gebhart/patrepeval huggingface dataset:
Capnography and Respiratory Depression (2008)

In order to determine whether opioid-naive patients at risk for respiratory depression are better monitored with either capnography or pulse oximetry and respiratory-rate assessment, the authors conducted a randomized, prospective trial. In 54 opioid-naive postoperative orthopedic patients at one hospital, capnography resulted in greater detection of respiratory depression, and the authors conclude that capnography may be more appropriate for use with postsurgical high-risk patients taking opioids on the general care nursing unit. Capnography's sensitivity in the detection of pauses in breathing in the sedated patient may have the added advantage of indicating those patients who may be at risk for obstructive sleep apnea. Further research is needed to confirm these results.
Molecular Profiling Reveals Low- and High-Grade Forms of Primary Melanoma (2012)

Abstract Purpose: For primary melanomas, tumor thickness, mitotic rate, and ulceration are well-laid cornerstones of prognostication. However, a molecular exposition of melanoma aggressiveness is critically missing. We recently uncovered a four-class structure in metastatic melanoma, which predicts outcome and informs biology. This raises the possibility that a molecular structure exists even in the early stages of melanoma and that molecular determinants could underlie histophenotype and eventual patient outcome. Experimental Design: We subjected 223 archival primary melanomas to a horizontally integrated analysis of RNA expression, oncogenic mutations at 238 lesions, histomorphometry, and survival data. Results: Our previously described four-class structure that was elucidated in metastatic lesions was evident within the expression space of primary melanomas. Because these subclasses converged into two larger prognostic and phenotypic groups, we used the metastatic lesions to develop a binary subtype-based signature capable of distinguishing between “high” and “low” grade forms of the disease. The two-grade signature was subsequently applied to the primary melanomas. Compared with low-grade tumors, high-grade primary melanomas were significantly associated with increased tumor thickness, mitotic rate, ulceration (all P &amp;lt; 0.01), and poorer relapse-free (HR = 4.94; 95% CI, 2.84–8.59), and overall (HR = 3.66; 95% CI, 2.40–5.58) survival. High-grade melanomas exhibited elevated levels of proliferation and BRCA1/DNA damage signaling genes, whereas low-grade lesions harbored higher expression of immune genes. Importantly, the molecular-grade signature was validated in two external gene expression data sets. Conclusions: We provide evidence for a molecular organization within melanomas, which is preserved across all stages of disease. Clin Cancer Res; 18(15); 4026–36. ©2012 AACR.
Rational Drug Design of Multifunctional Phosphoramidate Substituted Nucleoside Analogs (2004)

This review focuses on our approach to the study of the effect of a series of phosphoramidate substituted nucleoside analogs on model systems for cancer, HIV and fertility. This approach allowed the development of compound WHI-07, an arylphosphoramidate derivative of zidavudine. This compound is a multifunctional agent showing potent activity in the above mentioned model systems. Our rational drug design provided such a powerful derivative with all the necessary characteristic of a drug candidate. Importantly, we have experimental evidence that each of the groups associated with the molecular frame of WHI-07 imparts the multifunctional ability for this agent. In addition, we have also suggested a possible biological pathway for WHI-07 including various products with their therapeutic targets that are formed during the course of its metabolism inside the cell. We also propose which individual moieties in the structure of WHI-07 are responsible for the biological activity from the formation of these metabolites. A detailed structure-activity relationship is presented in the review in connection with various structural modifications of the agent. Application of this active agent in animal models shows the potential usefulness of this agent as a drug candidate. We further plan to utilize gene-chip technology to identify new targets and modes of action using microarrays to measure expression changes in thousands of gene products. In conclusion, we have demonstrated the power of multifunctional drug design to discover drugs to combat various diseases. We believe this is the future direction of the drug discovery process.
Role of the protein kinase C signaling pathway in high-density lipoprotein receptor-mediated efflux of intracellular cholesterol. (1991)

These studies provide evidence that binding of HDL3 to the HDL receptor stimulates translocation and efflux of intracellular cholesterol through mechanisms involving the activation of protein kinase C. This conclusion is supported by data demonstrating that HDL is able to increase cell diacylglycerol levels and activate protein kinase C. Sphingosine, a protein kinase C inhibitor, was able to inhibit HDL3-mediated cholesterol translocation and efflux, further suggesting a role for protein kinase C in HDL receptor-dependent cholesterol efflux. Inhibition of HDL-mediated diacylglycerol formation by pertussis toxin suggests the possible involvement of a G protein-activated phospholipase. Further studies are needed to understand how activation of protein kinase C promotes cholesterol translocation and to identify the target proteins for protein kinase C phosphorylation.
Routing Information Protocol (1988)

This RFC describes an existing protocol for exchanging routing information among gateways and other hosts. It is intended to be used as a basis for developing gateway software for use in the Internet community. Distribution of this memo is unlimited.
Gene-Enhanced Tissue Engineering (1999)

The treatment of difficult wounds remains a considerable clinical challenge. The goal of this study was to determine whether genetic augmentation of dermal cells on resorbable matrices can stimulate the healing process, leading to increased tissue repair in a rat full-thickness excisional wound repair model. The human platelet-derived growth factor B (PDGF-B) gene was the initial gene chosen to test this hypothesis. The human PDGF-B gene was obtained from human umbilical vein endothelial cells (HUVEC) by reverse transcriptase-polymerase chain reaction, cloned into retroviral vectors under control of either the cytomegalovirus promoter or the rat beta-actin promoter, and introduced into primary rat dermal cells. In vitro results demonstrate that rat dermal cells are transduced and selected readily using retroviral vectors, and engineered to secrete PDGF-B at a steady-state level of approximately 2 ng per milliliter culture per 1 million cells per 24 hours. Seeding of the gene-modified cells onto polyglycolic acid (PGA) scaffold matrices and introduction into the rat model resulted in substantially increased fibroblast hypercellularity over control wounds at both 7 and 14 days posttreatment. Our results demonstrate that gene augmentation of rat dermal fibroblasts with the PDGF-B gene introduced into this animal model via PGA matrices modulates wound healing and suggests that experimentation with additional genes for use separately or in combination with PDGF-B for additional, improved wound healing is warranted.
Multiple Domains Define the Expression and Regulatory Properties of Foxp1 Forkhead Transcriptional Repressors (2003)

The Foxp subfamily of forkhead/HNF3 transcription factors has recently been recognized because of its involvement in autoimmune disease, speech and language disorders, and lung development. Domains unique to this subfamily include a divergent DNA-binding winged helix, a leucine zipper, a zinc finger, and a polyglutamine tract. Little is known about the properties of these proteins that are fundamental to their function as transcription factors nor how the Foxp sequence motifs regulate their transcriptional regulatory properties. We report here a structure/function analysis of the Foxp1 protein. We have analyzed the alternative splice isoforms 1A and 1C and also report the cloning and characterization of a novel isoform Foxp1D that lacks the polyglutamine domain. We have isolated the preferred DNA-binding sites for Foxp1 transcription factors. Foxp1A, C, and D isoforms and the related Foxp2 protein repress gene transcription via binding to this consensus site or to a naturally occurring site within the SV40 and the interleukin-2 promoters. In some cases the strength of Foxp1 repression is mediated by the polyglutamine domain. Unlike previously characterized forkhead factors, Foxp1 proteins can form homodimers or heterodimers with subfamily members. The dimerization domain was localized to an evolutionarily conserved C2H2 zinc finger and leucine zipper motif. Finally, we demonstrate that Foxp1, although broadly expressed, is further regulated by tissue-specific alternative splicing of these functionally important sequence domains. These results suggest that Foxp1 proteins have diverse functional roles in different cell and tissue types.
Thin glass based packaging technologies for optoelectronic modules (2009)

The novel packaging approach glassPack is introduced as System-in-Package (SiP) technology. Wiring length can be reduced and integration density can be increased by stacking different assembled substrate layers and interconnecting them with one another resulting in 3D-SiP. Glass is an excellent material because of matched coefficient of thermal expansion (CTE) to silicon, high thermal load, dielectricity and high optical transparency over a wide wavelength range. Commercially available thin glass foils can be used as substrate material for electronic and optoelectronic modules. The goal of our ongoing development is making glass based packaging competitive with polymer based (e.g. chip-in-polymer) or silicon based packaging (e.g. silicon-through-via, stacked dies by wire bonding). Our work is focused on conductor trace and through-via realization as well as optical lightwave circuits integration using glass as substrate material. For through-vias in glass, holes were drilled in glass wafers by different laser technologies or etched using photosensitive glass and evaluated. Conductor traces and through-via interconnects were deposited on glass. Also, optical waveguide and fluidic channel integration in glass substrates were investigated. This paper presents the first demonstrator of our glass based packaging technology targeting sensor applications. Two silicon dies, a laser diode, two photodiodes and a fluidic-optical chip were mounted on a glass substrate and interconnected by 3D electrical wiring.
Decreased Uncoupling Protein Expression and Intramyocytic Triglyceride Depletion in Formerly Obese Subjects (2003)

The strong correlation of UCP expression and decrease in IMTG levels suggests that triglyceride content plays an even more important role in the regulation of UCP gene expression than the circulating levels of free fatty acids or the achieved degree of weight loss.
Profiling self-propagating worms via behavioral footprinting (2006)

This paper proposes behavioral footprinting, a new dimension of worm profiling based on worm infection sessions. A worm's infection session contains a number of steps (e.g., for probing, exploitation, and replication) that are exhibited in certain order in every successful worm infection. Behavioral footprinting complements content-based signature by enriching a worm's profile, which will be used in worm identification, an important task in post worm attack investigation and recovery. We propose an algorithm to extract a worm's behavioral footprint from the worm's traffic traces. Our evaluation with a number of real worms and their variants confirms the existence of worms' behavioral footprints and demonstrates their effectiveness in worm identification.
Phase III Comparative Study of High-Dose Cisplatin Versus a Combination of Paclitaxel and Cisplatin in Patients With Advanced Non–Small-Cell Lung Cancer (2000)

This large randomized phase III trial failed to show a significant improvement in survival for the paclitaxel/cisplatin combination compared with high-dose cisplatin in patients with advanced NSCLC. However, the paclitaxel/cisplatin combination did produce a better clinical response, resulting in an increased time to progression while providing a similar QOL.
Square Root Generator for Galois Field in Multiple-Valued Logic (2011)

In this paper, we present two pipelined square root circuits for Galois field in Multiple-Valued Logic (MVL). We use composite Galois fields in a MVL approach to generate the required square root value in the field. The fact that less literals are used in our approach speeds up the calculation operation. The MVL approach of calculating the square root in a composite Galois field is novel. In this review important patents are also discussed.
Single-nucleus gene expression (2016)

Neurogenomics
Identifying the genes expressed at the level of a single cell nucleus can better help us understand the human brain. Lake et al. developed a single-nuclei sequencing technique, which they applied to cells in classically defined Brodmann areas from a postmortem brain. Clustering of gene expression showed concordance with the area of origin and defining 16 neuronal subtypes. Both excitatory and inhibitory neuronal subtypes show regional variations that define distinct cortical areas and exhibit how gene expression clusters may distinguish between distinct cortical areas. This method opens the door to widespread sampling of the genes expressed in a diseased brain and other tissues of interest.

Science , this issue p. [1586][1]

 [1]: /lookup/doi/10.1126/science.aaf1204
Genital Herpes in Guinea Pigs: Pathogenesis of the Primary Infection and Description of Recurrent Disease (1982)

Guinea pigs inoculated intravaginally with herpes simplex virus type 2 (HSV-2) developed a self-limiting infection characterized by vesiculo-ulcerative lesions on the external genital skin, urinary retention, and hindlimb paralysis. Infection rarely resulted in death. Virologic, histologic, and immunoperoxidase data suggested the following scheme for viral pathogenesis: initial replication in the introitus, vagina, and bladder; spread via sensory nerves to the lumbosacral dorsal root ganglia and spinal cord, and transmission via peripheral nerves to the external genital skin to produce the characteristic lesions. After recovery from primary infection, animals developed recurrent vesicular lesions, shed virus from genital sites in the absence of lesions, and harbored latent HSV-2 in dorsal root ganglia. Genital infection in the guinea pig shares many features with genital herpes in humans and provides a model to explore mechanisms of latency and reactivation and to evaluate several methods for control of recurrent disease.
Expression of CSF-1, c-fms, and MCP-1 in the central nervous system of rats with experimental allergic encephalomyelitis (1993)

We have examined the expression of factors associated with the growth, differentiation, and chemotaxis of cells of the monocyte/macrophage series in the central nervous system of Lewis rats sensitized to develop experimental allergic encephalomyelitis. CSF-1 mRNA increased significantly over that found in control animals (sensitized with OVA in CFA or CFA alone). The elevation in the levels of this growth factor commenced immediately before the onset of early clinical signs and peaked immediately before maximal clinical incidence of disease. Expression of CSF-1 message declined to base-line values with resolution of the disease process. CSF-1 protein was also detected in the central nervous system at the height of clinical disease. Expression of the receptor for CSF-1, the proto-oncogene c-fms, also paralleled the early disease process. Elevated levels of c-fms mRNA were detected immediately before the onset and peaked at the height of clinical signs of disease. In contrast to CSF-1 levels, elevated c-fms message expression persisted after resolution of the acute phase of experimental allergic encephalomyelitis. Levels of macrophage chemotactic factor-1 message were also elevated immediately before the onset of clinical signs, peaked with the height of clinical disease, and declined with resolution of the disease. Unlike CSF-1 or c-fms, no endogenous macrophage chemotactic factor-1 message was detected in control animals. Macrophage chemotactic factor-1 protein was demonstrated by Western blot in the central nervous system at the height of clinical disease. The results support the conclusion that expression of factors that specifically target cells of the monocyte/macrophage series are an important component of the disease process in experimental allergic encephalomyelitis.
Activating Phosphoenolpyruvate Carboxylase and Phosphoenolpyruvate Carboxykinase in Combination for Improvement of Succinate Production (2013)

Phosphoenolpyruvate (PEP) carboxylation is an important step in the production of succinate by Escherichia coli. Two enzymes, PEP carboxylase (PPC) and PEP carboxykinase (PCK), are responsible for PEP carboxylation. PPC has high substrate affinity and catalytic velocity but wastes the high energy of PEP. PCK has low substrate affinity and catalytic velocity but can conserve the high energy of PEP for ATP formation. In this work, the expression of both the ppc and pck genes was modulated, with multiple regulatory parts of different strengths, in order to investigate the relationship between PPC or PCK activity and succinate production. There was a positive correlation between PCK activity and succinate production. In contrast, there was a positive correlation between PPC activity and succinate production only when PPC activity was within a certain range; excessive PPC activity decreased the rates of both cell growth and succinate formation. These two enzymes were also activated in combination in order to recruit the advantages of each for the improvement of succinate production. It was demonstrated that PPC and PCK had a synergistic effect in improving succinate production.
Metabolic Changes in Alzheimer's Disease (1988)

Patients with Alzheimer's disease (AD) and matched controls fasted for 24 hours, and serial glucose, pyruvate, lactate, beta-hydroxybutyrate, acetoacetate, insulin, and glucagon levels were measured. Patients with AD showed a glucose insulin correlation pattern over the 24 hours that differed from the control group. These differences may be secondary to weight loss or to other metabolic or nutritional factors affecting the AD patients.
Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA (2007)

Artificial biochemical circuits are likely to play as large a role in biological engineering as electrical circuits have played in the engineering of electromechanical devices. Toward that end, nucleic acids provide a designable substrate for the regulation of biochemical reactions. However, it has been difficult to incorporate signal amplification components. We introduce a design strategy that allows a specified input oligonucleotide to catalyze the release of a specified output oligonucleotide, which in turn can serve as a catalyst for other reactions. This reaction, which is driven forward by the configurational entropy of the released molecule, provides an amplifying circuit element that is simple, fast, modular, composable, and robust. We have constructed and characterized several circuits that amplify nucleic acid signals, including a feedforward cascade with quadratic kinetics and a positive feedback circuit with exponential growth kinetics.
Gabapentin augmentation therapy in bipolar depression (2002)

Open adjunctive GBP was effective and well tolerated in patients with mild to moderate bipolar depression. This open pilot study must be viewed with caution, and randomized controlled studies are warranted.
Carbon Nanotube Actuators (1999)

Electromechanical actuators based on sheets of single-walled carbon nanotubes were shown to generate higher stresses than natural muscle and higher strains than high-modulus ferroelectrics. Like natural muscles, the macroscopic actuators are assemblies of billions of individual nanoscale actuators. The actuation mechanism (quantum chemical-based expansion due to electrochemical double-layer charging) does not require ion intercalation, which limits the life and rate of faradaic conducting polymer actuators. Unlike conventional ferroelectric actuators, low operating voltages of a few volts generate large actuator strains. Predictions based on measurements suggest that actuators using optimized nanotube sheets may eventually provide substantially higher work densities per cycle than any previously known technology.
Ferromagnetic nanotubes by atomic layer deposition in anodic alumina membranes (2007)

In this paper, two methods for the synthesis of magnetic nanotubes inside the pores of anodic alumina membranes by atomic layer deposition (ALD) are compared. The precursors were nickelocene or cobaltocene, and H2O or O3. The first method consists of a three-step ALD cycle: First, the sample is exposed to the metal-organic precursor, subsequently to water, and finally, to hydrogen. In the second method, metal oxide is deposited by a conventional two-step ALD cycle. After the ALD process, the sample is reduced under hydrogen atmosphere. The magnetic nanotubes obtained by the second method have a smaller grain size and improved magnetic properties. The magnetic nanotubes with diameters ranging from 35to60nm exhibit a preferential magnetization direction along the nanowire axis. The Ni or Co nanotubes with larger diameters (around 160nm) show a nearly isotropic magnetic behavior, with the magnetic moments arranged in a vortex state at zero field.
Transcriptomes, transcription activators and microarrays (2001)

Gene-specific transcription activators are among the main factors which specifically shape the transcriptome profiles. It is tempting to take advantage of their properties to decipher the genome expression circuitry. The advent of microarray technology has offered fantastic opportunities to quickly analyze the expression profiles dictated by specific transcription factors. This review will first focus on the strategies which have been devised to control the activity of transcription factors and in the second part on the microarray experiments which addressed the role of these transcription factors in the genome-wide expression profile. This last part will mainly consider the case of the yeast Saccharomyces cerevisiae genome. All the collected data are available through the on-line database yTAFNET (http://transcriptome.ens.fr/ytafnet/). yTAFNET is designed to help the characterization of connections between the different yeast regulatory networks.
Effects of Low-Dose Ketamine Combined With Propofol on Phosphorylation of AMPA Receptor GluR1 Subunit and GABAA Receptor in Hippocampus of Stressed Rats Receiving Electroconvulsive Shock (2014)

Low-dose ketamine combined with propofol may play a role in enhancing the antidepressant efficacy of ECS in stressed rats, ameliorating the cognitive impairment associated with ECS by balancing the expression of p-GluR1 and p-GABAAR in the hippocampus of stressed rats.