gebhart/patrepeval huggingface dataset:
A recombinant calcitonin receptor independently stimulates 3',5'-cyclic adenosine monophosphate and Ca2+/inositol phosphate signaling pathways. (1992)

Calcitonin (CT), a polypeptide hormone, regulates calcium homeostasis by activating surface receptors coupled to stimulation of adenylyl cyclase in bone and kidney cells. CT has also been reported to increase cytoplasmic Ca2+ in osteoclasts and renal tubule cells. Signaling pathways activated by a recombinant porcine renal calcitonin receptor transiently expressed in HEK-293 cells were studied. In cells expressing the recombinant CT receptor, salmon CT stimulated cAMP accumulation (EC50, 0.16 nM) and synthesis of inositol phosphates (IP; EC50, 3.7 nM). Two other recombinant receptors, the m1-muscarinic acetylcholine receptor and the LH receptor, activated synthesis of either IP or cAMP, respectively, but not both. Stable expression of the CT receptor in a CT receptor-deficient cell line, M18, restored the cells' ability to increase cytoplasmic Ca2+ in response to salmon CT. These results show that a single recombinant CT receptor can independently activate effector pathways mediated by cAMP and IP/Ca2+.
Requirement of the DEAD-Box Protein Ded1p for Messenger RNA Translation (1997)

The DED1 gene, which encodes a putative RNA helicase, has been implicated in nuclear pre-messenger RNA splicing in the yeast Saccharomyces cerevisiae. It is shown here by genetic and biochemical analysis that translation, rather than splicing, is severely impaired in two newly isolated ded1 conditional mutants. Preliminary evidence suggests that the protein Ded1p may be required for the initiation step of translation, as is the distinct DEAD-box protein, eukaryotic initiation factor 4A (eIF4A). The DED1 gene could be functionally replaced by a mouse homolog, PL10, which suggests that the function of Ded1p in translation is evolutionarily conserved.
Chromosomal location of human kappa and lambda immunoglobulin light chain constant region genes (1982)

The chromosomal location of human constant region light chain immunoglobulin (Ig) genes has been determined by analyzing a group of human fibroblast/rodent somatic cell hybrids with nucleic acid probes prepared from cloned human kappa and lambda constant region genes. Human chromosomes in each cell line were identified by isoenzyme analysis. The DNA from hybrid cells was digested with restriction endonucleases, size fractionated by gel electrophoresis, transferred to nitrocellulose or DBM paper, and hybridized with (32)P-labeled nucleic acid probes. The C(kappa) gene was assigned to human chromosome 2 and the C(lambda) genes to chromosome 22, based upon analysis of these hybrid cell lines, and these assignments were confirmed by analysis of subclones. A group of previously unassigned loci can be mapped to chromosome 2 by virtue of their close linkage to C(kappa). The lambda and kappa light chain and heavy chain Ig genes have now been assigned to all three human chromosomes that are involved in translocations with chromosome 8 in human B cell neoplasms. These techniques and probes provide a means to study the detailed arrangement of human Ig genes and their pseudogenes.
A Hierarchical Data Structure for Representing the Spatial Decomposition of 3-D Objects (1985)

The polytree, a generalization of the octree data structure, retains most of the desirable features of the octree structure while offering several advantages.
Nitric Oxide Deficiency in Fenfluramine- and Dexfenfluramine-induced Pulmonary Hypertension (1998)

Dexfenfluramine and fenfluramine greatly increase the risk of developing pulmonary hypertension (PHT). The mechanism of anorexigen-associated PHT (AA-PHT) and the reason PHT occurs in a minority of people exposed are unknown. Anorexigens are weak pulmonary vasoconstrictors, but they become potent when synthesis of the endogenous vasodilator nitric oxide (NO) is suppressed. We hypothesized NO deficiency predisposes affected individuals to develop AA-PHT. A prospective, case-control, study was performed on consecutive patients with AA-PHT (n = 9). Two sex-matched control groups were selected: patients with primary PHT (P-PHT, n = 8) and normal volunteers (n = 12). Lung NO production (VNO) and systemic plasma oxidation products of NO (NOx) were measured at rest and during exercise. AA-PHT developed 17 +/- 6 mo after a short course of anorexigen (6 +/- 2 mo) and was irreversible. VNO was lower in AA-PHT than in P-PHT and correlated inversely with PVR (p < 0.05). The apparent VNO deficiency may have resulted from increased oxidative inactivation of NO in patients with AA-PHT, as their NOx levels were elevated (p < 0.05) in inverse proportion to VNO (r2 = 0. 55; p < 0.02). In susceptible persons, anorexigens can cause an irreversible syndrome of PHT, hypoxemia, and systemic vascular complications after brief exposures. These patients have a relative NO deficiency years after discontinuing the anorexigen, perhaps explaining their original susceptibility.
TaintDroid: an information-flow tracking system for realtime privacy monitoring on smartphones (2010)

Today's smartphone operating systems frequently fail to provide users with adequate control over and visibility into how third-party applications use their private data. We address these shortcomings with TaintDroid, an efficient, system-wide dynamic taint tracking and analysis system capable of simultaneously tracking multiple sources of sensitive data. TaintDroid provides realtime analysis by leveraging Android's virtualized execution environment. TaintDroid incurs only 14% performance overhead on a CPU-bound micro-benchmark and imposes negligible overhead on interactive third-party applications. Using TaintDroid to monitor the behavior of 30 popular third-party Android applications, we found 68 instances of potential misuse of users' private information across 20 applications. Monitoring sensitive data with TaintDroid provides informed use of third-party applications for phone users and valuable input for smartphone security service firms seeking to identify misbehaving applications.
Abdominal Wound with Enterocutaneous Fistula (1998)

In Brief The care of an elderly male surgical patient with an enterocutaneous fistula located in an abdominal wound is described. The fistula is believed to have been related to multiple surgeries, wound dehiscence, and malnutrition. This article presents a brief overview of enterocutaneous fistulas and a pictorial demonstration of an alternative wound management technique that was used intermittently over several months to contain corrosive intestinal effluent until a commercial wound manager could be instituted. A case study of a challenging enterocutaneous fistula located in an abdominal wound.
SEARNN: Training RNNs with Global-Local Losses (2017)

We propose SEARNN, a novel training algorithm for recurrent neural networks (RNNs) inspired by the "learning to search" (L2S) approach to structured prediction. RNNs have been widely successful in structured prediction applications such as machine translation or parsing, and are commonly trained using maximum likelihood estimation (MLE). Unfortunately, this training loss is not always an appropriate surrogate for the test error: by only maximizing the ground truth probability, it fails to exploit the wealth of information offered by structured losses. Further, it introduces discrepancies between training and predicting (such as exposure bias) that may hurt test performance. Instead, SEARNN leverages test-alike search space exploration to introduce global-local losses that are closer to the test error. We first demonstrate improved performance over MLE on two different tasks: OCR and spelling correction. Then, we propose a subsampling strategy to enable SEARNN to scale to large vocabulary sizes. This allows us to validate the benefits of our approach on a machine translation task.
A Soluble Tissue Factor Mutant Is a Selective Anticoagulant and Antithrombotic Agent (1997)

One approach to developing safer and more efficacious agents for the treatment of thrombotic disease involves the design and testing of inhibitors that block specific steps in the coagulation cascade. We describe here the development of a mutant of human tissue factor (TF) as a specific antagonist of the extrinsic pathway of blood coagulation and the testing of this mutant in a rabbit model of arterial thrombosis. Alanine substitutions of Lys residues 165 and 166 in human TF have been shown previously to diminish the cofactor function of TF in support of factor X (FX) activation catalyzed by factor VIIa (FVIIa). The K165A:K166A mutations have been incorporated into soluble TF (sTF; residues 1-219) to generate the molecule "hTFAA." hTFAA binds FVIIa with kinetics and affinity equivalent to wild-type sTF, but the hTFAA x FVIIa complex shows a 34-fold reduction in catalytic efficiency for FX activation relative to the activity measured for sTF x FVIIa. hTFAA inhibits the activation of FX catalyzed by the complex formed between FVIIa and relipidated TF(1-243). hTFAA prolongs prothrombin time (PT) determined with human plasma and relipidated TF(1-243) or membrane bound TF, and has no effect on activated partial thromboplastin time, but is 70-fold less potent as an inhibitor of PT with rabbit plasma. The rabbit homologue of this mutant ("rTFAA") was produced and shown to have greater potency with rabbit plasma. Both hTFAA and rTFAA display an antithrombotic effect in a rabbit model of arterial thrombosis with rTFAA giving full efficacy at a lower dose than hTFAA. Compared to heparin doses of equal antithrombotic potential, hTFAA and rTFAA cause less bleeding as judged by measurements of the cuticle bleeding time. These results indicate that TF x FVIIa is a good target for the development of new anticoagulant drugs for the treatment of thrombotic disease.
Nonlinear Disturbance Observer-Based Dynamic Surface Control of Mobile Wheeled Inverted Pendulum (2015)

In this brief, a dynamic model of a mobile wheeled inverted pendulum (MWIP) system is improved considering friction forces, and a nonlinear disturbance observer (NDO)-based dynamic surface controller is investigated to control the MWIP system. Using a coordinate transformation, this non-Class-I type underactuated system is presented as a semistrict feedback form, which is convenient for dynamic surface controller design. A dynamic surface controller together with an NDO is designed to stabilize the underactuated plant. The proposed approach can compensate the external disturbances and the model uncertainties to improve the system performance significantly. The stability of the closed-loop MWIP system is proved by Lyapunov theorem. Experiment results are presented to illustrate the feasibility and efficiency of the proposed method.
Molecular characterization of circulating tumor cells (CTC) and CTC subpopulations in progressive metastatic castration resistant prostate cancer (mCRPC). (2014)

132 Background: Numerous resistance mechanisms have been postulated in progressive mCRPC. Determining the presence of putative predictive biomarkers in patients requires a real-time tumor assessment because the biology changes under the influence of the specific therapy(ies) that a patient (Pt) has received. We examined CTC and CTC subpopulation incidence and molecular characterization of tumors from Pts with progressive mCRPC to assess if determinants of resistance can be assessed through a CTC test. Methods: 48 samples from 21 unique progressive mCRPC pts treated with androgen receptor targeted (AR tx) therapies, 9 (43%) on Abiraterone plus Prednisone (AA+P) and 12 (57%) on Enzalutamide (E). Samples were collected and shipped to Epic Sciences, where cells were stained and CTC identified by fluorescent scanners and algorithmic analysis. CTCs, defined as classic (CK+ CD45- w/intact DAPI nuclei and distinct), apopotic (CK+, CD45-, non-intact nuclei) and CK- (CK-, CD45-, intact and distinct) were identified. CTCs reported per mL of blood and were examined for AR, PTEN &amp; ERG. CTC data were analyzed in context of PSA, Veridex CTC (reported per 7.5mL of blood), and clinical history. Results: With Epic, all 21 pts had detectable CTCs (mdn 23 cells/ml, range 2 to 249), whereas with Veridex, 14 (67%) pts had &gt; 5 CTC/7.5 ml (mdn 5 cells/7.5 ml, range 0 to &gt;200). 0/7 (0%) with high AR responded to AA+P or E, 8/14 (53%) with low AR had a PSA decline and stable radiographic disease (median follow-up 12 wks). Variations in AR protein expression and localization heterogeneity was seen in all pts to varying degrees. 6/21 (29%) Pts demonstrated CK- CTC/CTC ratio &gt;50% (mdn 9 cells/ml, range 5-38). ERG rearrangement and PTEN loss were correlated. Conclusions: Epic CTC analysis provides higher detection rates, while enabling individual cell analyses for predictive biomarkers of sensitivity to AR directed therapies. Notable was the marked heterogeneity of detection of AR, ERG, and PTEN of individual CTCs. Studies are ongoing to further explore associations with outcomes. [Table: see text]
[Clinical study of fluconazole-injectable and -granules in pediatric patients]. (1994)

In this study, we have investigated the clinical effectiveness of fluconazole (FLCZ) given intravenously or orally to pediatric patients with systemic fungal infections. FLCZ was administered intravenously to two patients with acute leukemia (multiple hepatosplenic candidiasis and aspergillosis) and orally to two mycosis complicated with neuroblastoma and aplastic anemia, respectively. Clinical efficacies were excellent and no side effects were observed in any patients. Pharmacokinetic analysis in 6 neonates revealed that the plasma half-life is 37-41 hours after administration of single dose of intravenous infusion of 3 mg/kg of FLCZ.
Role of tobacco stems in the formation of N-nitrosamines in tobacco and cigarette mainstream and sidestream smoke (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRole of tobacco stems in the formation of N-nitrosamines in tobacco and cigarette mainstream and sidestream smokeKlaus D. Brunnemann, Joseph Masaryk, and Dietrich HoffmannCite this: J. Agric. Food Chem. 1983, 31, 6, 1221–1224Publication Date (Print):November 1, 1983Publication History Published online1 May 2002Published inissue 1 November 1983https://doi.org/10.1021/jf00120a020RIGHTS & PERMISSIONSArticle Views210Altmetric-Citations25LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (466 KB) Get e-Alerts Get e-Alerts
Herpes Simplex Virus Type 1/Adeno-Associated Virus Hybrid Vectors Mediate Site-Specific Integration at the Adeno-Associated Virus Preintegration Site, AAVS1, on Human Chromosome 19 (2002)

Herpes simplex virus type 1 (HSV-1)-based amplicon vectors have a large transgene capacity and can efficiently infect many different cell types. One disadvantage of HSV-1 vectors is their instability of transgene expression. By contrast, vectors based on adeno-associated virus (AAV) can either persist in an episomal form or integrate into the host cell genome, thereby supporting long-term gene expression. AAV expresses four rep genes, rep68, -78, -40, and -52. Of those, rep68 or rep78 are sufficient to mediate site-specific integration of the AAV DNA into the host cell genome. The major disadvantage of AAV vectors is the small transgene capacity ( approximately 4.6 kb). In this study, we constructed HSV/AAV hybrid vectors that contained, in addition to the standard HSV-1 amplicon elements, AAV rep68, rep78, both rep68 and -78, or all four rep genes and a reporter gene that was flanked by the AAV inverted terminal repeats (ITRs). Southern blots of Hirt DNA from cells transfected with the hybrid vectors and HSV-1 helper DNA demonstrated that both the AAV elements and the HSV-1 elements were functional in the context of the hybrid vector. All hybrid vectors could be packaged into HSV-1 virions, although those containing rep sequences had lower titers than vectors that did not. Site-specific integration at AAVS1 on human chromosome 19 was directly demonstrated by PCR and sequence analysis of ITR-AAVS1 junctions in hybrid vector-transduced 293 cells. Cell clones that stably expressed the transgene for at least 12 months could easily be isolated without chemical selection. In the majority of these clones, the transgene cassette was integrated at AAVS1, and no sequences outside the ITR cassette, rep in particular, were present as determined by PCR, ITR rescue/replication assays, and Southern analysis. Some of the clones contained random integrations of the transgene cassette alone or together with sequences outside the ITR cassette. These data indicate that the long-term transgene expression observed following transduction with HSV/AAV hybrid vectors is, at least in part, supported by chromosomal integration of the transgene cassette, both randomly and site specifically.
KRAS (but not BRAF) mutations in ovarian serous borderline tumour are associated with recurrent low‐grade serous carcinoma (2013)

BRAF and KRAS mutations in ovarian serous borderline tumours (OSBTs) and ovarian low-grade serous carcinomas (LGSCs) have been previously described. However, whether those OSBTs would progress to LGSCs or whether those LGSCs were developed from OSBT precursors in previous studies is unknown. Therefore, we assessed KRAS and BRAF mutations in tumour samples from 23 recurrent LGSC patients with a known initial diagnosis of OSBT. Paraffin blocks from both OSBT and LGSC samples were available for five patients, and either OSBTs or LGSCs were available for another 18 patients. Tumour cells from paraffin-embedded tissues were dissected out for mutation analysis by conventional polymerase chain reaction (PCR) and Sanger sequencing. Tumours that appeared to have wild-type KRAS by conventional PCR-Sanger sequencing were further analysed by full COLD (co-amplification at lower denaturation temperature)-PCR and deep sequencing. Full COLD-PCR was able to enrich the amplification of mutated alleles. Deep sequencing was performed with the Ion Torrent personal genome machine (PGM). By conventional PCR-Sanger sequencing, BRAF mutation was detected only in one patient and KRAS mutations were detected in ten patients. Full COLD-PCR deep sequencing detected low-abundance KRAS mutations in eight additional patients. Three of the five patients with both OSBT and LGSC samples available had the same KRAS mutations detected in both OSBT and LGSC samples. The remaining two patients had only KRAS mutations detected in their LGSC samples. For patients with either OSBT or LGSC samples available, KRAS mutations were detected in seven OSBT samples and six LGSC samples. Surprisingly, patients with the KRAS G12V mutation have shorter survival times. In summary, KRAS mutations are very common in recurrent LGSC, while BRAF mutations are rare. The findings indicate that recurrent LGSC can arise from proliferation of OSBT tumour cells with or without detectable KRAS mutations.
Channel state awareness based transmission power adaptation for efficient TCP dynamics in wireless networks (2005)

Although the problem of mal-performance of TCP in the wireless scenario has been extensively addressed, an integrated solution has remained undeciphered. Conventionally, measures have been suggested to either adapt or shield TCP from non-congestion losses over the wireless channel. On the other hand, the issues of wireless channel compensation and error control for achieving a better quality channel, have been extensively studied too. Recent efforts to investigate joint approaches do not model TCP dynamics over wireless channel, but study the impact of power control and link layer error correction mechanisms in relation to standard TCP throughput models. In this work, we propose and evaluate transmission power adaptation as an integrated solution to mal-performance of TCP in wireless networks. The congestion control dynamics of bulk-transfer TCP flow are modeled for the wireless channel, and an optimization framework is delineated. Based on dynamic programming solutions and low-complexity heuristics, adaptive power control measures are suggested and analyzed for their merit. Via simulations, we demonstrate that suitable power adaptation can lead to a considerable improvement in TCP throughput for slow and fast fading channels.
Diversity of P450 enzymes in the biosynthesis of natural products (2012)

Diverse oxygenation patterns of natural products generated by secondary metabolic pathways in microorganisms and plants are largely achieved through the tailoring reactions catalysed by cytochrome P450 enzymes (P450s). P450s are a large family of oxidative hemoproteins found in all life forms from prokaryotes to humans. Understanding the reactivity and selectivity of these fascinating C-H bond-activating catalysts will advance their use in generating valuable pharmaceuticals and products for medicine, agriculture and industry. A major strength of this P450 group is its set of established enzyme-substrate relationships, the source of the most detailed knowledge on how P450 enzymes work. Engineering microbial-derived P450 enzymes to accommodate alternative substrates and add new functions continues to be an important near- and long-term practical goal driving the structural characterization of these molecules. Understanding the natural evolution of P450 structure-function should accelerate metabolic engineering and directed evolutionary approaches to enhance diversification of natural product structures and other biosynthetic applications.
A spoken language system for automated call routing (2002)

We are interested in the problem of understanding fluently spoken language. In particular, we consider people's responses to the open-ended prompt of "How may I help you?". We then further restrict the problem to classifying and automatically routing such a call, based on the meaning of the user's response. Thus, we aim at extracting a relatively small number of semantic actions from the utterances of a very large set of users who are not trained to the system's capabilities and limitations. In this paper, we describe the main components of our speech understanding system: the large vocabulary recognizer and the language understanding module performing the call-type classification. In particular, we propose automatic algorithms for selecting phrases from a training corpus in order to enhance the prediction power of the standard word n-gram. The phrase language models are integrated into stochastic finite state machines which outperform standard word n-gram language models. From the speech recognizer output we recognize and exploit automatically-acquired salient phrase fragments to make a call-type classification. This system is evaluated on a database of 10 K fluently spoken utterances collected from interactions between users and human agents.