gebhart/patrepeval huggingface dataset:
Scanning tunneling microscope tip as a positionable contact: Probing a Josephson-junction array at subkelvin temperatures (1998)

We describe an experiment in which a scanning tunneling microscope (STM) is employed to selectively contact a lithographically fabricated structure at 350 mK. The STM enables us to probe the structure, a Josephson-junction array, at various positions. The experiment demonstrates that it is possible to combine the use of a scanning tunneling microscope with transport measurements on lithographically fabricated structures at temperatures below 1 K. We focus on the strategy to position the tip above the structure of interest, the influence of the STM on the electronic noise, and on the effective temperature of the sample.
Endothelin-1 and F2-isoprostane relate to and predict renal dysfunction in hypertensive patients (2008)

Our findings are a clear-cut demonstration of a strong and negative correlation of both oxidative stress and ET-1 with renal function stages in HT. ET-1 and 8-isoprostane are predictive of eGFR.
Efficient Delivery of Cyclic Peptides into Mammalian Cells with Short Sequence Motifs (2012)

Cyclic peptides hold great potential as therapeutic agents and research tools, but their broad application has been limited by poor membrane permeability. Here, we report a potentially general approach for intracellular delivery of cyclic peptides. Short peptide motifs rich in arginine and hydrophobic residues (e.g., FΦRRRR, where Φ is l-2-naphthylalanine), when embedded into small- to medium-sized cyclic peptides (7–13 amino acids), bound to the plasma membrane of mammalian cultured cells and were subsequently internalized by the cells. Confocal microscopy and a newly developed peptide internalization assay demonstrated that cyclic peptides containing these transporter motifs were translocated into the cytoplasm and nucleus at efficiencies 2–5-fold higher than that of nonaarginine (R9). Furthermore, incorporation of the FΦRRRR motif into a cyclic peptide containing a phosphocoumaryl aminopropionic acid (pCAP) residue generated a cell permeable, fluorogenic probe for detecting intracellular protein tyrosine phosphatase activities.
Light scattering by polydisperse cylindrical micelles (1970)

Angular light-scattering measurements have been analyzed using the Rayleigh-Gans theory to obtain information on the structure and polydispersity of the micelles formed in aqueous solutions of [graphic ommitted]. The cylindrical micelles have a radius equal to the extended length of the monomer molecule and a polydispersity which is consistent with the predictions of the multiple equilibrium thermodynamic treatment of micelle formation.
Prevalence, Complications, and Hospital Charges Associated With Use of Bone-Morphogenetic Proteins in Spinal Fusion Procedures (2009)

Bone-morphogenetic protein was used in approximately 25% of all spinal fusions nationally in 2006, with use associated with more frequent complications for anterior cervical fusions and with greater hospital charges for all categories of fusions.
Reanimating Faces in Images and Video (2003)

Abstract This paper presents a method for photo‐realistic animation that can be applied to any face shown in a single imageor a video. The technique does not require example data of the person's mouth movements, and the image to beanimated is not restricted in pose or illumination. Video reanimation allows for head rotations and speech in theoriginal sequence, but neither of these motions is required. In order to animate novel faces, the system transfers mouth movements and expressions across individuals, basedon a common representation of different faces and facial expressions in a vector space of 3D shapes and textures.This space is computed from 3D scans of neutral faces, and scans of facial expressions. The 3D model's versatility with respect to pose and illumination is conveyed to photo‐realistic image and videoprocessing by a framework of analysis and synthesis algorithms: The system automatically estimates 3D shape andall relevant rendering parameters, such as pose, from single images. In video, head pose and mouth movements aretracked automatically. Reanimated with new mouth movements, the 3D face is rendered into the original images. Categories and Subject Descriptors (according to ACM CCS): I.3.7 [Computer Graphics]: Animation
Micropatterning of biomedical polymer surfaces by novel UV polymerization techniques (2001)

The "living" radical polymerization with an iniferter was used to create micropatterned biomedical surfaces. Novel, photosensitive biomedical polymers were created by the incorporation of dithiocarbamate groups from iniferters. A second monomer layer was then irradiated onto the photosensitive polymer substrate created with the iniferter to form a copolymer. Patterns were created on the films by application of modified microfabrication-based photolithographic techniques. The technique was used to create patterns with depths from 5 to 80 microm. In addition, various polymers were incorporated, including polyethylene glycol methacrylates, styrene, and methacrylic acid, to synthesize regions with different physico-chemical properties. Applications include novel surfaces for biosensors and biomaterials for the selective adhesion of cells and proteins.
On the performance of different detection techniques for OFDM-CDMA in fading channels (2002)

The combination of orthogonal frequency division multiplexing (OFDM) with code division multiple access (CDMA) systems has attained increasing significance in mobile radio communications. In this paper basic OFDM-CDMA detection techniques based on simple equalization algorithms, and improved detection techniques, such as the newly proposed iterative detection applying the minimum mean square error (MMSE) criterion, are analyzed in the mobile radio environment. This analysis enables one a comparison between known and new OFDM-CDMA detection techniques in terms of spectral efficiency and receiver complexity.
Evaluation of the safety and immunogenicity of different COVID-19 vaccine combinations in healthy individuals: study protocol for a randomized, subject-blinded, controlled phase 3 trial [PRIBIVAC] (2022)

ClinicalTrials.gov NCT05142319 . Registered on 2 Dec 2021.
Transferred melanoma-specific CD8 + T cells persist, mediate tumor regression, and acquire central memory phenotype (2012)

Adoptively transferred tumor-specific T cells offer the potential for non-cross-resistant therapy and long-term immunoprotection. Strategies to enhance in vivo persistence of transferred T cells can lead to improved antitumor efficacy. However, the extrinsic (patient conditioning) and intrinsic (effector cell) factors contributing to long-term in vivo persistence are not well-defined. As a means to enhance persistence of infused T cells in vivo and limit toxicity, 11 patients with refractory, progressive metastatic melanoma received cyclophosphamide alone as conditioning before the infusion of peripheral blood mononuclear cell-derived, antigen-specific, CD8(+) cytotoxic T-lymphocyte (CTL) clones followed by low-dose or high-dose IL-2. No life-threatening toxicities occurred with low-dose IL-2. Five of 10 evaluable patients had stable disease at 8 wk, and 1 of 11 had a complete remission that continued for longer than 3 y. On-target autoimmune events with the early appearance of skin rashes were observed in patients with stable disease or complete remission at 4 wk or longer. In vivo tracking revealed that the conditioning regimen provided a favorable milieu that enabled CTL proliferation early after transfer and localization to nonvascular compartments, such as skin and lymph nodes. CTL clones, on infusion, were characterized by an effector memory phenotype, and CTL that persisted long term acquired phenotypic and/or functional qualities of central memory type CTLs in vivo. The use of a T-cell product composed of a clonal population of antigen-specific CTLs afforded the opportunity to demonstrate phenotypic and/or functional conversion to a central memory type with the potential for sustained clinical benefit.
Microalgae as biodiesel & biomass feedstocks: Review & analysis of the biochemistry, energetics & economics (2010)

Following scrutiny of present biofuels, algae are seriously considered as feedstocks for next-generation biofuels production. Their high productivity and the associated high lipid yields make them attractive options. In this review, we analyse a number aspects of large-scale lipid and overall algal biomass production from a biochemical and energetic standpoint. We illustrate that the maximum conversion efficiency of total solar energy into primary photosynthetic organic products falls in the region of 10%. Biomass biochemical composition further conditions this yield: 30 and 50% of the primary product mass is lost on producing cell protein and lipid. Obtained yields are one third to one tenth of the theoretical ones. Wasted energy from captured photons is a major loss term and a major challenge in maximising mass algal production. Using irradiance data and kinetic parameters derived from reported field studies, we produce a simple model of algal biomass production and its variation with latitude and lipid content. An economic analysis of algal biomass production considers a number of scenarios and the effect of changing individual parameters. Our main conclusions are that: (i) the biochemical composition of the biomass influences the economics, in particular, increased lipid content reduces other valuable compounds in the biomass; (ii) the “biofuel only” option is unlikely to be economically viable; and (iii) among the hardest problems in assessing the economics are the cost of the CO2 supply and uncertain nature of downstream processing. We conclude by considering the pressing research and development needs.
Lupus autoantibodies to native DNA cross-react with the A and D SnRNP polypeptides. (1994)

Antibodies to native DNA (nDNA) in sera from patients with systemic lupus erythematosus have been found to frequently correlate with antibodies to the A and D SnRNP proteins measured in Western blot assays. 40 of 54 SLE (74.1%) sera with anti-nDNA bound to A and D proteins, while 9 of 113 sera (8%) without anti-nDNA bound the A and D proteins, P < 10(-8) by Fisher's exact test. Antibodies to nDNA correlated closely with anti-A and anti-D in seven of eight patients followed sequentially, r = 0.7865. Nine human polyclonal anti-nDNA populations were isolated from DNA cellulose columns. Seven reacted equally with A and D, and two reacted predominantly with D. Two of three murine monoclonal anti-DNA antibodies isolated from NZB/NZW F1 hybrid mice bound A and D equally in Western blot with a titer > 1/40,000. These reactions were directed to the unfolded A and D proteins measurable in Western blot since these monoclonals (and several of the human anti-nDNA populations) failed to react with native U1RNP in ELISA or in RNA immunoprecipitation experiments. These newly recognized cross reactions of anti-nDNA may amplify the immune response to DNA and be part of the original immunogenic drive.
Volume Changes of Corpus Striatum, Thalamus, Hippocampus and Lateral Ventricles in Posttraumatic Stress Disorder (PTSD) Patients Suffering from Headaches and without Therapy (2010)

The present study revealed a bilateral volume decrease of the caudate nucleus, putamen and hippocampus in PTSD male subjects without therapy. Intensity of volume alterations correlated with Hamilton's depression rating score; regression analysis uncovered correlated changes in the caudate nucleus, putamen and hippocampus, and an inverse correlation with the volume of the lateral ventricle in the PTSD patients.
CD133: molecule of the moment (2007)

CD133 (prominin-1) was the first in a class of novel pentaspan membrane proteins to be identified in both humans and mice, and was originally classified as a marker of primitive haematopoietic and neural stem cells. Due to the highly restricted expression of CD133 family molecules on plasma membrane protrusions of epithelial and other cell types, in association with membrane cholesterol, a role in the organization of plasma membrane topology has also recently been assigned to this family. Studies have now confirmed the utility of CD133 as a marker of haematopoietic stem cells for human allogeneic transplantation. In addition, CD133 represents a marker of tumour-initiating cells in a number of human cancers, and therefore it may be possible to develop future therapies towards targeting cancer stem cells via this marker. The development of such therapies will be aided by a clearer understanding of the molecular mechanisms and signalling pathways that regulate the behaviour of CD133-expressing cells, and new data outlining the role of Wnt, Notch, and bone morphogenetic protein (BMP) signalling in CD133(+) cancer stem cell regulation are discussed within.
Elevated CSF TDP-43 levels in amyotrophic lateral sclerosis: Specificity, sensitivity, and a possible prognostic value (2010)

TAR DNA binding protein of 43 kDa (TDP-43) is likely to be the major pathogenetic protein in amyotrophic lateral sclerosis (ALS). A previous study has shown that levels of TDP-43 in CSF measured by an ELISA are significantly higher for ALS patients than for controls. The aim of this study was to investigate whether elevated CSF TDP-43 levels are specific to ALS, and are associated with clinical profiles in ALS patients. We measured CSF TDP-43 levels by the same ELISA in 27 ALS patients and 50 neurodegenerative or inflammatory disease controls such as Parkinson's disease, multiple sclerosis, and Guillain-Barré syndrome. Results showed that the CSF TDP-43 levels were increased only in ALS patients. Receiver operating characteristic (ROC) analyses showed a sensitivity of 59.3% and a specificity of 96.0%. We also found that lower CSF TDP-43 levels may be associated with shorter survival time. In conclusion, the CSF TDP-43 is a potential biomarker that supports a diagnosis of ALS. Moreover, among ALS patients, lower levels of CSF TDP-43 may reflect the accumulation of TDP-43 in the cortical and spinal motor neurons and thereby shorter survival time, although this should be confirmed in larger prospective studies.
On Constructing Long Words (1987)

Of perennial interest to Word Ways readers are very long English words - words of 27 or more letters, written solidly, without hyphens, apostrophes, or other letter separations. Unfortunately, categories: obscure medical terms: even obscurer medical terms: weird place names of Amerind, Welsh, Maori, Thai, or other equally exotic provenance, resembling nothing even remotely English: fictitious words listed and defined by dictionaries. Examples of fictitious words include: HONORICICABILITUDINATATIBUS (Web 1 and 2) FLOCCIPAUCINIHILIPILIFICATION (Oxford English Dictionary) SUPERCALIFRAGILISTICEXPIALIDOCIOUS (Random House) PNEUMONOULTRAMICROSCOPICSILICOVOCANOKONISOSIS (Web 2) PNEUMONOULTRAMICROSCOPICSILICOVOLCANOCONIOSIS (Web 3)
Doping-Free Fabrication of Carbon Nanotube Based Ballistic CMOS Devices and Circuits (2007)

We have fabricated ballistic n-type carbon nanotube (CNT)-based field-effect transistors (FETs) by contacting semiconducting single wall CNTs using Sc. Together with the demonstrated ballistic p-type CNT FETs using Pd contacts, our work closes the gap for doping-free fabrication of CNT-based ballistic complementary metal-oxide semiconductor (CMOS) devices and circuits. We demonstrated the feasibility of this doping-free CMOS technology by fabricating a simple CMOS inverter on a SiO2/Si substrate using the back-gate geometry, but in principle much more complicated CMOS circuits may be integrated on a CNT on any suitable insulator substrate using the top-gate geometry and high-κ dielectrics. This CNT-based CMOS technology only requires the patterning of arrays of parallel semiconducting CNTs with moderately narrow diameter range, for example, 1.6−2.4 nm, which is within the reach of current nanotechnology. This may lead to the integration of CNT-based CMOS devices with increasing complexity and possibly find its way into the computers brain: the logic circuit.
Escherichia coli DNA polymerase III holoenzyme footprints three helical turns of its primer (1994)

Escherichia coli DNA polymerase III holoenzyme in the presence of ATP and E. coli single-stranded DNA-binding protein forms an initiation complex on a primed template capable of rapid and highly processive DNA replication. DNase I digestion of initiation complexes demonstrated that holoenzyme protected 27-30 nucleotides of primer. Like the formation of initiation complexes, this protection required both ATP and E. coli single-stranded DNA-binding protein. Initiation complexes assembled with core DNA polymerase III (alpha, epsilon, and theta subunits), gamma-complex (gamma, delta, delta', chi, and omega) and the beta subunit produced a footprint identical to that formed with intact holoenzyme, indicating that initiation complexes formed with reconstituted enzyme and those formed with holoenzyme were equivalent. The presence of the tau subunit in reconstituted initiation complexes did not alter the DNase I footprint. Preinitiation complexes (gamma-complex plus beta subunit) assembled onto primer-template in an ATP-dependent reaction protected a larger region of the primer than did holoenzyme. The addition of core DNA polymerase III to preintiation complexes restored the 30-nucleotide footprint observed with intact holoenzyme. These results suggest that holoenzyme subunits rearrange during initiation complex formation.
Design, synthesis, and in vitro evaluation of cytotoxic analogs of bombesin-like peptides containing doxorubicin or its intensely potent derivative, 2-pyrrolinodoxorubicin (1997)

Five peptide fragments, based on the C-terminal sequence of bombesin (BN)-(6-14) or BN-(7-14), were selected as carriers for radicals doxorubicin (DOX) and 2-pyrrolino-DOX to create hybrid cytotoxic analogs. All these compounds had a reduced peptide bond (CH2-NH or CH2-N) between positions 13 (Phe or Leu) and 14 (Phe, Leu, or Tac) (Tac = thiazolidine-4-carboxylic acid). Three pseudononapeptide carriers contained N-terminal D-Phe or D-Tpi at position 6 (Tpi = 2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid). Two pseudooctapeptides had Gln7 at the N terminus. The conjugation of N-(9-fluorenylmethoxycarbonyl) doxorubicin (N-Fmoc-DOX)-14-O-hemiglutarate to the peptide carriers at the N terminus resulted in cytotoxic hybrids of BN-like peptides containing DOX. These hybrids could then be converted to analogs with 2-pyrrolino-DOX by a reaction with 4-iodobutyraldehyde. The ability of the carriers and the conjugates to inhibit the binding of 125I-labeled [Tyr4]BN to receptors for BN/gastrin releasing peptide (GRP) on Swiss 3T3 cells was determined. Cytotoxic conjugates of pseudooctapeptide carrier analogs displayed the highest binding affinity (KD approximately 1 nM). The cytotoxic BN analogs and their corresponding cytotoxic radicals exerted similar inhibitory effects on the in vitro growth of CFPAC-1 human pancreatic cancer, DMS-53 human lung cancer, PC-3 human prostate cancer, and MKN-45 human gastric cancer cell lines that have receptors for BN/GRP. In DMS-53 cells, the activity of 2-pyrrolino-DOX and its conjugates was approximately 2500 times higher than that of DOX and its hybrids. These highly potent cytotoxic analogs of BN have been designed as targeted anti-tumor agents for the treatment of various cancers that possess receptors for BN/GRP.
Validation of microarray-based resequencing of 93 worldwide mitochondrial genomes (2008)

The human mitochondrial genome consists of a multicopy, circular dsDNA molecule of 16,569 base pairs. It encodes for 13 proteins, two ribosomal genes, and 22 tRNAs that are essential in the generation of cellular ATP by oxidative phosphorylation in eukaryotic cells. Germline mutations in mitochondrial DNA (mtDNA) are an important cause of maternally inherited diseases, while somatic mtDNA mutations may play important roles in aging and cancer. mtDNA polymorphisms are also widely used in population and forensic genetics. Therefore, methods that allow the rapid, inexpensive and accurate sequencing of mtDNA are of great interest. One such method is the Affymetrix GeneChip Human Mitochondrial Resequencing Array 2.0 (MitoChip v.2.0) (Santa Clara, CA). A direct comparison of 93 worldwide mitochondrial genomes sequenced by both the MitoChip and dideoxy terminator sequencing revealed an average call rate of 99.48% and an accuracy of > or =99.98% for the MitoChip. The good performance was achieved by using in-house software for the automated analysis of additional probes on the array that cover the most common haplotypes in the hypervariable regions (HVR). Failure to call a base was associated mostly with the presence of either a run of > or =4 C bases or a sequence variant within 12 bases up- or downstream of that base. A major drawback of the MitoChip is its inability to detect insertions/deletions and its low sensitivity and specificity in the detection of heteroplasmy. However, the vast majority of haplogroup defining polymorphism in the mtDNA phylogeny could be called unambiguously and more rapidly than with conventional sequencing.
A Hypergeometric Probability Model for Protein Identification and Validation Using Tandem Mass Spectral Data and Protein Sequence Databases (2003)

We present a new probability-based method for protein identification using tandem mass spectra and protein databases. The method employs a hypergeometric distribution to model frequencies of matches between fragment ions predicted for peptide sequences with a specific (M + H)+ value (at some mass tolerance) in a protein sequence database and an experimental tandem mass spectrum. The hypergeometric distribution constitutes null hypothesis-all peptide matches to a tandem mass spectrum are random. It is used to generate a score characterizing the randomness of a database sequence match to an experimental tandem mass spectrum and to determine the level of significance of the null hypothesis. For each tandem mass spectrum and database search, a peptide is identified that has the least probability of being a random match to the spectrum and the corresponding level of significance of the null hypothesis is determined. To check the validity of the hypergeometric model in describing fragment ion matches, we used chi2 test. The distribution of frequencies and corresponding hypergeometric probabilities are generated for each tandem mass spectrum. No proteolytic cleavage specificity is used to create the peptide sequences from the database. We do not use any empirical probabilities in this method. The scores generated by the hypergeometric model do not have a significant molecular weight bias and are reasonably independent of database size. The approach has been implemented in a database search algorithm, PEP_PROBE. By using a large set of tandem mass spectra derived from a set of peptides created by digestion of a collection of known proteins using four different proteases, a false positive rate of 5% is demonstrated.
Phenotypic marker for early disease detection in dominant late-onset retinal degeneration. (2001)

Dark-adaptation abnormalities can precede symptoms and funduscopic signs of L-ORD by at least a decade. Short-term, high-dose vitamin A accelerates the kinetics of dark adaptation to a limited degree. The results contribute clues about early pathophysiology of this retinal degeneration and provide additional power for genetic mapping of the L-ORD locus.