gebhart/patrepeval huggingface dataset:
Development of a Closed Bioreactor System for Culture of Tissue-Engineered Skin at an Air–Liquid Interface (2005)

A bioreactor has been developed for the production of tissue-engineered skin at an air-liquid interface for clinical and experimental use. In this closed system, scaffold and bioreactor sterilization, cell seeding, and medium perfusion were all performed with a peristaltic pump. Natural and synthetic dermal substitutes were seeded directly with skin cells without opening the bioreactor and fed either by continuous medium perfusion or by batch-feed. The system was validated by monoculture of human dermal fibroblasts and keratinocytes and the coculture of both cell types in acellular human dermis, Azowipes, electrospun polystyrene, and an electrospun composite of polystyrene and poly-DL-lactide fibers. A comparison was made of culture at an air-liquid interface versus submerged culture and of medium change by continuous perfusion versus batch-feed. Fibroblast and endothelial cells showed greater viability under submerged rather than air-liquid conditions whereas keratinocytes favored culture at an air-liquid interface as did cocultured keratinocytes and fibroblasts. Total cellular viability for reconstructed skin with keratinocytes and fibroblasts was greatest with continuous perfusion rather than batch-feed and with electrospun scaffolds compared with acellular human dermis. The bioreactor could also be easily configured to give replicate small areas for experimental use or one continuous area of construct for clinical use.
Viscoelastic Properties and Dynamics of Porcine Gastric Mucin (2005)

Gastric mucin is a glycoprotein known to undergo a pH-dependent sol-gel transition that is crucial to the protective function of the gastric mucus layer in mammalian stomachs. We present microscope-based dynamic light scattering data on porcine gastric mucin at pH 6 (solution) and pH 2 (gel) with and without the presence of tracer particles. The data provide a measurement of the microscale viscosity and the shear elastic modulus as well as an estimate of the mesh size of the gel formed at pH 2. We observe that the microscale viscosity in the gel is about 100-fold lower than its macroscopic viscosity, suggesting that large pores open up in the gel reducing frictional effects. The data presented here help to characterize physiologically relevant viscoelastic properties of an important biological macromolecule and may also serve to shed light on diffusive motion of small particles in the complex heterogeneous environment of a polymer gel network.
Structural Basis of Transcription Initiation: RNA Polymerase Holoenzyme at 4 Å Resolution (2002)

The crystal structure of the initiating form of Thermus aquaticus RNA polymerase, containing core RNA polymerase (alpha2betabeta'omega) and the promoter specificity sigma subunit, has been determined at 4 angstrom resolution. Important structural features of the RNA polymerase and their roles in positioning sigma within the initiation complex are delineated, as well as the role played by sigma in modulating the opening of the RNA polymerase active-site channel. The two carboxyl-terminal domains of sigma are separated by 45 angstroms on the surface of the RNA polymerase, but are linked by an extended loop. The loop winds near the RNA polymerase active site, where it may play a role in initiating nucleotide substrate binding, and out through the RNA exit channel. The advancing RNA transcript must displace the loop, leading to abortive initiation and ultimately to sigma release.
Characterization and Biocompatibility Studies of Novel Humic Acids Based Films as Membrane Material for an Implantable Glucose Sensor (2001)

Multilayered films of humic acids (HAs) (naturally occurring biopolymers) were investigated as a potential semipermeable membrane for implantable glucose sensors. These films were grown using a layer-by-layer self-assembly process of HAs and oppositely charged ferric ions. The growth of these assemblies exhibited strong dependence on the pH and ionic strength of HAs solutions, which correlated with the degree of ionization of the carboxyl groups and neutralization-induced surface spreading. Quartz crystal microbalance (QCM) and ellipsometric studies have shown repeatable, stepwise increase in mass (as high as 5.63 microg/cm(2)) and in film thickness (ca. 24.3 nm per layer) for these assemblies. The permeability of glucose through these membranes can be regulated by varying the number of self-assembled HAs/Fe(3+) layers. Moreover, a 200 nm thick HAs/Fe(3+) film (in its hydrated state) had a shear modulus of about 80 MPa, implying stability upon implantation. These films were determined to be biocompatible since in vivo studies indicated only mild tissue reaction along with some neovascularization.
Location and Chemical Synthesis of a Binding Site for HIV-1 on the CD4 Protein (1988)

The human immunodeficiency virus type 1 (HIV-1) uses the CD4 protein as a receptor for infection of susceptible cells. A candidate structure for the HIV-1 binding site on the CD4 protein was identified by epitope mapping with a family of eight functionally distinct CD4-specific monoclonal antibodies in conjunction with a panel of large CD4-derived synthetic peptides. All of the seven epitopes that were located reside within two immunoglobulin-like disulfide loops situated between residues 1 and 168 of the CD4 protein. The CD4-specific monoclonal antibody OKT4A, a potent inhibitor of HIV-1 binding, recognized a site between residues 32 and 47 on the CD4 protein. By analogy to other members of the immunoglobulin superfamily of proteins, this particular region has been predicted to exist as a protruding loop. A synthetic analog of this loop (residues 25 to 58) showed a concentration-dependent inhibition of HIV-1-induced cell fusion. It is proposed that a loop extending from residues 37 to 53 of the CD4 protein is a binding site for the AIDS virus.
Catalytic DNAs as potential therapeutic agents and sequence-specific molecular tools to dissect biological function (2000)

Apolipoprotein AI CD44 FGF-2 Fibronectin Intercellular adhesion molecule-1 Membrane type
Antigenic Epitopes Fused to Cationic Peptide Bound to Oligonucleotides Facilitate Toll-Like Receptor 9-Dependent, but CD4+ T Cell Help-Independent, Priming of CD8+ T Cells (2003)

A priority in current vaccine research is the development of adjuvants that support the efficient priming of long-lasting, CD4(+) T cell help-independent CD8(+) T cell immunity. Oligodeoxynucleotides (ODN) with immune-stimulating sequences (ISS) containing CpG motifs facilitate the priming of MHC class I-restricted CD8(+) T cell responses to proteins or peptides. We show that the adjuvant effect of ISS(+) ODN on CD8(+) T cell priming to large, recombinant Ag is enhanced by binding them to short, cationic (arginine-rich) peptides that themselves have no adjuvant activity in CD8(+) T cell priming. Fusing antigenic epitopes to cationic (8- to 10-mer) peptides bound to immune-stimulating ISS(+) ODN or nonstimulating NSS(+) ODN (without CpG-containing sequences) generated immunogens that efficiently primed long-lasting, specific CD8(+) T cell immunity of high magnitude. Different MHC class I-binding epitopes fused to short cationic peptides of different origins showed this adjuvant activity. Quantitative ODN binding to cationic peptides strikingly reduced the toxicity of the latter, suggesting that it improves the safety profile of the adjuvant. CD8(+) T cell priming supported by this adjuvant was Toll-like receptor 9 dependent, but required no CD4(+) T cell help. ODN (with or without CpG-containing sequences) are thus potent Th1-promoting adjuvants when bound to cationic peptides covalently linked to antigenic epitopes, a mode of Ag delivery prevailing in many viral nucleocapsids.
Elevated levels of mitochondrial mortalin and cytosolic HSP70 in blood as risk factors in patients with colorectal cancer (2013)

Mortalin/GRP75 is a ubiquitous mitochondrial chaperone related to the cytosolic heat shock protein 70 (HSP70). It protects cells from senescence and apoptosis and is overexpressed in cancer cells. Cell resistance to complement-dependent cytotoxicity depends on mortalin and during complement attack mortalin is released from cells. Our goal was to determine whether cancer patients have circulating mortalin in blood. The significance of mortalin in blood to survival prospects of colorectal cancer patients was evaluated. Occurrence of extracellular soluble HSP70 (sHSP70) is documented. We developed a sensitive ELISA for mortalin. The association between mortalin level and survival was subjected to the Cox proportional hazards analysis (univariate and multivariate analyses). Mortalin concentration in serum of colorectal cancer patients was 10-214 ng/ml. Survival data of the patients were known from an earlier study of sHSP70 in these samples. Cox regression analysis indicated that high mortalin (>60 ng/ml) is a risk factor for shorter survival. Serum levels of sHSP70 and mortalin in patients were independent variables. Concurrence of high sHSP70 and mortalin was associated with rapid disease progression (HR = 4, 2.04-8.45, p < 0.001). Addition of high sHSP70 and mortalin to a baseline model of age, sex and TNM stage, significantly (p < 0.001) enhanced the risk score to 8 (3.26-20.46). This is the first demonstration of circulating mortalin in cancer patients. Analysis of mortalin in blood, and even more so of mortalin and sHSP70, adds a high prognostic value to the TNM stage and will identify colorectal cancer patients at high risk of poor survival.
Development of through silicon via (TSV) interposer technology for large die (21&#x00D7;21mm) fine-pitch Cu/low-k FCBGA package (2009)

Because of Moore's (scaling/integration) law, the Cu/low-k silicon chip is getting bigger, the pin-out is getting higher, and the pitch is getting finer. Thus, the conventional organic buildup substrates cannot support these kinds of silicon chips anymore. To address these needs, Si interposer with TSV has emerged as a good solution to provide high wiring density interconnection, to minimize CTE mismatch to the Cu/low-k chip that is vulnerable to thermal-mechanical stress, and to improve electrical performance due to shorter interconnection from the chip to the substrate. This paper presents the development of TSV interposer technology for a 21 times 21 mm Cu/low-k test chip on FCBGA package. The Cu/low-k chip is a 65 nm, 9-metal layer chip with 150 mum SnAg bump pitch of total 11,000 I/O, with via chain and daisy chain for interconnect integrity monitoring and reliability testing. The TSV interposer size is 25 times 25 times 0.3 mm with CuNiAu as UBM on the top side, and SnAgCu bumps on the underside. The conventional BT substrate size is 45 times 45 mm with BGA pad pitch of 1 mm and core thickness of 0.8 mm. Mechanical and thermal modeling and simulation for the FCBGA package with TSV interposer have been performed. TSV interposer fabrication processes and assembly process of the large die mounted on TSV interposer with Pb-free micro solder bumps and underfill have been set up. The FCBGA samples have been subjected to moisture sensitivity test and thermal cycling (TC) reliability assessments.
Identification of Novel Small Molecules That Bind to Two Different Sites on the Surface of Tetanus Toxin C Fragment (2002)

A combination of computational methods, electrospray ionization mass spectroscopy (ESI-MS), and NMR spectroscopy has been used to identify novel small molecules that bind to two adjacent sites on the surface of the C fragment of tetanus toxin (TetC). One of these sites, Site-1, binds gangliosides present on the surface of motor neurons, while Site-2 is a highly conserved deep cleft in the structures of the tetanus (TeNT) and botulinum (BoNT) neurotoxins. ESI-MS was used to experimentally determine which of the top 11 computationally predicted Site-2 candidates bind to TetC. Each of the six molecules that tested positive was further screened, individually and as mixtures, for binding to TetC in aqueous solutions by NMR. A trNOESY competition assay was developed that used doxorubicin as a marker for Site-1 to provide insight into whether the predicted Site-2 ligands bound to a different site. Of the six predicted Site-2 ligands tested, only four were observed to bind. Naphthofluorescein-di-beta-galactopyranoside was insoluble under conditions compatible with TetC. Sarcosine-Arg-Gly-Asp-Ser-Pro did not appear to bind, but its binding affinity may have been outside the range detectable by the trNOESY experiment. Of the remaining four, three [3-(N-maleimidopropionyl)biocytin, lavendustin A, and Try-Glu-Try] bind in the same site, presumably the predicted Site-2. The fourth ligand, Ser-Gln-Asn-Tyr-Pro-Ile-Val, binds in a third site that differs from Site-1 or predicted Site-2. The results provide a rational, cost- and time-effective strategy for the selection of an optimal set of Site-1 binders and predicted Site-2 binders for use in synthesizing novel bidendate antidotes or detection reagents for clostridial neurotoxins, such as TeNT and BoNT.
Psychiatric in-patient care and suicide in England, 1997 to 2008: a longitudinal study (2012)

The rate of suicide among psychiatric in-patients in England has fallen considerably. Possible explanations include falling general population rates, changes in the at-risk population or improved in-patient safety. However, a transfer of risk to the period after discharge or other clinical settings such as crisis resolution teams cannot be ruled out.
Lipid Nanoparticles as Carriers for RNAi against Viral Infections: Current Status and Future Perspectives (2014)

The efforts made to develop RNAi-based therapies have led to productive research in the field of infections in humans, such as hepatitis C virus (HCV), hepatitis B virus (HBV), human immunodeficiency virus (HIV), human cytomegalovirus (HCMV), herpetic keratitis, human papillomavirus, or influenza virus. Naked RNAi molecules are rapidly digested by nucleases in the serum, and due to their negative surface charge, entry into the cell cytoplasm is also hampered, which makes necessary the use of delivery systems to exploit the full potential of RNAi therapeutics. Lipid nanoparticles (LNP) represent one of the most widely used delivery systems for in vivo application of RNAi due to their relative safety and simplicity of production, joint with the enhanced payload and protection of encapsulated RNAs. Moreover, LNP may be functionalized to reach target cells, and they may be used to combine RNAi molecules with conventional drug substances to reduce resistance or improve efficiency. This review features the current application of LNP in RNAi mediated therapy against viral infections and aims to explore possible future lines of action in this field.
Site-specific binding constants for actinomycin D on DNA determined from footprinting studies (1992)

We report site-specific binding constants for the intercalating anticancer drug actinomycin D (Act-D), binding to a 139-base-pair restriction fragment from pBR 322 DNA. The binding constants are derived from analysis of footprinting experiments, in which the radiolabeled 139-mer is cleaved using DNase I, the cleavage products undergo gel electrophoresis, and, from the gel autoradiogram, spot intensities, proportional to amounts of cleaved fragments, are measured. A bound drug prevents DNase I from cleaving at approximately 7 bonds, leading to decreased amounts of corresponding fragments. With the radiolabel on the 3' end of the noncoding strand (A-label), we measured relative amounts of 54 cleavage products at 25 Act-D concentrations. For cleavage of the 139-mer with the label on the 3' end of the coding strand (G-label), relative amounts of 43 cleavage products at 11 Act-D concentrations were measured. These measurements give information about approximately 120 base pairs of the restriction fragment (approximately 12 turns of the DNA helix); in this region, 14 strong and weak Act-D binding sites were identified. The model used to interpret the footprinting plots is derived in detail. Binding constants for 14 sites on the fragment are obtained simultaneously. It is important to take into account the effect of drug binding at its various sites on the local concentration of probe elsewhere. It is also necessary to include in the model weak as well as strong Act-D sites on the carrier DNA which is present, since the carrier DNA controls the free-drug concentration. As expected, the strongest sites are those with the sequence (all sequences are 5'----3') GC, with TGCT having the highest binding constant, 6.4 x 10(6) M-1. Sites having the sequence GC preceded by G are weak binding sites, having binding constants approximately 1 order of magnitude lower than those of the strong sites. Also, the non-GC-containing sequences CCG and CCC bind Act-D with a binding constant comparable to those of the weak GGC sites. The analysis may reveal drug-induced structural changes on the DNA, which are discussed in terms of the mechanism of Act-D binding.
Glass half-full: On-road glance metrics differentiate crashes from near-crashes in the 100-Car data (2017)

This work may have important implications for attention management in the context of the increasing prevalence of in-vehicle demands as well as of vehicle automation.
The Role of Trophoblast Interferons in the Maintenance of Early Pregnancy in Ruminants (1997)

Negative regulation of gene expression may be a general strategy in IFN activity. This may explain the similar activities of IFN-tau and IFN-alpha on a broad variety of cell types, including ruminant uterine endometrium.
NP1 Protein of the Bocaparvovirus Minute Virus of Canines Controls Access to the Viral Capsid Genes via Its Role in RNA Processing (2015)

The Parvovirinae are small nonenveloped icosahedral viruses that are important pathogens in many animal species, including humans. Although parvoviruses have only subtle early-to-late expression shifts, they all regulate access to their capsid genes. Minute virus of canines (MVC) is an autonomous parvovirus in the genus Bocaparvovirus. It has a single promoter generating a single pre-mRNA which is processed via alternative splicing and alternative polyadenylation to generate at least 8 mRNA transcripts. MVC contains two polyadenylation sites, one at the right-hand end of the genome, (pA)d, and another, (pA)p, within the capsid-coding region. It had not been clear how the potent internal polyadenylation motif is suppressed to allow processing, export, and accumulation of the spliced capsid protein-encoding mRNAs. We show here that MVC NP1, the first parvovirus protein to be implicated in RNA processing, governs access to the MVC capsid gene by facilitating splicing and suppressing internal polyadenylation of MVC pre-mRNAs.
Obstrüktif uyku apnesi sendromunda septoplasti ile birlikte modifiye Fujita uvulopalatoplasti tekniğinin başarısı (2012)

Objective: The aim of this study was to investigate the clinical efficacy of modified Fujita technique uvulopalatoplasty (UPPP) with nasal surgery in patients with simple snoring and obstructive sleep apnea syndrome (OSAS). Methods: A total of 12 consecutive OSAS patients (mean age 46.08±7.16 years) who underwent modified Fujita technique UPPP with nasal surgery were included in the study. Pre and postoperative subjective symptoms and polysomnographic data were compared. Results: Following simultaneous nasal-oropharyngeal surgery, the AHI significantly decreased (from 41.8±22.5 to 19.3±12.6 events per hour; p0.05). Conclusion: Single-staged modified UPPP with nasal surgery is an available and relatively safe surgical approach in OSAS patients with nasal obstruction.
UPF1-like helicase grip on nucleic acids dictates processivity (2018)

Helicases are molecular engines which translocate along nucleic acids (NA) to unwind double-strands or remodel NA-protein complexes. While they have an essential role in genome structure and expression, the rules dictating their processivity remain elusive. Here, we developed single-molecule methods to investigate helicase binding lifetime on DNA. We found that UPF1, a highly processive helicase central to nonsense-mediated mRNA decay (NMD), tightly holds onto NA, allowing long lasting action. Conversely, the structurally similar IGHMBP2 helicase has a short residence time. UPF1 mutants with variable grip on DNA show that grip tightness dictates helicase residence time and processivity. In addition, we discovered via functional studies that a decrease in UPF1 grip impairs NMD efficiency in vivo. Finally, we propose a three-state model with bound, sliding and unbound molecular clips, that can accurately predict the modulation of helicase processivity.
siRNA-mediated MDM2 inhibition sensitizes human lung cancer A549 cells to radiation (2007)

MDM2 (murine double minute 2) is well-documented to play a key role in radiation response and tumor radiosensitivity, thus offering an attractive clinic drug target to enhance tumor sensitivity to anti-cancer radiotherapy. In this study, we designed and tested two siRNA fragments against human MDM2 in non-small cell human lung cancer A549 cells. Transfection of mammalian expression vector pUR/U6 containing either MDM2 siRNA1 or siRNA2 fragment was shown to reduce MDM2 mRNA levels by 72% and 31%, respectively. Western blotting detected a similar inhibition of MDM2 protein levels in cells transfected with MDM2 siRNA1. A549 cells transfected with the expression vector for siRNA1 significantly decreased cell proliferation and rendered cells more sensitive to radiation. The basal apoptotic and necrotic cells, 1% and 2%, respectively, detected among A549 cells were increased to 2.6% and 14.4% after gamma-irradiation with 5 Gy. Transfection of MDM2 siRNA1 induced 30.1% apoptosis and 12.7% necrosis while combined treatment of siRNA1 and 5-Gy radiation increased apoptosis and necrosis to 45.9% and 15.2%, respectively. These data provide the first evidence that specific siRNA fragment (MDM2 siRNA1) targeting human MDM2 mRNA is able to enhance lung cancer radiosensitivity.
43.2: Light Output Feedback Solution for RGB LED Backlight Applications (2003)

Abstract It is well known that backlights for Liquid Crystal Displays (LCDs) based on Red, Green and Blue Light Emitting Diodes (RGB LEDs) render superior color quality but do require control of white point over temperature and lifetime [3], [4], [5]. We have developed a novel backlighting system utilizing RGB LED lightsources, a color sensor and a feedback controller. The main result of using optical feedback is a color stability Δ u'v' &lt; 0.002 (CIE1976) over temperature. Optionally, brightness can be maintained constant. The system can control any color point or brightness required.
Isolation and characterization of the E2F‐like gene in plants (1999)

The transcription factor E2F regulates the expression of genes involved in the progression of G1/S transition and DNA replication in mammalian cells. We cloned and characterized a cDNA ( NtE2F ) corresponding to a E2F homolog of tobacco ( Nicotiana tabacum ). The transcription of NtE2F was induced as cells progressed from G1 to the S phase and expressed much earlier than that of the proliferating cell nuclear antigen (PCNA) gene. We demonstrated that NtE2F can interact with the tobacco retinoblastoma (Rb)‐related protein in a yeast two‐hybrid assay. To further characterize NtE2F, the trans ‐activation activity of NtE2F was examined by using a transient assay in the tobacco Bright Yellow‐2 (BY‐2) cells with NtE2F fused to the DNA‐binding domain of the yeast transcriptional activator GAL4. NtE2F activated the transcription of the β‐glucuronidase (GUS) reporter gene driven by a cauliflower mosaic virus (CaMV) 35S core promoter containing the GAL4‐binding sequence. This is the first report of the identification of a functionally equivalent E2F‐like gene in plants.