gebhart/patrepeval huggingface dataset:
Potentially Lethal Damage versus Sublethal Damage: Independent Repair Processes in Actively Growing Chinese Hamster Cells (1979)

H. Utsumi, M. M. Elkind, Potentially Lethal Damage versus Sublethal Damage: Independent Repair Processes in Actively Growing Chinese Hamster Cells, Radiation Research, Vol. 77, No. 2 (Feb., 1979), pp. 346-360
Transgenic expression of aminoglycoside adenine transferase in the chloroplast: a selectable marker for site-directed transformation of chlamydomonas (1991)

Expression vectors for Chlamydomonas reinhardtii chloroplast transformation have been constructed with transcription and translation signals from chloroplast genes. The bacterial aadA sequence, coding for aminoglycoside 3" adenyl transferase, was inserted in these vectors and introduced into the C. reinhardtii chloroplast by particle gun transformation. The stable transgenic expression of this foreign protein in the chloroplast confers spectinomycin and streptomycin resistance to the transformed cells. This new marker can be used as a reporter of gene expression, and as a portable selectable cassette for chloroplast reverse genetics. Targetted gene disruption mutants of loci required for photosynthesis, tscA and psaC, were thus obtained. A gene disruption of an unidentified open reading frame, ORF472, remained heteroplasmic, suggesting that it has a vital function.
A new concept in colonic drug targeting: a combined pH‐responsive and bacterially‐triggered drug delivery technology (2008)

The dual-mechanism (pH/bacterial) coating provides colon-specificity. Each trigger mechanism has the capacity to act as a failsafe, ensuring appropriate targeting in the gastrointestinal tract. This platform technology has potential for systemic applications or the treatment of local disorders of the large intestine, such as inflammatory bowel disease.
Evaluation of regional gastrointestinal absorption of edoxaban using the enterion capsule (2015)

Two studies in healthy subjects assessed the absorption of edoxaban when delivered to specific locations within the gastrointestinal tract using Enterion capsules. In study 1 (single-dose, 4-way crossover), 8 participants received edoxaban 60 mg as immediate-release (IR) tablets (treatment A), as powder formulation delivered to the distal small bowel (treatment B) or ascending colon (treatment C), or as an aqueous suspension delivered to the ascending colon (treatment D). In study 2 (single-dose, 2-way crossover), 10 participants received edoxaban 30 mg as IR tablets (treatment E) or in granulate formulation with fumaric acid 50 mg, added to acidify the local gastrointestinal tract and enhance solubility, delivered to the ascending colon (treatment F). Peak and total exposure following targeted drug delivery to the distal gastrointestinal tract were significantly lower than with IR tablet delivery. In study 1, total exposure ratios of treatments B, C, and D compared with A were 14.9%, 7.9%, and 6.1%, respectively. In study 2, relative total exposure was 12.6% for treatment F despite the fumaric acid. Time to peak concentration was longer with higher variability for edoxaban delivered to the distal gastrointestinal tract compared with the IR tablet. These data indicate that edoxaban absorption occurs predominantly in the proximal small intestine.
Mammary epithelial-specific disruption of the focal adhesion kinase blocks mammary tumor progression (2007)

Elevated expression and activation of the focal adhesion kinase (FAK) occurs in a large proportion of human breast cancers. Although several studies have implicated FAK as an important signaling molecule in cell culture systems, evidence supporting a role for FAK in mammary tumor progression is lacking. To directly assess the role of FAK in this process, we have used the Cre/loxP recombination system to disrupt FAK function in the mammary epithelium of a transgenic model of breast cancer. Using this approach, we demonstrate that FAK expression is required for the transition of premalignant hyperplasias to carcinomas and their subsequent metastases. This dramatic block in tumor progression was further correlated with impaired mammary epithelial proliferation. These observations provide direct evidence that FAK plays a critical role in mammary tumor progression.
Fluorine compounds in anaesthesia (9) (1982)

Six heavily fluorinated aliphatic compounds and four heavily fluorinated derivatives of diethyl ether have been examined as anaesthetics, using mice. Two compounds are felt to be worth further examination. These are 1,1,1,-trifluoro-2,2-dichloroethane (halothane with the bromine atom replaced by a second chlorine) and 1,1,2,2,4,5,5-heptafluoro-3-oxapentane (ordinary diethyl ether with seven hydrogen atoms replaced by fluorine).
Prospective controlled study of microbial colonization of the trachea in tracheotomized and laryngectomized patients with HME (heat and moisture exchanger) (2008)

In all three groups, Staphylococcus aureus and Candida albicans were most frequently demonstrated. The microbial count of facultative pathogenic agents ranged between 3×10(2) colony forming units (cfu)/ml and 10(6) cfu/ml and was similar in the three groups. With respect to the absence of inflammatory symptoms in every patient, all isolates could be regarded as colonizers. Among the antibiotics tested with each isolate, cefuroxime proved to be the most effective against the facultative pathogenic bacteria.
Growth and Differentiation of Human Adipose Stromal Cells in Culture (2003)

Human adipose stromal cells provide an excellent model for studying a variety of metabolic processes in an in vitro system These are normal cells derived from subcutaneous or omental adipose tissue. Under specific culture condition, they will differentiate without replication into cells resembling mature adipocytes or will replicate, become confluent, and grow in subculture. The initial observation that the stromal vascular fraction of human omental adipose tissue contained a fibroblast-like cell that was a possible adipocyte precursor was made by Poznanski et al (1). Subsequent studies demonstrated enzymological and morphological properties that developed during differentiation (2-4). The primary interest has focused on the conditions required to stimulate these cells to differentiate into adipocytes, which can accumulate lipid and possess the enzymes involved in lipogenesis, including glycerol-3-phosphate dehydrogenase (GPDH) and lipoprotein lipase (LPL).
A Physically Transient Form of Silicon Electronics (2012)

A remarkable feature of modern silicon electronics is its ability to remain physically invariant, almost indefinitely for practical purposes. Although this characteristic is a hallmark of applications of integrated circuits that exist today, there might be opportunities for systems that offer the opposite behavior, such as implantable devices that function for medically useful time frames but then completely disappear via resorption by the body. We report a set of materials, manufacturing schemes, device components, and theoretical design tools for a silicon-based complementary metal oxide semiconductor (CMOS) technology that has this type of transient behavior, together with integrated sensors, actuators, power supply systems, and wireless control strategies. An implantable transient device that acts as a programmable nonantibiotic bacteriocide provides a system-level example.
Metal-Semiconductor Nanocontacts: Silicon Nanowires (2000)

Silicon nanowires assembled from clusters or etched from the bulk, connected to aluminum electrodes and passivated, are studied with large-scale local-density-functional simulations. Short ( approximately 0.6 nm) wires are fully metallized by metal-induced gap states resulting in finite conductance ( approximately e(2)/h). For longer wires ( approximately 2.5 nm) nanoscale Schottky barriers develop with heights larger than the corresponding bulk value by 40% to 90%. Electric transport requires doping dependent gate voltages with the conductance spectra exhibiting interference resonances due to scattering of ballistic channels by the contacts.
CLOSTRIDIUM DIFFICILE TOXINS A AND B CAN ALTER EPITHELIAL PERMEABILITY AND PROMOTE BACTERIAL PARACELLULAR MIGRATION THROUGH HT-29 ENTEROCYTES (2000)

Clostridium difficile toxins A and B are the widely recognized etiologic agents of antibiotic-associated diseases ranging from diarrhea to pseudomembranous colitis. We hypothesized that C. difficile toxins may alter intestinal epithelial permeability and facilitate bacterial penetration of the intestinal epithelial barrier. Experiments were designed to clarify the effects of C. difficile toxins A and B on the flux of inert particles across HT-29 enterocyte monolayers, and to correlate these results with bacteria-enterocyte interactions. In all experiments, mature, confluent HT-29 cultures were preincubated 16 h with toxin A or B (1-100 ng/mL). To study alterations in epithelial permeability, toxin-treated enterocytes were incubated with 5 pM solutions of 10- and 40-kD inert dextran particles. Toxin A, but not toxin B, was associated with increased dextran flux through enterocyte monolayers. To study bacteria-enterocyte interactions, toxin-treated enterocytes were incubated with 10(8) Salmonella typhimurium, Proteus mirabilis, or Escherichia coli. Although numbers of internalized bacteria were generally unaffected, both toxins were associated with increased bacterial adherence, as well as increased bacterial transmigration through enterocyte monolayers. Bacterial transmigration was significantly greater using toxin A- compared to toxin B-treated enterocytes, consistent with the observation that dextran flux was significantly greater using toxin A- compared to toxin B-treated enterocytes. Thus intestinal colonization with toxigenic C. difficile may facilitate bacterial penetration of the intestinal epithelium by a mechanism involving increased permeability of the intestinal epithelial barrier.
A “Click Chemistry” Approach to the Efficient Synthesis of Multiple Imaging Probes Derived from a Single Precursor (2009)

Different imaging modalities can provide complementary information on biological processes at the cellular or molecular level in vitro and in vivo. However, specific molecular probes suitable for a comparison of different imaging modalities are often not readily accessible because their preparation is usually accomplished by individually developed and optimized syntheses. Herein, we present a general, modular synthetic approach that provides access to multiple probes derived from a single precursor by application of the same, efficient functionalization strategy, the Cu(I)-catalyzed cycloaddition of terminal alkynes and azides (click chemistry). To demonstrate the viability and efficiency of this approach, folic acid (FA) was selected as a targeting vector because the preparation of FA-based imaging probes used for SPECT, PET, MRI, and NIRF by reported synthetic strategies is usually difficult to achieve and often results in low overall yields. We prepared a versatile γ-azido-FA precursor as well as a set of alkyne functionalized probes and precursors including ligand systems suitable for the chelation of various (radio)metals, an NIR dye and (18)F- and (19)F-derivatives, which enabled the parallel development of new FA-imaging probes. The Cu(I)-mediated coupling of the alkynes with the γ-azido-FA precursor was accomplished in high yields and with minimal use of protective groups. The various probes were fully characterized spectroscopically as well as in vitro and in vivo. In vitro, all new FA-derivatives exhibited high affinity toward the folic acid receptor (FR) and/or were specifically internalized into FR-overexpressing KB cells. In vivo experiments with nude mice showed that all probes (except the MRI probes which have not been tested yet) accumulated specifically in FR-positive organs and human KB-cell xenografts. However, in vivo imaging revealed significant differences between the various FA-derivatives with respect to unspecific, off-target localization. In general, the comparison of different probes proved the superiority of the more hydrophilic, radiometal-based imaging agents, a result which will guide future efforts for the development of FA-based imaging probes and therapeutic agents. In addition, the strategy presented herein should be readily applicable to other molecules of interest for imaging and therapeutic purposes and thus represents a valuable alternative to other synthetic approaches.
Contact leakage and open monitoring with an advanced e-beam inspection system (2007)

In this study, we used optimized negative mode to detect N+/P-well contact open and P+/N-well contact leakage. We found the optimized contact process condition to eliminate both contact open and leakage. Electron beam (e-beam) inspection results strongly correlate with die yield. We implemented negative mode e-beam defect inspection along with positive mode inspection for effective inline monitoring to accelerate the 65 nm process yield ramp.
Identification of the SecA protein homolog in pea chloroplasts and its possible involvement in thylakoidal protein transport. (1994)

Recently, we identified the SecA and SecY proteins in the cyanobacterium Synechococcus PCC7942. Antibodies raised against cyanobacterial SecA specifically reacted with a 110-kDa protein of pea chloroplasts, suggesting the presence of SecA in higher plant chloroplasts. A part of the pea secA cDNA was polymerase chain reaction-amplified with degenerated oligonucleotide primers and with pea cDNA as a template. The deduced amino acid sequence shows 62% identity with cyanobacterial SecA and 52% identity with Escherichia coli SecA. Antibodies raised against the pea SecA fragment, which was expressed in E. coli cells from the obtained polymerase chain reaction-amplified cDNA, reacted with the 110-kDa chloroplast protein; the 110-kDa protein was mainly found in the stroma but partly in the thylakoid membrane. The anti-pea SecA IgG inhibited the in vitro import of the 33-kDa protein of the oxygen-evolving complex, but not of the 23-kDa protein of the oxygen-evolving complex, into thylakoids. These results suggest that SecA facilitates transport of a subset of thylakoid lumenal proteins including the 33-kDa protein into thylakoids. We propose that a bacterial-type Sec protein-dependent transport system operates for protein transport into thylakoids in higher plant chloroplasts.
Histone Deacetylase Inhibitors through Click Chemistry (2008)

Histone deacetylase inhibitors (HDACi) are a relatively new class of chemotherapy agents. Herein, we report a click-chemistry based approach to the synthesis of HDACi. Fourteen agents were synthesized from the combination of two alkyne and seven azido precursors. The inhibition of HDAC1 and HDAC8 was then determined by in vitro enzymatic assays, after which the cytotoxicity was evaluated in the NCI human cancer cell line screen. A lead compound 5 g (NSC746457) was discovered that inhibited HDAC1 at an IC(50) value of 104 +/- 30 nM and proved quite potent in the cancer cell line screen with GI(50) values ranging from 3.92 microM to 10 nM. Thus, this click HDACi design has provided a new chemical scaffold that has not only revealed a lead compound, but one which is easily amendable to further structural modifications given the modular nature of this approach.
Expression profiles of MUC1, MUC2, and MUC4 mucins in human neoplasms and their relationship with biological behavior (2008)

Mucins are high molecular weight glycoproteins that play important roles in carcinogenesis or tumor invasion. To clarify the relationship of the expression patterns of mucins in human neoplasms with their biological behavior, we examined the expression profiles of MUC1, MUC2, and MUC4 mucins in various human neoplasms using immunohistochemistry and in situ hybridization, and compared them with clinicopathologic factors including outcome of the patients. MUC1 or MUC4 expression is related with the aggressive behavior of human neoplasms and a poor outcome of the patients. In contrast, MUC2 expression tends to be related with the indolent behavior of human neoplasms and a favorable outcome of the patients, although indolent pancreatobiliary neoplasms sometimes show invasive growth with MUC1 expression in the invasive areas. The expression of MUC2 mucin in indolent pancreatobiliary neoplasms coincided with expression of MUC2 mRNA. Our recent studies to clarify the MUC2 gene regulation mechanism disclosed that DNA methylation and histone modification in the 5' flanking region of the MUC2 promoter may play an important role. Further studies of the epigenetics also in MUC1 and MUC4 gene expression may be needed to understand the relationship between the expression of mucins in human neoplasms with their biological behavior.
Environment matting extensions (2000)

Environment matting is a generalization of traditional bluescreen matting. By photographing an object in front of a sequence of structured light backdrops, a set of approximate light-transport paths through the object can be computed. The original environment matting research chose a middle ground—using a moderate number of photographs to produce results that were reasonably accurate for many objects. In this work, we extend the technique in two opposite directions: recovering a more accurate model at the expense of using additional structured light backdrops, and obtaining a simplified matte using just a single backdrop. The first extension allows for the capture of complex and subtle interactions of light with objects, while the second allows for video capture of colorless objects in motion.
Communication-optimal parallel and sequential QR and LU factorizations (2008)

We present parallel and sequential dense QR factorization algorithms that are both optimal (up to polylogarithmic factors) in the amount of communication they perform, and just as stable as Householder QR. We prove optimality by extending known lower bounds on communication bandwidth for sequential and parallel matrix multiplication to provide latency lower bounds, and show these bounds apply to the LU and QR decompositions. We not only show that our QR algorithms attain these lower bounds (up to polylogarithmic factors), but that existing LAPACK and ScaLAPACK algorithms perform asymptotically more communication. We also point out recent LU algorithms in the literature that attain at least some of these lower bounds.
T-cell receptor genes in autoimmune mice: T-cell subsets have unexpected T-cell receptor gene programs. (1987)

Two unique cell subsets have been identified in the autoimmune-prone MRL/MP lpr/lpr and C3H/HeJ gld/gld murine strains that have the Lyt-2-,L3T4-,Thy-1+, and Lyt-2-,L3T4-,Ia-,Thy-1- phenotypes, respectively. We have now found that these cells express T-cell receptor proteins on their surface. Our observations further indicate that the expression of the Thy-1 antigen does not correlate with the expression of alpha-chain and beta-chain T-cell receptor polypeptides. Interestingly, T-cell receptor gamma-chain RNA expression may be influenced or correlate with Thy-1 molecular expression. These studies indicate unusual relationships of different cell-surface structures that may reflect unexpected developmental programs.
NMR Solution Structure and Membrane Interaction of the N-Terminal Sequence (1−30) of the Bovine Prion Protein (2004)

The structure and membrane interaction of the N-terminal sequence (1−30) of the bovine prion protein (bPrPp) has been investigated by NMR spectroscopy in phospholipid membrane mimetic systems. CD spectroscopy revealed that the peptide adopts a largely α-helical structure in zwitterionic bicelles as well as in DHPC micelles but has a less degree of α-helix structure in partly charged bicelles. The solution structure of bPrPp was determined in DHPC micelles, and an α-helix was found between residues Ser8 and Ile21. The residues within the helical region show slow amide hydrogen exchange. Translational diffusion measurements in zwitterionic q = 0.5 bicelles show that the peptide does not induce aggregation of the bicelles. Increased quadrupolar splittings were observed in the outer part of the 2H spectrum of DMPC in q = 3.5 bicelles, indicating that the peptide induces a certain degree of order in the bilayer. The amide hydrogen exchange and the 2H NMR results are consistent with a slight positive hydrophobic mismatch and that bPrPp forms a stable helix that inserts in a transmembrane location in the bilayer. The structure of bPrPp and its position in the membrane may be relevant for the understanding of how the N-terminal (1−30) part of the bovine PrP functions as a cell-penetrating peptide. These findings may lead to a better understanding of how the prion protein accumulates at the membrane surface and also how the conversion into the scrapie form is carried out.
All digital phase-locked loop: concepts, design and applications (1989)

The concepts of an all digital phase-locked loop (DPLL), which contains a purely digital phase detector, loop filter and voltage-controlled oscillator, are explained. A second order DPLL is considered and analysed using the Z-transform technique. Implementation of the DPLL, based on the CMOS digital signal processor TMS 320C25, and the experimental results, are presented. Potential applications are also discussed.
Polymorphic variation at the serotonin 1-A receptor gene is associated with comorbid depression and generalized anxiety (2011)

In our study, the HTR1A C(-1019)G polymorphism was found to be associated to the frequent clinical presentation of comorbid MD and GAD, suggesting a common genetic background for mixed depression and anxiety states. These findings should be considered as preliminary. Future replications in independent samples would be needed to confirm or discard such association.
cDNA structures and regulation of two interferon-induced human Mx proteins. (1989)

Human cells treated with interferon synthesize two proteins that exhibit high homology to murine Mx1 protein, which has previously been identified as the mediator of interferon-induced cellular resistance of mouse cells against influenza viruses. Using murine Mx1 cDNA as a hybridization probe, we have isolated cDNA clones originating from two distinct human Mx genes, designated MxA and MxB. In human fibroblasts, expression of MxA and MxB is strongly induced by alpha interferon (IFN-alpha), IFN-beta, Newcastle disease virus, and, to a much lesser extent, IFN-gamma, MxA and MxB proteins have molecular masses of 76 and 73 kilodaltons, respectively, and their sequences are 63% identical. A comparison of human and mouse Mx proteins revealed that human MxA and mouse Mx2 are the most closely related proteins, showing 77% sequence identity. Near their amino termini, human and mouse Mx proteins contain a block of 53 identical amino acids and additional regions of very high sequence similarity. These conserved sequences are also present in a double-stranded RNA-inducible fish gene, which suggests that they may constitute a functionally important domain of Mx proteins. In contrast to mouse Mx1 protein, which accumulates in the nuclei of IFN-treated mouse cells, the two human Mx proteins both accumulate in the cytoplasm of IFN-treated cells.