gebhart/patrepeval huggingface dataset:
Cell-free DNA in healthy individuals, noncancerous disease and strong prognostic value in colorectal cancer (2014)

The purpose was to investigate total cell-free DNA (cfDNA) in colorectal cancer (CRC) patients during treatment with second-line chemotherapy and in healthy controls and patients with different comorbidities. Patient treated with second-line irinotecan for metastatic CRC (n = 100), a cohort of healthy controls with and without comorbidity (n = 70 and 100, respectively) were included. cfDNA was quantified by an in-house developed quantitative polymerase chain reaction from plasma samples drawn prior to the first cycle of chemotherapy and at time of progression. cfDNA levels were significantly higher in CRC compared to controls, with a clear capability for discriminating between the groups (receiver operation curve analysis; area under the curve 0.82, p < 0.0001). Patients with high levels had a shorter survival from irinotecan compared to those with lover levels. The cohort independent upper normal limit divided patients into high and low risk groups. The progression-free survival (PFS) was 2.1 months [95% confidence interval (CI) 2.0-3.4] and 6.5 (95% CI 4.2-7.2) months [hazard ratio (HR) 2.53; 95% CI 1.57-4.06, p < 0.0001] and overall survival (OS) 7.4 months (95% CI 4.3-8.7) and 13.8 months (95% CI 11.9-18.9; HR 2.52; 95% CI 1.54-4.13, p < 0.0000), respectively. Cox regression multivariate analysis showed a PFS HR of 1.4 (95% CI 1.1-1.7) for each increase in cfDNA quartile, p = 0.03 and 1.6 (1.3-2.0) for OS, p < 0.0001, respectively. A combined marker analysis with plasma KRAS mutations added further prognostic impact, which was consistent when performed on the samples drawn at time of progression. In conclusion, cfDNA measurement holds important clinical information and could become a useful tool for prediction of outcome from chemotherapy in mCRC.
Inhibition of gamma-glutamyl transpeptidase activity at the surface of human myeloid cells is correlated with macrophage maturation and transforming growth factor beta production. (1995)

The protease gamma-glutamyl transpeptidase (gamma-GT) activity was detected at the surface of human blood granulocytes and monocytes and myeloblastic HL-60 and monoblastic U937 leukemia cell lines using an enzymatic assay (cleavage of gamma-glu-p-nitroanilide and inhibition by the specific irreversible inhibitor of gamma-GT, i.e., acivicin). Flow cytometric analysis of gamma-GT expression and detection of a 2.4-kb gamma-GT mRNA species by Northern blot analysis confirmed the presence of gamma-GT in cells of the monocytic-granulocytic lineage. Differentiation of HL-60, U937 cells, and blood monocytes along the macrophage pathway or granulocytic maturation of HL-60 cells was accompanied by an increase in gamma-GT mRNA levels without modulation of cell surface gamma-GT activity and protein. When added to leukemic cell cultures, acivicin produced a dose- and time-dependent inhibitory growth effect associated with the induction of morphological features characteristic of macrophage maturation and enhanced surface expression of phenotypic markers CD11b and CD71 characteristic of monocyte development. When cultured in the presence of acivicin, freshly isolated monocytes also underwent characteristic changes in morphology and antigenic phenotype (increase in CD71 and HLA-DR class II) consistent with their differentiation into macrophages. In parallel, a marked production of latent transforming growth factor (TGF)-beta was observed in supernatants of cells cultured with acivicin, although TGF-beta 1 mRNA species were expressed in these cells at a level almost similar to that in unstimulated cell cultures. Moreover, acivicin-treated cells still differentiated into macrophages in the presence of a neutralizing antibody to TGF-beta 1/beta 2.(ABSTRACT TRUNCATED AT 250 WORDS)
Community-Acquired Pneumonia (1994)

Journal Article Community-Acquired Pneumonia Get access Thomas J. Marrie Thomas J. Marrie From the Departments of Medicine and Microbiology, Dalhousie University, and Victoria General Hospital, Halifax, Nova Scotia, Canada Reprints or correspondence: Dr. T. J. Marrie, Room 5014 ACC, 1278 Tower Road, Halifax, Nova Scotia B3H 2Y9, Canada. Search for other works by this author on: Oxford Academic PubMed Google Scholar Clinical Infectious Diseases, Volume 18, Issue 4, April 1994, Pages 501–515, https://doi.org/10.1093/clinids/18.4.501 Published: 01 April 1994 Article history Received: 19 November 1993 Published: 01 April 1994
Central Sleep Apnea in a Geriatric Patient Treated With Aripiprazole (2009)

We report a case of central sleep apnea in a geriatric patient that was associated with treatment with aripiprazole for an episode of major depressive disorder with psychotic features. The patient was a 72-year-old man who was started on aripiprazole and developed central sleep apnea that improved significantly when the medication was stopped. A rechallenge with aripiprazole led to a worsening of the central sleep apnea, which again improved off the aripiprazole. We postulate that the central sleep apnea was due to aripiprazole. There have been numerous case reports in the literature of obstructive sleep apnea associated with atypical antipsychotics. To our knowledge, this is the first published case of central sleep apnea. We caution clinicians to be aware that there is potential risk of atypical antipsychotics like aripiprazole inducing or exacerbating central sleep apnea.
Phylogeny of human intestinal bacteria that activate the dietary lignan secoisolariciresinol diglucoside (2006)

The human intestinal microbiota is essential for the conversion of the dietary lignan secoisolariciresinol diglucoside (SDG) via secoisolariciresinol (SECO) to the enterolignans enterodiol (ED) and enterolactone (EL). However, knowledge of the species that catalyse the underlying reactions is scant. Therefore, we focused our attention on the identification of intestinal bacteria involved in the conversion of SDG. Strains of Bacteroides distasonis, Bacteroides fragilis, Bacteroides ovatus and Clostridium cocleatum, as well as the newly isolated strain Clostridium sp. SDG-Mt85-3Db, deglycosylated SDG. Demethylation of SECO was catalysed by strains of Butyribacterium methylotrophicum, Eubacterium callanderi, Eubacterium limosum and Peptostreptococcus productus. Dehydroxylation of SECO was catalysed by strains of Clostridium scindens and Eggerthella lenta. Finally, the newly isolated strain ED-Mt61/PYG-s6 catalysed the dehydrogenation of ED to EL. The results indicate that the activation of SDG involves phylogenetically diverse bacteria, most of which are members of the dominant human intestinal microbiota.
Cell-based therapy for heart failure (2006)

Cell therapy for patients with heart failure is still in its infancy. While early clinical studies suggest that stem and progenitor cell transfer to the failing heart may be feasible, firm conclusions regarding efficacy cannot be drawn at this time. The cell types that have undergone clinical testing so far, i.e. bone marrow cells and skeletal myoblasts, cannot promote true tissue regeneration. Further research into cell types with true cardiac transdifferentiation capacity is necessary in order to realize the prospects of cell therapy in this patient population.
Distinct bacteriocin groups correlate with different groups of Streptococcus mutans plasmids (1985)

A correlation between the presence of 5.6-kilobase plasmids and bacteriocin activity was found in human-derived strains of Streptococcus mutans. Compared with bacteriocin activity of randomly selected clinical isolates of plasmid-negative strains, bacteriocin activity of plasmid-positive strains significantly inhibited not only two laboratory strains of S. mutans, OMZ176 and AHT (P less than 0.0001 and P = 0.038, respectively), but most plasmid-negative clinical isolates as well (P = 0.0005). Comparisons of inhibition between pairs of plasmid-positive strains revealed two groups, group I and group II, that produced distinct bacteriocins we designated as mutacin I and mutacin II, respectively. Within each group, a strain produced inhibitory activity against all the members of the other group but against no members of its own group. Plasmid DNA from plasmid-positive strains of each group was isolated and analyzed by restriction endonuclease digestion. Plasmids from the two groups that were apparently identical in size differed in digestion patterns for EcoRI, HaeIII, and TaqI, even though six TaqI fragments appeared to be common to all. Based on bacteriocin profiles and restriction enzyme digests, two distinct groups of plasmid-positive S. mutans strains emerged. Although the bacteriocin activity of plasmid-positive strain LM7 (serotype e) placed it in group I, clear differences in restriction digests distinguished it from the other plasmid-containing strains.
Clues to Neuro-Degeneration in Niemann-Pick Type C Disease from Global Gene Expression Profiling (2006)

Many genes involved in the trafficking and processing of amyloid precursor protein and the microtubule binding protein, tau, were more highly expressed. Numerous genes important for membrane traffic and the cellular regulation of calcium, metals and other ions were upregulated. Finally, NPC fibroblasts exhibited a gene expression profile indicative of oxidative stress. These changes are likely contributors to the pathophysiology of Niemann-Pick Type C disease.
Mechanical hysteresis of a polyether polyurethane thermoplastic elastomer (1993)

Abstract The mechanical hysteresis of a polyether polyurethane thermoplastic elastomer was studied as a function of temperature, percent strain, and deformation energy. Hysteresis values remained small at low temperatures when the extent of the sample deformation did not disrupt the glassy matrix. This was readily evident at temperatures below the glass transition temperature, T g of the polymer where the material did not formally yield. At temperatures above the T g of the polymer, hysteresis remained small even at substantial strains levels and demonstrated the capabilities of the hard segment domains to act as physical crosslinks. At elevated temperatures, percent hysteresis increased as the hydrogen‐bonded hard segment domains weakened. When mechanical hysteresis was considered on the basis of constant deformation energies, hysteresis values reached a maximum in the vicinity of the T g of the polymer. These maxima existed as a consequence of two opposing trends: the decreasing resiliency of the polymer as it becomes a glass and the increase in the resistance of that glass to undergo deformations sufficient to cause plastic flow. Finally, a hysteresis response surface constructed as a function of deformation energy and temperature was found to be sensitive to both the strain‐induced crystallization of the rubbery soft segment matrix and to the strain‐induced yielding of the glassy soft segment matrix.
AltiVec extension to PowerPC accelerates media processing (2000)

There is a clear trend in personal computing toward multimedia-rich applications. These applications will incorporate a wide variety of multimedia technologies, including audio and video compression, 2D image processing, 3D graphics, speech and handwriting recognition, media mining, and narrow/broadband signal processing for communication. In response to this demand, major microprocessor vendors have announced architectural extensions to their general-purpose processors in an effort to improve their multimedia performance. Intel extended IA-32 with MMX and SSE (alias KNI), Sun enhanced Sparc with VIS, Hewlett-Packard added MAX to its PA-RISC architecture, Silicon Graphics extended the MIPS architecture with MDMX, and Digital (now Compaq) added MVI to Alpha. This article describes the most recent, and what we believe to be the most comprehensive, addition to this list: PowerPC's AltiVec, AltiVec speeds not only media processing but also nearly any application in which data parallelism exists, as demonstrated by a cycle-accurate simulation of Motorola's MPC 7400, the heart of Apple G4 systems.
Anterior chamber flare after femtosecond laser–assisted cataract surgery (2013)

Anterior segment inflammation was less after femtosecond laser-assisted cataract surgery than after manual cataract surgery, and this appeared to be due to a reduction in phacoemulsification energy.
Benefits of Immediate Jejunostomy Feeding after Major Abdominal Trauma???A Prospective, Randomized Study (1986)

Benefits of immediate postinjury nutritional support remain ill defined. Seventy-five consecutive patients undergoing emergent celiotomy with an abdominal trauma index (A.T.I.) greater than 15 were randomized prospectively to a control group (no supplemental nutrition during first 5 days) or enteral-fed group. The enteral patients had a needle catheter jejunostomy (N.C.J.) placed at laparotomy with the constant infusion of an elemental diet (Vivonex HN) begun at 18 hours and advanced to 3,000 ml/day (3,000 kcal, 20 gm N2) within 72 hours. Control and enteral-fed groups were comparable with respect to demographic features, trauma mechanism, shock, colon injury, splenectomy, A.T.I., and initial nutritional assessment. Twenty (63%) of the enteral patients were maintained on the elemental diet greater than 5 days; four (12%) needed total parenteral nutrition (T.P.N.). Nine (29%) of the control patients required T.P.N. Nitrogen balance was markedly improved (p less than 0.001) in the enteral-fed group. Although visceral protein markers and overall complication rate were not significantly different, septic morbidity was greater (p less than 0.025) in the control group (abdominal infection in seven and pneumonia in two) compared to the enteral-fed patients (abdominal abscess in three). Analysis of patients with A.T.I. 15-40 disclosed sepsis in seven (26%) of the control versus one (4%) of the enteral-fed group (p less than 0.01). Our clinical experience demonstrates the feasibility of immediate postoperative enteral feeding via N.C.J. after major abdominal trauma, and suggests this early nutrition reduces septic complications in critically injured patients.
Conjugated Polymer Inverse Opals for Potentiometric Biosensing (2002)

Colloidal crystals of poly(styrene) spheres can be used as templates to fabricate a conjugated polymer inverse opal potentiometric biosensor (see Figure) incorporating an enzyme. After core removal, a seven‐fold increase in sensitivity relative to conventional films is measured for analyte concentrations varying from 1 to 100 μM. The presence of large pores enables the formation of a Schottky junction, which governs the sensing response.
CCAAT-Enhancer Binding Protein: A Component of a Differentiation Switch (1991)

The CCAAT-enhancer binding protein (C/EBP) has now been found to promote the terminal differentiation of adipocytes. During the normal course of adipogenesis, C/EBP expression is restricted to a terminal phase wherein proliferative growth is arrested, and specialized cell phenotype is first manifested. A conditional form of C/EBP was developed, making it feasible to test its capacity to regulate the differentiation of cultured adipocytes. Premature expression of C/EBP in adipoblasts caused a direct cessation of mitotic growth. Moreover, when abetted by the effects of three adipogenic hormones, C/EBP promoted terminal cell differentiation. Since C/EBP is expressed in a variety of tissues, it may have a fundamental role in regulating the balance between cell growth and differentiation in higher animals.
Generation of programmable, picosecond-resolution shaped laser pulses by fiber-grating pulse compression (1987)

We demonstrate that fiber-optic compression can be sufficiently well characterized to permit generation of an arbitrarily shaped, 1-psec-resolution laser pulse from a predistorted, much longer pulse. Coupled with our previously demonstrated capability to generate an arbitrary shape with 10-psec resolution and software control, this technique provides significant advantages over conventional mode-locked, cavity-dumped, synchronously pumped laser systems.
Import of amber and ochre suppressor tRNAs into mammalian cells: A general approach to site-specific insertion of amino acid analogues into proteins (2001)

A general approach to site-specific insertion of amino acid analogues into proteins in vivo would be the import into cells of a suppressor tRNA aminoacylated with the analogue of choice. The analogue would be inserted at any site in the protein specified by a stop codon in the mRNA. The only requirement is that the suppressor tRNA must not be a substrate for any of the cellular aminoacyl-tRNA synthetases. Here, we describe conditions for the import of amber and ochre suppressor tRNAs derived from Escherichia coli initiator tRNA into mammalian COS1 cells, and we present evidence for their activity in the specific suppression of amber (UAG) and ochre (UAA) codons, respectively. We show that an aminoacylated amber suppressor tRNA (supF) derived from the E. coli tyrosine tRNA can be imported into COS1 cells and acts as a suppressor of amber codons, whereas the same suppressor tRNA imported without prior aminoacylation does not, suggesting that the supF tRNA is not a substrate for any mammalian aminoacyl-tRNA synthetase. These results open the possibility of using the supF tRNA aminoacylated with an amino acid analogue as a general approach for the site-specific insertion of amino acid analogues into proteins in mammalian cells. We discuss the possibility further of importing a mixture of amber and ochre suppressor tRNAs for the insertion of two different amino acid analogues into a protein and the potential use of suppressor tRNA import for treatment of some of the human genetic diseases caused by nonsense mutations.
Quality-of-life improvements in cataract patients with bilateral blue light–filtering intraocular lenses: Clinical trial (2005)

The blue light-filtering IOL improved color vision, driving, and other aspects of HRQOL in a manner similar to that of a lens that does not filter blue light.
In-Situ NH3 Generation for SCR NOx Applications (2002)

<div class="htmlview paragraph">There is currently a need for a practical solution for NOx abatement in automotive diesel engines. Technologies developed thus far suffer from inherent technical limitations. The selective catalytic reduction (SCR) of NOx under lean conditions has been proven to be successful for stationary applications.</div> <div class="htmlview paragraph">A new approach is described to efficiently remove NOx from the exhaust of a diesel engine powered vehicle and convert it to nitrogen and oxygen. The key to the approach is the development of an on board (in-situ) ammonia generating catalyst. The ammonia is then used as a reagent to react with exhaust NO over a secondary SCR catalyst downstream. The system can remove over 85% of the exhaust NO under achievable diesel engine operating conditions, while eliminating the potential for ammonia slip with a minimal system of sensors and feedback controls.</div>
Interactions ofCandida albicans with bacteria and salivary molecules in oral biofilms (1995)

The yeast Candida albicans coaggregates with a variety of streptococcal species, an interaction that may promote oral colonization by yeast cells. C. albicans and Candida tropicalis are the yeasts most frequently isolated from the human oral cavity and our data demonstrate that both these species bind to Streptococcus gordonii NCTC 7869 while two other Candida species (Candida krusei and Candida kefyr) do not. Adherence of C. albicans was greatest when the yeast had been grown at 30 degrees C to mid-exponential growth phase. For 21 strains of C. albicans there was a positive correlation between the ability to adhere to S. gordonii and adherence to experimental salivary pellicle. Whole saliva either stimulated or slightly inhibited adherence of C. albicans to S. gordonii depending on the streptococcal growth conditions. The results suggest that the major salivary adhesins and coaggregation adhesins of C. albicans are co-expressed.
Molecular cloning, nucleotide sequence, and expression of the gene encoding human eosinophil differentiation factor (interleukin 5). (1987)

The human eosinophil differentiation factor (EDF) gene was cloned from a genomic library in lambda phage EMBL3A by using a murine EDF cDNA clone as a probe. The DNA sequence of a 3.2-kilobase BamHI fragment spanning the gene was determined. The gene contains three introns. The predicted amino acid sequence of 134 amino acids is identical with that recently reported for human interleukin 5 but shows no significant homology with other known hemopoietic growth regulators. The amino acid sequence shows strong homology (approximately 70% identity) with that of murine EDF. Recombinant human EDF, expressed from the human EDF gene after transfection into monkey COS cells, stimulated the production of eosinophils and eosinophil colonies from normal human bone marrow but had no effect on the production of neutrophils or mononuclear cells (monocytes and lymphoid cells). The apparent specificity of human EDF for the eosinophil lineage in myeloid hemopoiesis contrasts with the properties of human interleukin 3 and granulocyte/macrophage and granulocyte colony-stimulating factors but is directly analogous to the biological properties of murine EDF. Human EDF therefore represents a distinct hemopoietic growth factor that could play a central role in the regulation of eosinophilia.
HIGHLY STEREOSELECTIVE PROCEDURE FOR (6R)-TETRAHYDROBIOPTERIN COFACTOR (1984)

Abstract (6R)-Tetrahydrobiopterin cofactor for aromatic amino acid hydroxylases was synthesized stereoselectively by catalytic hydrogenation of biopterin over platinum oxide at pH 11.4 and subsequent crystallization from hydrochloric acid and ethanol.
A Comparison of Internet Resource Discovery Approaches (1992)

In the past several years, the number and variety of resources available on the Internet have increased dramatically. With this increase, many new systems have been developed that allow users to search for and access these resources. As these systems begin to interconnect with one another through &amp;quot;information gateways&amp;quot;, the conceptual relationships between the systems come into question. Understanding these relationships is important, because they address the degree to which the systems can be made to interoperate seamlessly, without the need for users to learn the details of each system. In this paper we present a taxonomy of approaches to resource discovery. The taxonomy provides insights into the interrelated problems of organizing, browsing, and searching for information. Using this taxonomy, we compare a number of resource discovery systems, and examine several gateways between existing systems.
Parallel Networks that Learn to Pronounce English Text (1987)

This paper describes NETtalk, a class of massively-parallel network systems that learn to convert English text to speech. The memory representations for pronunciations are learned by practice and are shared among many processing units. The performance of NETtalk has some similarities with observed human performance. (i) The learning follows a power law. (;i) The more words the network learns, the better it is at generalizing and correctly pronouncing new words, (iii) The performance of the network degrades very slowly as connections in the network are damaged: no single link or processing unit is essential. (iv) Relearning after damage is much faster than learning during the original training. (v) Distributed or spaced practice is more effective for long-term retention than massed practice. Network models can be constructed that have the same performance and learning characteristics on a particular task, but differ completely at the levels of synaptic strengths and single-unit responses. However, hierarchical clustering techniques applied to NETtalk reveal that these different networks have similar internal representations of letter-to-sound correspondences within groups of processing units. This suggests that invariant internal representations may be found in assemblies of neurons intermediate in size between highly localized and completely distributed representations.