRNAs showed a strong preference for adenine at nucleotide 10. Comparisons between AGO3- and Aub-associated rasiRNAs revealed pairs of rasiRNAs showing complementarities in their first 10 nucleotides. Aub and AGO3 exhibited Slicer activity in vitro. These data support a model in which formation of a 5' terminus within rasiRNA precursors is guided by rasiRNAs originating from transcripts of the other strand in concert with the Slicer activity of PIWI.
Whole genome amplification - Review of applications and advances (2001)

The concept of Whole Genome Amplification is something that has arisen in the past few years as modifications to the polymerase chain reaction (PCR) have been adapted to replicate regions of genomes which are of biological interest.The applications here are many -forensics, embryonic disease diagnosis, bio terrorism genome detection, 'imoralization' of clinical samples, microbial diversity, and genotyping.The key question is if DNA can be replicated a genome at a time without bias or non random distribution of the target.Several papers published in the last year and currently in preparation may lead to the conclusion that whole genome amplification may indeed be possible and therefore open up a new avenue to molecular biology.
Realization of atomic layer etching of silicon (1996)

An experimental system and methodology were developed to realize dry etching of single crystal silicon with monolayer accuracy. Atomic layer etching of silicon is a cyclic process composed of four consecutive steps: reactant adsorption, excess reactant evacuation, ion irradiation, and product evacuation. When successful, completion of one cycle results in removal of one monolayer of silicon. The process was self-limiting with respect to both reactant and ion dose. Control of the ion energy was the most important factor in realizing etching of one monolayer per cycle.
Indirect evidence of TTV replication in bone marrow cells, but not in hepatocytes, of a subacute hepatitis/aplastic anemia patient (2000)

The presence of a new DNA virus (TTV) has been reported in sera from patients with posttransfusion hepatitis of unknown etiology. The precise replication site of TTV, however, has not been established. In this study, the presence of TTV in liver autopsy material, and in bone marrow biopsy and autopsy samples taken from a subacute hepatitis/aplastic anemia patient was determined by PCR and Southern blot analyses. Liver cells were found to contain only TTV DNA and not mRNA. Bone marrow material, especially that taken at biopsy, contained high levels of TTV DNA. It is suggested that the TTV replication site was in the bone marrow rather than in the liver, and that TTV infection was the cause of this patient's aplastic anemia. The precise etiological association of TTV with hepatitis remains to be established. J. Med. Virol. 61:165–170, 2000. © 2000 Wiley-Liss, Inc.
Tissue-specific Expression of Unique mRNAs That Encode Proglucagon-derived Peptides or Exendin 4 in the Lizard (1997)

Glucagon-like peptide 1 stimulates insulin secretion and inhibits glucagon secretion, gastric emptying, and feeding, suggesting it may be biologically useful for the treatment of diabetes. A lizard glucagon-like peptide 1 (GLP-1)-related peptide, exendin 4, binds to the GLP-1 receptor and mimics the actions of GLP-1 in vivo. To determine the genetic relationship between exendin 4 and GLP-1, we analyzed the structure and expression of pancreatic and intestinal proglucagon mRNAs in the reptile Heloderma suspectum. Two different proglucagon cDNAs (lizard proglucagon I (LPI) and lizard proglucagon II (LPII)), with unique 3'-untranslated regions were identified. Two LPI mRNA transcripts, approximately 1.6 and 2.1 kilobases, encoded glucagon and GLP-1 but not GLP-2 and were restricted in expression to the pancreas. In contrast, a 1.1-kilobase LPII mRNA transcript, encoding glucagon, GLP-1, and GLP-2 utilized a different 3'-untranslated region and was expressed in both pancreas and intestine. Lizard proglucagon mRNA transcripts were not detectable by reverse transcription-polymerase chain reaction or Northern blotting in salivary gland. A single class of lizard salivary gland proexendin cDNAs encoded the sequence of exendin 4 and a 45-amino acid exendin NH2-terminal peptide. Exendin mRNA transcripts were expressed in the salivary gland, but not pancreas or intestine. These data demonstrate that GLP-1 and exendin 4 represent related yet distinct peptides encoded by different genes in the lizard.
Molecular insights into cancer invasion: strategies for prevention and intervention. (1995)

The diagnosis and treatment of solid tumors usually begins at a late stage when most patients already have occult or overt metastasis. Many years of cancer progression precede diagnosis of most solid tumors. Novel noncytotoxic therapeutics may be specially suited for administration during this interval. An important window of intervention can be defined as the period during which transition from a hyperproliferative state to acquisition of the capacity for invasion and metastasis occurs. Investigation of the molecular basis of invasion is uncovering strategies for delaying progression of preinvasive carcinoma and treatment of primary tumors and established metastasis. Although tumor cell invasion might not be rate limiting for the growth of metastasis, anti-invasive agents can block tumor angiogenesis and thereby indirectly block metastasis growth. Two classes of molecular anti-invasion targets exist: (a) cell surface and extracellular proteins, which mediate sensing, adhesion, and proteolysis; and (b) signal transduction pathways, which regulate invasion, angiogenesis, and proliferation. Both categories of targets yield treatment approaches that are now being tested in the clinic. Metalloproteinase inhibitors, such as BB94, are based on the recognition that metalloproteinases play a necessary role in invasion and angiogenesis. The orally active signal transduction inhibitor carboxyamidotriazole modulates non-voltage-gated calcium influx-regulated signal pathways and reversibly inhibits tumor invasion, growth, and angiogenesis. Blockade of invasion, angiogenesis, or cellular signal pathways is likely to generate a cytostatic, rather than a cytotoxic effect. Cytostatic therapy constitutes an alternative paradigm for clinical translation that may complement conventional cytotoxic therapy. For patients with newly diagnosed solid tumors, long-term cytostatic therapy could potentially create a state of metastasis dormancy or delay the time to overt relapse following cytotoxic agent-induced remission. Clinical toxicity and pharmacology using oral cytostatic agents in phase I trials and in adjuvant settings will provide an important foundation for the translation of this approach to the preinvasive carcinoma period.
Species-Crossreactive scFv Against the Tumor Stroma Marker “Fibroblast Activation Protein” Selected by Phage Display From an Immunized FAP−/− Knock-Out Mouse (2001)

MB M036, derived from phage display selected species crossreactive scFv, is suitable for tumor stroma targeting and will be a valuable tool in the analyses of the functional role of FAP in tumor biology as well as in the evaluation of the suitability of FAP for drug targeting.
Beta cell mass and growth after syngeneic islet cell transplantation in normal and streptozocin diabetic C57BL/6 mice. (1993)

In islet transplantation, nonimmunological factors such as limited growth capacity or increased death rate could reduce the beta cell mass in the graft and lead to failure of the transplant. We studied the evolution of beta cell replication and mass after transplantation of insufficient, minimally sufficient, or excessive islet tissue. Streptozocin diabetic C57BL/6 mice received 150 or 300 syngeneic islets under the kidney capsule and normal mice received 300 islets. In streptozocin diabetic mice 300 islets restored normoglycemia; beta cell replication in transplanted islets was similar to replication in normal pancreas and beta cell mass in the graft remained constant. In contrast, 150 islets were insufficient to achieve normoglycemia; beta cell replication was increased initially but not by 18 or 30 d despite persistent hyperglycemia, and beta cell mass fell progressively. When islets were transplanted into normal recipients, beta cell replication remained normal but beta cells underwent atrophy and mass in the graft was substantially reduced. Therefore, with a successful islet transplant, in diabetic mice beta cell replication and mass remain constant. In contrast, when insufficient islet tissue is transplanted an initial increase in beta cell replication can not compensate for a decline in beta cell mass. When excessive islet tissue is transplanted, beta cell mass is reduced despite normal beta cell replication.
Loss of β-III Spectrin Leads to Purkinje Cell Dysfunction Recapitulating the Behavior and Neuropathology of Spinocerebellar Ataxia Type 5 in Humans (2010)

Mutations in SPTBN2, the gene encoding beta-III spectrin, cause spinocerebellar ataxia type 5 in humans (SCA5), a neurodegenerative disorder resulting in loss of motor coordination. How these mutations give rise to progressive ataxia and what the precise role beta-III spectrin plays in normal cerebellar physiology are unknown. We developed a mouse lacking full-length beta-III spectrin and found that homozygous mice reproduced features of SCA5 including gait abnormalities, tremor, deteriorating motor coordination, Purkinje cell loss, and cerebellar atrophy (molecular layer thinning). In vivo analysis reveals an age-related reduction in simple spike firing rate in surviving beta-III(-/-) Purkinje cells, whereas in vitro studies show these neurons to have reduced spontaneous firing, smaller sodium currents, and dysregulation of glutamatergic neurotransmission. Our data suggest an early loss of EAAT4- (protein interactor of beta-III spectrin) and a subsequent loss of GLAST-mediated uptake may play a role in neuronal pathology. These findings implicate a loss of beta-III spectrin function in SCA5 pathogenesis and indicate that there are at least two physiological effects of beta-III spectrin loss that underpin a progressive loss of inhibitory cerebellar output, namely an intrinsic Purkinje cell membrane defect due to reduced sodium currents and alterations in glutamate signaling.