gebhart/patrepeval huggingface dataset:
Lateral diffusion of minority carriers in InAsSb-based nBn detectors (2010)

We report on the investigation of lateral diffusion of minority carriers in InAsSb based photodetectors with the nBn design. Diffusion lengths (DLs) were extracted from temperature dependent I-V measurements. The behavior of DL as a function of applied bias, temperature, and composition of the barrier layer was investigated. The obtained results suggest that lateral diffusion of minority carriers is not the limiting factor for InAsSb based nBn mid-wave infrared detector performance at high temperatures (&amp;gt;200 K). The detector with an As mole fraction of 10% in the barrier layer has demonstrated values of DL as low as 7 μm (Vb=0.05 V) at 240 K.
Sequence analysis and molecular characterization of the temperate lactococcal bacteriophage r1t (1996)

The temperate lactococcal bacteriophage r1t was isolated from its lysogenic host and its genome was subjected to nucleotide sequence analysis. The linear r1t genome is composed of 33,350 bp and was shown to possess 3' staggered cohesive ends. Fifty open reading frames (ORFs) were identified which are, probably, organized in a life-cycle-specific manner. Nucleotide sequence comparisons, N-terminal amino acid sequencing and functional analyses enabled the assignment of possible functions to a number of DNA sequences and ORFs. In this way, ORFs specifying regulatory proteins, proteins involved in DNA replication, structural proteins, a holin, a lysin, an integrase, and a dUTPase were putatively identified. One ORF seems to be contained within a self-splicing group I intron. In addition, the bacteriophage att site required for site-specific integration into the host chromosome was determined.
Targeting the Binding Function 3 (BF3) Site of the Human Androgen Receptor through Virtual Screening. (2011)

The androgen receptor (AR) is the best studied drug target for the treatment of prostate cancer. While there are a number of drugs that target the AR, they all work through the same mechanism of action and are prone to the development of drug resistance. There is a large unmet need for novel AR inhibitors which work through alternative mechanism(s). Recent studies have identified a novel site on the AR called binding function 3 (BF3) that is involved into AR transcriptional activity. In order to identify inhibitors that target the BF3 site, we have conducted a large-scale in silico screen followed by experimental evaluation. A number of compounds were identified that effectively inhibited the AR transcriptional activity with no obvious cytotoxicity. The mechanism of action of these compounds was validated by biochemical assays and X-ray crystallography. These findings lay a foundation for the development of alternative or supplementary therapies capable of combating prostate cancer even in its antiandrogen resistant forms.
Complete nucleotide sequence of human reg gene and its expression in normal and tumoral tissues. The reg protein, pancreatic stone protein, and pancreatic thread protein are one and the same product of the gene. (1990)

We previously identified a novel gene, reg (i.e. regenerating gene), in the screening of a rat regenerating islet-derived cDNA library, and isolated its human cDNA homologue which encodes a 166-amino acid protein (Terazono, K., Yamamoto, H., Takasawa, S., Shiga, K., Yonemura, Y., Tochino, Y., and Okamoto, H. (1988) J. Biol. Chem. 263, 2111-2114). In the present study, we have isolated the human reg gene, determined its complete nucleotide sequence, and examined its expression in human tissues. The functional human reg gene is a single copy gene, spans approximately 3.0 kilobase pairs, and is composed of six exons and five introns. TATA box and CCAAT box-like sequences are located at 27 and 100 base pairs upstream from the transcriptional initiation site. The human reg mRNA was detected predominantly in the pancreas, and at lower levels in the gastric mucosa and the kidney. Furthermore, the reg gene was found to be expressed ectopically in colon and rectal tumors. Immunoblot analysis demonstrated several molecular forms (15-18 kDa) of the reg protein in the pancreas. The 166-amino acid sequence encoded by the human reg gene contains the 144-amino acid sequence of pancreatic stone protein determined by De Caro et al. (De Caro, A. M., Adrich, Z., Fournet, B., Capon, C., Bonicel, J. J., De Caro, J. D., and Rovery, M. (1989) Biochim. Biophys. Acta 994, 281-284) and the partially determined 45-amino acid sequence of pancreatic thread protein (Gross, J., Carlson, R. I., Brauer, A. W., Margolies, M. N., Warshaw, A. L., and Wands, J. R. (1985) J. Clin. Invest. 76, 2115-2126), indicating that the reg protein, pancreatic stone protein, and pancreatic thread protein are simply different names for a single protein deriving from the reg gene.
Switching and Finite Automata Theory (2009)

Understand the structure, behaviour, and limitations of logic machines with this thoroughly updated third edition. Many new topics are included, such as CMOS gates, logic synthesis, logic design for emerging nanotechnologies, digital system testing, and asynchronous circuit design, to bring students up-to-speed with modern developments. The intuitive examples and minimal formalism of the previous edition are retained, giving students a text that is logical and easy to follow, yet rigorous. Kohavi and Jha begin with the basics, and then cover combinational logic design and testing, before moving on to more advanced topics in finite-state machine design and testing. Theory is made easier to understand with 200 illustrative examples, and students can test their understanding with over 350 end-of-chapter review questions.
Phosphoinositides as Regulators in Membrane Traffic (1996)

Phosphorylated products of phosphatidylinositol play critical roles in the regulation of membrane traffic, in addition to their classical roles as second messengers in signal transduction at the cell surface. Growing evidence suggests that phosphorylation-dephosphorylation of the polar heads of phosphoinositides (polyphosphorylated inositol lipids) in specific intracellular locations signals either the recruitment or the activation of proteins essential for vesicular transport. Cross talk between phosphatidylinositol metabolites and guanosine triphosphatases is an important feature of these regulatory mechanisms.
Mutants of the CMP-sialic Acid Transporter Causing the Lec2 Phenotype (1998)

Chinese hamster ovary (CHO) mutants belonging to the Lec2 complementation group are unable to translocate CMP-sialic acid to the lumen of the Golgi apparatus. Complementation cloning in these cells has recently been used to isolate cDNAs encoding the CMP-sialic acid transporter from mouse and hamster. The present study was carried out to determine the molecular defects leading to the inactivation of CMP-sialic acid transport. To this end, CMP-sialic acid transporter cDNAs derived from five independent clones of the Lec2 complementation group, were analyzed. Deletions in the coding region were observed for three clones, and single mutants were found to contain an insertion and a point mutation. Epitope-tagged variants of the wild-type transporter protein and of the mutants were used to investigate the effect of the structural changes on the expression and subcellular targeting of the transporter proteins. Mutants derived from deletions showed reduced protein expression and in immunofluorescence showed a diffuse staining throughout the cytoplasm in transiently transfected cells, while the translation product derived from the point-mutated cDNA (G189E) was expressed at the level of the wild-type transporter and co-localized with the Golgi marker alpha-mannosidase II. This mutation therefore seems to directly affect the transport activity. Site-directed mutagenesis was used to change glycine 189 into alanine, glutamine, and isoleucine, respectively. While the G189A mutant was able to complement CMP-sialic acid transport-deficient Chinese hamster ovary mutants, the exchange of glycine 189 into glutamine or isoleucine dramatically affected the transport activity of the CMP-sialic acid transporter.
Theoretically informed coarse grain simulations of block copolymer melts: method and applications (2009)

A newly developed formalism is described, in which models that have been traditionally addressed using field-theoretic methods are solved by resorting to Monte Carlo simulations in arbitrary ensembles. In the context of block copolymer melts, the formalism starts from a standard, field-based Hamiltonian, but describes the polymeric chains explicitly, as collections of beads connected by springs, and incorporates the effects of fluctuations. The general applicability of the method is illustrated by discussing several examples from the recent literature, including the effect of fluctuations on the order–disorder transition of diblock copolymers, the morphology of linear triblock copolymers, the directed assembly of copolymer on nanopatterned substrates, and the hierarchical assembly of nanoparticle-copolymer mixtures.
Experience in the use of clobazam in the treatment of Lennox–Gastaut syndrome (2014)

Clobazam is a 1,5-benzodiazepine used successfully worldwide since the 1970s as an anxiolytic and antiepileptic drug. Since its recent Food and Drug Administration (FDA) approval in the United States in 2011 as adjunctive treatment for Lennox-Gastaut syndrome, it has continued to show sustained efficacy and a better safety and tolerability profile compared with other benzodiazepines. The two randomized, controlled studies that led to the US FDA approval, as well as the follow-up multicenter, open-label study of clobazam, showed ≥50% seizure reduction for more than 50% of Lennox-Gastaut syndrome patients, while none of the other FDA-approved treatments for LGS have demonstrated efficacy rates better than 50%. Clobazam appears to have a safe profile and sustained effectiveness over the first 3 years of use in LGS and other epilepsy syndromes with intractable seizures, which makes it a viable long-term treatment option.
Identification of Apoptosis-associated Proteins in a Human Burkitt Lymphoma Cell Line (1998)

Apoptosis or programmed cell death is essential in the process of controlling lymphocyte growth and selection. We identified proteins that are involved in anti-IgM antibody-mediated apoptosis using a subclone of the human Burkitt lymphoma cell line BL60. Apoptosis-associated proteins were detected by high resolution two-dimensional gel electrophoresis on a micropreparative scale. Comparison of the high resolution two-dimensional gel electrophoresis protein patterns from apoptotic and non-apoptotic cells showed differences in approximately 80 spots including protein modifications. Analysis of the predominantly altered proteins was performed by internal Edman microsequencing and/or by peptide mass fingerprinting using matrix-assisted laser desorption/ionization mass spectrometry. Analysis was significantly improved by using new micropreparative high resolution two-dimensional gels employing high protein concentrations. The following 12 apoptosis-associated proteins were identified: heterogeneous nuclear ribonucleoprotein (hnRNP) A1, hnRNP C1/C2, FUSE-binding protein, dUTPase, lymphocyte-specific protein LSP1, UV excision repair protein RAD23 homologue B (HHR23B), 60 S acidic ribosomal protein P0 (L10E), heterochromatin protein 1 homologue alpha (HP1alpha), nucleolin, lamin, neutral calponin, and actin. Fragmentation of actin, hnRNP A1, hnRNP C1/C2, 60 S acidic ribosomal protein P0, lamin, and nucleolin could be inhibited by benzyloxycarbonyl-Asp(OMe)-Glu(OMe)-Val-Asp(OMe)-fluoromethyl ketone, a selective irreversible inhibitor of CPP32 (caspase 3).
A Tonic Hyperpolarization Underlying Contrast Adaptation in Cat Visual Cortex (1997)

The firing rate responses of neurons in the primary visual cortex grow with stimulus contrast, the variation in the luminance of an image relative to the mean luminance. These responses, however, are reduced after a cell is exposed for prolonged periods to high-contrast visual stimuli. This phenomenon, known as contrast adaptation, occurs in the cortex and is not present at earlier stages of visual processing. To investigate the cellular mechanisms underlying cortical adaptation, intracellular recordings were performed in the visual cortex of cats, and the effects of prolonged visual stimulation were studied. Surprisingly, contrast adaptation barely affected the stimulus-driven modulations in the membrane potential of cortical cells. Moreover, it did not produce sizable changes in membrane resistance. The major effect of adaptation, evident both in the presence and in the absence of a visual stimulus, was a tonic hyperpolarization. Adaptation affects a class of synaptic inputs, most likely excitatory in nature, that exert a tonic influence on cortical cells.
Effects of Size and Number Density of Micro-reentrant Cavities on Boiling Heat Transfer from a Silicon Chip Immersed in Degassed and Gas-dissolved FC-72 (1999)

Boiling heat transfer of FC-72 from newly developed treated surfaces with micro-reentrant cavities was studied experimentally. The surface structure was fabricated on a silicon chip by use of microelectronic fabrication techniques. Four kinds of treated surfaces with the combinations of two cavity mouth diameters (about 1.6 μm and 3.1 μm) and two number densities of the micro-reentrant cavities (81 l/cm2 and 96 × 103 l/cm2) were tested along with a smooth surface. Experiments were conducted at the liquid subcoolings of 3 K and 25 K with degassed and gas-dissolved FC-72. While the wall superheat at boiling incipience was strongly dependent on the dissolved gas content; it was little affected by the cavity mouth diameter and the liquid subcooling. The heat transfer performance of the treated surface was considerably higher than that of the smooth surface. The highest performance was obtained with a treated surface with a larger cavity mouth diameter and a larger cavity number density. The results were compared with those for previously developed treated surfaces.
Switching base preferences of mismatch cleavage in endonuclease V: an improved method for scanning point mutations (2006)

Endonuclease V (endo V) recognizes a broad range of aberrations in DNA such as deaminated bases or mismatches. It nicks DNA at the second phosphodiester bond 3' to a deaminated base or a mismatch. Endonuclease V obtained from Thermotoga maritima preferentially cleaves purine mismatches in certain sequence context. Endonuclease V has been combined with a high-fidelity DNA ligase to develop an enzymatic method for mutation scanning. A biochemical screening of site-directed mutants identified mutants in motifs III and IV that altered the base preferences in mismatch cleavage. Most profoundly, a single alanine substitution at Y80 position switched the enzyme to essentially a C-specific mismatch endonuclease, which recognized and cleaved A/C, C/A, T/C, C/T and even the previously refractory C/C mismatches. Y80A can also detect the G13D mutation in K-ras oncogene, an A/C mismatch embedded in a G/C rich sequence context that was previously inaccessible using the wild-type endo V. This investigation offers insights on base recognition and active site organization. Protein engineering in endo V may translate into better tools in mutation recognition and cancer mutation scanning.
Imaging-based stereotaxic serial biopsies in untreated intracranial glial neoplasms (1987)

Forty patients with previously untreated intracranial glial neoplasms underwent stereotaxic serial biopsies assisted by computerized tomography (CT) and magnetic resonance imaging (MRI). Tumor volumes defined by computer reconstruction of contrast enhancement and low-attenuation boundaries on CT and T1 and T2 prolongation on MRI revealed that tumor volumes defined by T2-weighted MRI scans were larger than those defined by low-attenuation or contrast enhancement on CT scans. Histological analysis of 195 biopsy specimens obtained from various locations within the volumes defined by CT and MRI revealed that: contrast enhancement most often corresponded to tumor tissue without intervening parenchyma; hypodensity corresponded to parenchyma infiltrated by isolated tumor cells or in some instances to tumor tissue in low-grade gliomas or to simple edema; and isolated tumor cell infiltration extended at least as far as T2 prolongation on magnetic resonance images. This information may be useful in planning surgical procedures and radiation therapy in patients with intracranial glial neoplasms.
Realizing the full potential of electronic health records: the role of natural language processing (2011)

Meaningful use of electronic health records (EHRs) for patient care or for research requires data to be comparable. Many portions of EHRs continue to be unstructured, presenting significant challenges for biomedical informatics. This issue of the journal displays several solutions to this problem that are based on natural language processing (NLP) techniques. A high-level review by Nadkarni ( see page 544 ) is intended to introduce the main components of NLP for the novice, and to briefly describe machine learning methods that are successfully being employed in the field. It includes a discussion on Watson, a contestant on ‘Jeopardy!,’ a popular question-and-answer TV show, and the ensuing speculations about its potential extensions to medical NLP. However, despite some notable examples of successful NLP applications in clinical care, progress in the field has been relatively slow.

Chapman and colleagues ( see page 540 ) discuss the need to steer current NLP research efforts so that new developments can be accelerated, and research products can become readily usable in healthcare applications. The authors advocate for a concerted, collaborative effort to develop open-source software components and infrastructure to share annotated data and tools. The guest editorial raises important questions …
Delivering hydrophilic and hydrophobic chemotherapeutics simultaneously by magnetic mesoporous silica nanoparticles to inhibit cancer cells (2012)

Using nanoparticles to deliver chemotherapeutics offers new opportunities for cancer therapy, but challenges still remain when they are used for the delivery of multiple drugs, especially for the synchronous delivery of hydrophilic and hydrophobic drugs in combination therapies. In this paper, we developed an approach to deliver hydrophilic-hydrophobic anticancer drug pairs by employing magnetic mesoporous silica nanoparticles (MMSNs). We prepared 50 nm-sized MMSNs with uniform pore size and evaluated their capability for the loading of two combinations of chemotherapeutics, namely doxorubicin-paclitaxel and doxorubicin-rapamycin, by means of sequential adsorption from the aqueous solution of doxorubicin and nonaqueous solutions of paclitaxel or rapamycin. Experimental results showed that the present strategy successfully realized the co-loading of hydrophilic and hydrophobic drugs with high-loading content and widely tunable ratio range. We elaborate on the theory behind the molecular interaction between the silica hydroxyl groups and drug molecules, which underlie the controllable loading, and the subsequent release of the drug pairs. Then we demonstrate that the multidrug-loaded MMSNs could be easily internalized by A549 human pulmonary adenocarcinoma cells, and produce enhanced tumor cell apoptosis and growth inhibition as compared to single-drug loaded MMSNs. Our study thus realized simultaneous and dose-tunable delivery of hydrophilic and hydrophobic drugs, which were endowed with improved anticancer efficacy. This strategy could be readily extended to other chemotherapeutic combinations and might have clinically translatable significance.
Light‐dependent Oxygen Consumption in Bacteriochlorophyll‐Serine‐treated Melanoma Tumors: On‐line Determination Using a Tissue‐inserted Oxygen Microsensor (1997)

Successful application of anticancer therapy, and especially photodynamic therapy (PDT) mediated by type II (PDTII) processes, depends on the oxygen content within the tumor before, during and after treatment. The high consumption of oxygen during type II PDT imposes constraints on therapy strategies. Although rates of oxygen consumption and repletion during PDTII were suggested by theoretical studies, direct measurements have not been reported. Application of a novel oxygen sensor allowed continuous and direct in situ measurements (up to a depth of 8-9 mm from the tumor surface and for several hours) of temporal variations in the oxygen partial pressure (pO2) during PDT. Highly pigmented M2R mouse melanoma tumors implanted in CD1 nude mice were treated with bacteriochlorophyll-serine (Bchl-Ser; a new photodynamic reagent) and were subjected to fractionated illumination (700 < lambda < 900 nm) at a fluence rate of 12 mW cm-2. This illumination led to total oxygen depletion with an average consumption rate of 7.2 microM(O2) s-1. Spontaneous reoxygenation (at an average rate of 2.5 microM(O2)/s) was observed during the following dark period. These rates are in good agreement with theoretical considerations (Foster et al., Radiat. Res. 126, 296, 1991 and Henning et al., Radiat. Res. 142, 221, 1995). The observed patterns of oxygen consumption and recovery during prolonged periods of light/dark cycles were interpreted in terms of vasculature damage and sensitizer clearance. The presented data support the previously suggested advantages of fractionated illumination for type II photodynamic processes.
Frequent amplification of the bcl-1 locus in head and neck squamous cell carcinomas. (1989)

The bcl-1 locus on chromosome 11 at band q13 has been shown to be rearranged in some chronic B lymphoid malignancies with the t(11;14)(q13;q32). Chromosome 11 abnormalities also occur in squamous cell carcinomas including tumors from the head and neck region. In this investigation, we analysed the arrangement, copy number and expression of this locus in 23 fresh head and neck cancers and six established head and neck squamous cell carcinoma cell lines. Bcl-1 was found to be amplified two- to 10-fold in eight fresh tumors and two cell lines, UM-SCC-8 and UM-SCC-22A. Moreover, amplification was more frequently observed in poorly differentiated fresh tumors. None of the fresh tumors or cell lines showed rearrangement of bcl-1. In addition, these tumors and cell lines did not contain amplification of the c-myc or Ha-ras oncogenes.
Infliximab for patients with refractory ulcerative colitis (2001)

Conventional treatment options for patients with severe corticosteroid-refractory ulcerative colitis (UC) include intravenous cyclosporine, which is frequently limited by toxicity, or colectomy. The efficacy of infliximab was investigated in the treatment of 16 patients with severely active UC refractory to conventional therapy; 7 of these patients were considered for colectomy pending medical failure. All patients received a single infusion of infliximab, 5 mg/kg; 6 of 16 patients (38%) received a second infusion approximately 5 months later. Efficacy was assessed by clinical response (defined as the lack of symptoms) as well as endoscopic and histologic outcomes. Clinical, endoscopic, and histologic improvement was observed in 14 of 16 patients (88%) after treatment with infliximab. Surgery was avoided in six of seven surgical candidates (86%). Clinical remission was maintained in 14 of 16 patients (88%) for > or = 4 months, and 4 of 16 patients (25%) for 7-10 months. Most of the treated patients were completely withdrawn from corticosteroid therapy. Treatment with infliximab induced endoscopic remission at 30 days and a significant improvement from baseline in mean histologic score (p < 0.001). In conclusion, infliximab improved clinical, endoscopic, and histologic outcomes in patients with severely active UC refractory to conventional therapy, allowing corticosteroid sparing and reducing the need for colectomy.