gebhart/patrepeval huggingface dataset:
Roles of Phosphatidylethanolamine and of Its Several Biosynthetic Pathways in<i>Saccharomyces cerevisiae</i> (2001)

Three different pathways lead to the synthesis of phosphatidylethanolamine (PtdEtn) in yeast, one of which is localized to the inner mitochondrial membrane. To study the contribution of each of these pathways, we constructed a series of deletion mutants in which different combinations of the pathways are blocked. Analysis of their growth phenotypes revealed that a minimal level of PtdEtn is essential for growth. On fermentable carbon sources such as glucose, endogenous ethanolaminephosphate provided by sphingolipid catabolism is sufficient to allow synthesis of the essential amount of PtdEtn through the cytidyldiphosphate (CDP)-ethanolamine pathway. On nonfermentable carbon sources, however, a higher level of PtdEtn is required for growth, and the amounts of PtdEtn produced through the CDP-ethanolamine pathway and by extramitochondrial phosphatidylserine decarboxylase 2 are not sufficient to maintain growth unless the action of the former pathway is enhanced by supplementing the growth medium with ethanolamine. Thus, in the absence of such supplementation, production of PtdEtn by mitochondrial phosphatidylserine decarboxylase 1 becomes essential. In psd1Delta strains or cho1Delta strains (defective in phosphatidylserine synthesis), which contain decreased amounts of PtdEtn, the growth rate on nonfermentable carbon sources correlates with the content of PtdEtn in mitochondria, suggesting that import of PtdEtn into this organelle becomes growth limiting. Although morphological and biochemical analysis revealed no obvious defects of PtdEtn-depleted mitochondria, the mutants exhibited an enhanced formation of respiration-deficient cells. Synthesis of glycosylphosphatidylinositol-anchored proteins is also impaired in PtdEtn-depleted cells, as demonstrated by delayed maturation of Gas1p. Carboxypeptidase Y and invertase, on the other hand, were processed with wild-type kinetics. Thus, PtdEtn depletion does not affect protein secretion in general, suggesting that high levels of nonbilayer-forming lipids such as PtdEtn are not essential for membrane vesicle fusion processes in vivo.
Acceptance of direct physician access to a computer-based patient record in a managed care setting. (1993)

Kaiser Permanente Mid-Atlantic States has developed a fully integrated outpatient information system which currently runs on an IBM ES9000 on a VM platform written in MUMPS. The applications include Lab, Radiology, Transcription, Appointments. Pharmacy, Encounter tracking, Hospitalizations, Referrals, Phone Advice, Pap tracking, Problem list, Immunization tracking, and Patient demographics. They are department specific and require input and output from a dumb terminal. We have developed a physician's work station to access this information using PC compatible computers running Microsoft Windows and a custom Microsoft Visual Basic 2.0 environment which draws from these 14 applications giving the physician a comprehensive view of all electronic medical records. Through rapid prototyping, voluntary participation, formal training and gradual implementation we have created an enthusiastic response. 95% of our physician PC users access the system each month. The use ranges from 0.2 to 3.0 screens of data viewed per patient visit. This response continues to drive the process toward still greater user acceptance and further practice enhancement.
Novel isoforms of the β and γ subunits of the <i>Xenopus</i> epithelial Na channel provide information about the amiloride binding site and extracellular sodium sensing (1997)

We have previously identified three homologous subunits alpha, beta, and gamma of the highly selective amiloride-sensitive Na channel from the Xenopus laevis kidney A6 cell line, which forms a tight epithelium in culture. We report here two novel genes, termed beta2 and gamma2, which share 90 and 92% sequence identity with the previously characterized beta and gamma XENaC, respectively. beta2 and gamma2 transcripts were detected in lung, kidney, and A6 cells grown on porous substrate. The physiological and pharmacological profile of the Na channel expressed after alphabeta2gamma XENaC cRNA injection in Xenopus oocyte did not differ from alphabetagamma XENaC. By contrast, the channel expressed after alphabetagamma2 injection showed: (i) a lower maximal amiloride-sensitive sodium current, (ii) a higher apparent affinity for external sodium and inactivation of the sodium current by high sodium concentrations, and (iii) a lower apparent affinity for amiloride (KI alphabetagamma2; 1.34 microM versus alphabetagamma 0.35 microM). These data indicate that the gamma (and/or gamma2) subunit participates in amiloride binding and the sensing of the extracellular sodium concentration. The close homology between gamma and gamma2 will help to define the domains involved in sensing external sodium and in the structure of this important drug receptor.
Phosphoric Acid-Doped Ion-Pair Coordinated PEMs with Broad Relative Humidity Tolerance (2020)

Proton exchange membrane (PEM) capable of working over a broad operating condition window is critical for successful adoption of PEM-based electrochemical devices. In this work, phosphoric acid (PA)-doped biphenyl-backbone ion-pair coordinated PEMs were prepared by quaternization of BPBr-100, a precursor polymer, with three different tertiary amines including trimethylamine, 1-methylpiperidine, and 1,2-dimethylimidazole followed by membrane casting, ion exchange reaction to hydroxide ion, and doping with PA. The resulting PA-doped ion-pair PEMs were characterized in terms of PA doping level, proton conductivity, relative humidity (RH) tolerance, thermal stability, and mechanical properties. PA doping levels were between six and eight according to acid-base titration. The size and structure of the cation group of ion-pair polymers were found to affect the PA doping level and water uptake. Proton conductivity was studied as a function of RH over a wide range of 5% to 95% RH. Stable conductivity at 80 °C was observed up to 70% RH for 10 h. Mechanical property characterization indicates that the PA doping process resulted in more ductile membranes with significantly increased elongation at break due to the plasticization effect of PA. A combination of high proton conductivity at low RH conditions, and good humidity tolerance makes this new class of PEMs great potential candidates for use in electrochemical devices such as proton exchange membrane fuel cells and electrochemical hydrogen compressors.
Surfactant Protein A, Phosphatidylcholine, and Surfactant Inhibitors in Epithelial Lining Fluid: Correlation with Surface Activity, Severity of Respiratory Distress Syndrome, and Outcome in Small Premature Infants (1991)

Although surfactant deficiency at birth is the major cause of respiratory distress syndrome (RDS), there is insufficient data on surfactant and surfactant inhibitors after birth. In the present study, a total of 345 airway specimens (AS) from 61 neonates of gestational age of 24 to 29 wk (54 with RDS) were analyzed for concentrations of phosphatidylcholine (PC), saturated PC (SPC), surfactant protein A (SP-A), nonsedimentable protein, and free amino acids in epithelial lining fluid (ELF). The relationship between surfactant indices, surface activity, and severity of RDS was studied. Treatment with human surfactant containing SP-A increased [PC]ELF and [SPC]ELF to levels found in infants without RDS. In placebo-treated infants similar concentrations were first reached between Days 4 and 7. Surfactant treatment increased the low SP-A/SPC ratio, although this ratio remained lower than that in exogenous surfactant. In RDS, the concentrations of free amino acids in ELF were 6 to 31 times higher than in infants without RDS. The nonsedimentable proteins of AS and cationic amino acids increased the minimum surface tension of SP-A-deficient surfactant from AS. Addition of SP-A improved the surface activity. According to multiple regression analysis, In [PC]ELF (p less than 0.0001), SPC/PC ratio (p less than 0.0001), In SP-A/SPC ratio (p less than 0.0002), and [protein]ELF (p less than 0.01) correlated with alveolar-arterial oxygen pressure gradient. Of the infants weighing less than 1,000 g, those who were going to die or develop bronchopulmonary dysplasia had a strikingly lower SP-A/SPC ratio during the first week (less than 25 ng/nmol) than those surviving without BPD.(ABSTRACT TRUNCATED AT 250 WORDS)
A Rapid and Simple Procedure for the Routine Detection of ras Point Mutations in Formalin-Fixed, Paraffin-Embedded Tissues (1992)

The use of the polymerase chain reaction (PCR) to detect specific DNA sequences in small amounts of tissues or cells has become a widespread tool in the field of molecular biology. With the better understanding of the clinical significance of oncogene activations in human tumors, the application of PCR in a routine setting is rapidly gaining importance. We have developed a rapid and simple procedure for the detection of mutated ras oncogenes in routinely fixed, paraffin-embedded tissue samples. DNA is isolated from three 10 microns tissue sections by incubation with a nonionic detergent and proteinase K, and can be directly used for amplification by PCR. The amplified DNA fragments are then dot-blotted onto nylon membranes and are hybridized to radioactively labeled oligodeoxynucleotides, specific for each of the mutated ras sequences. After a selective washing procedure, only fully matched oligodeoxynucleotides remain bound to the membrane, thus revealing the nature of the sequences that were present in the starting material. With this method, the detection of point mutations in ras genes can be performed in a routine setting, and the results of the analyses can be available in as few as 3-4 days.
A Novel Technology (2013)

In this study, we examined the effectiveness of percutaneous injected fibrin glue as a treatment for frontal sinus cerebrospinal fluid (CSF) rhinorrhea in a series of 4 cases. All 4 patients had fracture in the posterior wall of the frontal sinus. The anterior wall of the frontal sinus was punctured following high-resolution computed tomography imaging. In 3 out of 4 patients with defective skull due to prior frontal craniotomy, direct percutaneous puncture of the frontal sinus was used. Fibrin glue was injected to close the fistula and to seal the rhinorrhea. Surgery procedures lasted for 15-35 minutes (average 27.6 min). Rhinorrhea was stopped in all patients after the surgery, with no recurrence at a 10-month follow-up visit. In 1 case, the glue was expelled by coughing at 2 days after the surgery but was completely stopped with no recurrence after a second attempt. One patient with no recurrence at a 10-month follow-up died of tumor relapse at 12 months. In summary, fibrin glue could be used as a novel treatment for frontal sinus CSF rhinorrhea.
Basin-scale tomography: A new tool for studying weather and climate (1990)

Measurements of acoustic travel time across the northeast Pacific Ocean are used to detect large-scale (&gt;500 km) thermal trends in the ocean interior. The trends are novel observations, and there is probably no method to verify them with other data sets. The results demonstrate the practicality of a new and powerful means to observe ocean temperature and to investigate its relation to weather, climate, and greenhouse warming.
Classified Separation of Lignin Hydrothermal Liquefied Products (2011)

Alkaline lignin was liquefied under hydrothermal conditions, and the liquefied products were effectively separated into four main types of substances: benzenediols, monophenolic hydroxyl products, weak-polar products, and water-soluble products (low-molecular-weight organic acids, alcohols, etc.). The production process and yield of each classified products are discussed. More than half of the yields of the oil products consisted of phenolics. A mechanism for phenolic production from lignin liquefaction is proposed. It suggests that the decomposition of lignin under hydrothermal conditions occurs mainly by three steps: hydrolysis and cleavage of the ether bond and the C–C bond, demethoxylation, and alkylation.
Speech-to-text transcription in support of pervasive computing (2004)

Speech recognition technology can help transcribe discussions, interviews, meetings, and conversations. This paper describes
Plasma selenium and skin neoplasms: A case‐control study (1985)

Although experimental studies in animals show that selenium may prevent cancer, case-control studies of internal human cancers have been difficult to interpret because neoplastic tissue sequesters selenium. We therefore conducted a case-control study to examine the association between plasma selenium level and skin cancer, a neoplasm with minimal tumor mass at the time of diagnosis. The mean selenium level among patients with either basal cell epithelioma (N = 142), squamous cell carcinoma (N = 48), or both (N = 50), was 0.141 micrograms/g. This was significantly lower than the mean plasma selenium level of the 103 control subjects, which was 0.155 micrograms/g. The noncancer control groups were drawn from current clinic patients and past clinic patients. The logistic estimate of the odds ratio for the lowest versus the highest decile of selenium for all cases combined versus the group of current patient controls was 4.39; for all cases combined versus the past patient controls, the logistic estimate of the odds ratio was 5.81.
Three NF-χB sites in the IχB-α promoter are required for induction of gene expression by TNFα (1994)

NF-kappa B was first identified as a postive regulator which bound to a 10 bp sequence in the first intron of the Ig kappa light chain gene. Further characterization of this transcription factor has revealed that NF-kappa B is kept from binding to its consensus sequence by its inhibitor, IkB-alpha, which retains NF-kappa B in the cytoplasm. Upon receiving various extra- and intracellular signals, I kappa B-alpha is rapidly degraded and NF-kappa B is induced to translocate into the nucleus. This process precedes the rapid induction of I kappa B-alpha mRNA and protein. To understand how I kappa B-alpha is replenished, we have cloned and sequenced the 5' flanking region of the I kappa B-alpha gene and have identified the transcription start site and three NF-kappa B sites in this region. Further characterization of these NF-kappa B sites show that they have different affinities for three specific protein complexes which we identify here to consist of various members of the Rel family. In transient assays, cotransfection with a p65 expression vector is able to activate an I kappa B-alpha promoter-CAT reporter construct and all three NF-kappa B sites are required for full activation of the I kappa B-alpha gene following stimulation with TNF-alpha. Our data confirm a transcriptional autoregulatory loop involved in maintaining appropriate NF-kappa B and I kappa B-alpha levels in the cell.
Antagonistic metal-directed inductions in catalytic asymmetric aziridination by manganese and iron tetramethylchiroporphyrins (1999)

Catalytic asymmetric aziridination of styrene by [N-(p-toluenesulfonyl)imino]phenyliodinane was achieved by manganese and iron tetramethylchiroporphyrins; opposite enantioselectivities were obtained with the two metal centers, and possible mechanisms are proposed to explain this unexpected result.
Polyclonality of BRAF mutations in primary melanoma and the selection of mutant alleles during progression (2011)

Acquisition of a BRAF mutation is not a founder event, but may be one of the multiple clonal events in melanoma development, which is selected for during the progression.
Another overnight sensation: Australian TV comedy (1990)

According to the weekend press, the weekly and monthly magazines, and Sixty Minutes, Australians are in the middle of a boom in television comedy at the moment. Suddenly, comedians have appeared from nowhere to entertain us in these depressive times, and the most surprising thing of all is that many of them are women! Journalists everywhere have been caught asking silly and essentialising questions: why comedy now? what makes things funny now? and the inevitable, '... do you think there is such a thing as an Australian sense of humour'? For those producers and writers who have been trying to establish Australian comedy's foothold in Australian television for years, the current naive enthusiasm about its 'overnight success' must be less than gratifying. The fact is, of course, Australian comedy has not just suddenly improved and thus come to dominate our screens. What may have happened is that the commercial networks have finally acknowledged that comedy can be produced in Australia, that it might be able to develop its own formats, and that it has to be given more than a couple of weeks to secure its audience.
Phenotyping of Lesions of Melanocyte Origin With Monoclonal Antibodies to Melanoma-Associated Antigens and to HLA Antigens<xref ref-type="fn" rid="FN2">2</xref> (1984)

The antigenic profiles of a large number of surgically removed human benign and malignant lesions of melanocyte origin have been analyzed with the use of monoclonal antibodies (MoAb) against la antigens, against the HLA-A,B,C-beta 2-microglobulin molecular complex, against a cytoplasmic melanoma-associated antigen (MAA), and against membrane-bound MAA. Membrane-bound MAA include a high-molecular-weight MAA (HMW-MAA), a 115K MAA, and a 100K MAA. Appearance of the HMW-MAA and of the cytoplasmic MAA, as well as cytoplasmic distribution or loss of HLA-A,B,C antigens, occurs in benign lesions. Additional appearance of Ia antigens is associated with malignant transformation of melanocytes. The antigenic profile defined by the battery of MoAb used displays differences among benign lesions of different histogenesis, between benign and malignant lesions, and among malignant lesions with different histopathologic properties. These results suggest that phenotyping of surgically removed lesions with anti-MAA and anti-HLA MoAb may contribute to the understanding of the steps involved in tumor progression of melanocytes and may aid in the diagnosis of lesions with unusual histopathologic features.
Liquid Haskell: Haskell as a Theorem Prover (2016)

Code deficiencies and bugs constitute an unavoidable part of software systems. In safety-critical systems, like aircrafts or medical equipment, even a single bug can lead to catastrophic impacts such as injuries or death. Formal verification can be used to statically track code deficiencies by proving or disproving correctness properties of a system. However, at its current state formal verification is a cumbersome process that is rarely used by mainstream developers, mostly because it targets non general purpose languages (e.g., Coq, Agda, Dafny).We present Liquid Haskell, a usable program verifier that aims to establish formal verification as an integral part of the development process. Liquid Haskell naturally integrates the specification of correctness propertiesas logical refinements of Haskell's types. Moreover, it uses the abstract interpretation framework of liquid types to automatically check correctness of specifications via Satisfiability Modulo Theories (SMT) solversrequiring no explicit proofs or complicated annotations. Finally, the specification language is arbitrary expressive, allowing the user to write general correctness properties about their code, thus turning Haskell into a theorem prover. Transforming a mature language --- with optimized libraries and highly tuned parallelism --- into a theorem prover enables us to verify a wide variety of properties on real world applications. We used Liquid Haskell to verify shallow invariants of existing Haskell code, e.g., memory safety of the optimized string manipulation library ByteString. Moreover, we checked deep, sophisticated properties of parallel Haskell code, e.g., program equivalence of a naive string matcher and its parallelized version. Having verified about 20K of Haskell code, we present how Liquid Haskell serves as a prototype verifier in a future where formal techniques will be used to facilitate, instead of hinder, software development.
Submillisecond unmasked subliminal visual stimuli evoke electrical brain responses (2014)

Subliminal perception is strongly associated to the processing of meaningful or emotional information and has mostly been studied using visual masking. In this study, we used high density 256-channel EEG coupled with an liquid crystal display (LCD) tachistoscope to characterize the spatio-temporal dynamics of the brain response to visual checkerboard stimuli (Experiment 1) or blank stimuli (Experiment 2) presented without a mask for 1 ms (visible), 500 µs (partially visible), and 250 µs (subliminal) by applying time-wise, assumption-free nonparametric randomization statistics on the strength and on the topography of high-density scalp-recorded electric field. Stimulus visibility was assessed in a third separate behavioral experiment. Results revealed that unmasked checkerboards presented subliminally for 250 µs evoked weak but detectable visual evoked potential (VEP) responses. When the checkerboards were replaced by blank stimuli, there was no evidence for the presence of an evoked response anymore. Furthermore, the checkerboard VEPs were modulated topographically between 243 and 296 ms post-stimulus onset as a function of stimulus duration, indicative of the engagement of distinct configuration of active brain networks. A distributed electrical source analysis localized this modulation within the right superior parietal lobule near the precuneus. These results show the presence of a brain response to submillisecond unmasked subliminal visual stimuli independently of their emotional saliency or meaningfulness and opens an avenue for new investigations of subliminal stimulation without using visual masking.
Mechanisms of Membrane Curvature Sensing (2011)

Bacteria and eukaryotic cells contain geometry-sensing tools in their cytosol: protein motifs or domains that recognize the curvature, concave or convex, deep or shallow, of lipid membranes. These sensors contrast with classical lipid-binding domains by their extended structure and, sometimes, counterintuitive chemistry. Among the sensors are long amphipathic helices, such as the ALPS motif and the N-terminal region of α-synuclein, whose apparent "design defects" translate into a remarkable ability to specifically adsorb to the surface of small vesicles. Fundamental differences in the lipid composition of membranes of the early and late secretory pathways probably explain why some sensors use mostly electrostatics whereas others take advantage of the hydrophobic effect. Membrane curvature sensors help to organize very diverse reactions, such as lipid transfer between membranes, the tethering of vesicles at the Golgi apparatus, and the assembly-disassembly cycle of protein coats.
Free and lipid <i>myo</i>-inositol in tissues from rats with acute and less severe streptozotocin-induced diabetes (1977)

Acute diabetes with ketosis was induced in rats by intraperitoneal streptozotocin and also a milder form of diabetes without ketosis by injecting less of the drug. The acutely diabetic rats were killed 72h after injection and the others after either 2 or 13 weeks. Free and lipid myo-inositol was then measured in various tissues and body fluids by g.l.c. of the trimethylsilyl ether. Serum inositol was increased in the acutely diabetic group, whereas liver inositol was decreased. Brain and kidney inositol concentrations were increased in the mildly diabetic animals at 13 weeks and there was a progressive decrease in sciatic-nerve inositol. Lipid inositol of sciatic nerve was decreased in the acutely diabetic group only. Brain lipid inositol concentration was decreased in mild diabetes at 13 weeks. Possible implications of these findings in relation to diabetic neuropathy was discussed.