gebhart/patrepeval huggingface dataset:
Nanostructured Liquid Crystals Combining Ionic and Electronic Functions (2010)

New molecular materials combining ionic and electronic functions have been prepared by using liquid crystals consisting of terthiophene-based mesogens and terminal imidazolium groups. These liquid crystals show thermotropic smectic A phases. Nanosegregation of the pi-conjugated mesogens and the ionic imidazolium moieties leads to the formation of layered liquid-crystalline (LC) structures consisting of 2D alternating pathways for electronic charges and ionic species. These nanostructured materials act as efficient electrochromic redox systems that exhibit coupled electrochemical reduction and oxidation in the ordered bulk states. For example, compound 1 having the terthienylphenylcyanoethylene mesogen and the imidazolium triflate moiety forms the smectic LC nanostructure. Distinct reversible electrochromic responses are observed for compound 1 without additional electrolyte solution on the application of double-potential steps between 0 and 2.5 V in the smectic A phase at 160 degrees C. In contrast, compound 2 having a tetrafluorophenylterthiophene moiety and compound 3 having a phenylterthiophene moiety exhibit irreversible cathodic reduction and reversible anodic oxidation in the smectic A phases. The use of poly(3,4-ethylenedioxythiophene)-poly(4-styrene sulfonate) (PEDOT-PSS) as an electron-accepting layer on the cathode leads to the distinct electrochromic responses for 2 and 3. These results show that new self-organized molecular redox systems can be built by nanosegregated pi-conjugated liquid crystals containing imidazolium moieties with and without electroactive thin layers on the electrodes.
Development of a rapid and efficient restriction endonuclease analysis typing system for Clostridium difficile and correlation with other typing systems (1993)

A HindIII restriction endonuclease analysis (REA) typing system for total genomic Clostridium difficile DNA including a rapid and efficient method of DNA extraction and a scheme for organizing unique electrophoretic DNA band patterns was developed. REA typing was performed by two extraction methods for 1,965 C. difficile isolates obtained from patients with symptomatic C. difficile disease, asymptomatic patients who were C. difficile culture positive, and environmental surfaces. This isolate collection yielded 206 unique REA types, which were organized into 75 groups. A reference strain representing each unique REA type was chosen for DNA band pattern comparisons, cytotoxin testing, and plasmid analysis. The DNA band patterns utilizing a guanidine thiocyanate-EDTA-Sarkosyl DNA extraction method were 94% reproducible, while the original and sporadically problematic diethyl pyrocarbonate-sodium dodecyl sulfate DNA extraction method was 98% reproducible when readable patterns were obtained. Reference strains from 43 of the 75 groups were cytotoxin positive, 28 groups were cytotoxin negative, and 4 groups included both toxigenic and nontoxigenic strains. Cytotoxicity of isolates with a particular REA type was always consistent with the toxicity of the reference strain for that type. REA typing was able to discriminate strain differences within types identified by the immunoblot (89 isolates), bacteriophage-bacteriocin (44 isolates), and ribotyping (23 isolates) methods. REA typing is a sensitive, discriminating, reproducible, and rapid method for differentiating C. difficile strains and is suitable for large-scale epidemiologic studies.
Mapping Drug Interactions at the Covalent Topoisomerase II-DNA Complex by Bisantrene/Amsacrine Congeners (1998)

To identify structural determinants for the sequence-specific recognition of covalent topoisomerase II-DNA complexes by anti-cancer drugs, we investigated a number of bisantrene congeners, including a 10-azabioisoster, bearing one or two 4, 5-dihydro-1H-imidazol-2-yl hydrazone side chains at positions 1, 4, or 9 of the anthracene ring system. The studied bisantrene/amsacrine (m-AMSA) hybrid and bisantrene isomers were able to poison DNA topoisomerase II with an intermediate activity between those of bisantrene and m-AMSA. Moving the side chain from the central to a lateral ring (from C-9 to C-1/C-4) only slightly modified the drug DNA affinity, whereas it dramatically affected local base preferences of poison-stimulated DNA cleavage. In contrast, switching the planar aromatic systems of bisantrene and m-AMSA did not substantially alter the sequence specificity of drug action. A computer-assisted steric and electrostatic alignment analysis of the test compounds was in agreement with the experimental data, since a common pharmacophore was shared by bisantrene, m-AMSA, and 9-substituted analogs, whereas the 1-substituted isomer showed a radically changed pharmacophoric structure. Thus, the relative space occupancy and electron distribution of putative DNA binding (aromatic rings) and enzyme binding (side chains) moieties are fundamental in directing the specific action of topoisomerase II poisons and in determining the poison pharmacophore.
Harnessing human CD1d restricted T cells for tumor immunity: progress and challenges (2009)

Glycolipid reactive CD1d restricted natural killer T (NKT) cells represent a distinct population of T cells implicated in the regulation of immune responses in a broad range of diseases including cancer. Several studies have demonstrated the capacity of NKT cells bearing an invariant T cell receptor (iNKT cells) to recruit both innate and adaptive anti-tumor immunity and mediate tumor rejection in mice. Early phase clinical studies in humans have demonstrated the capacity of dendritic cells (DCs) to mediate expansion of NKT cells in vivo. However several challenges need to be overcome in order to effectively harness the properties of these cells in the clinic.
Interstitial fluid: the overlooked component of the tumor microenvironment? (2010)

Access to fluid that reliably reflects the local microenvironment enables us to identify substances that can be used in early detection and monitoring of disease.
Detection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates (2015)

Whole-cell biosensors have several advantages for the detection of biological substances and have proven to be useful analytical tools. However, several hurdles have limited whole-cell biosensor application in the clinic, primarily their unreliable operation in complex media and low signal-to-noise ratio. We report that bacterial biosensors with genetically encoded digital amplifying genetic switches can detect clinically relevant biomarkers in human urine and serum. These bactosensors perform signal digitization and amplification, multiplexed signal processing with the use of Boolean logic gates, and data storage. In addition, we provide a framework with which to quantify whole-cell biosensor robustness in clinical samples together with a method for easily reprogramming the sensor module for distinct medical detection agendas. Last, we demonstrate that bactosensors can be used to detect pathological glycosuria in urine from diabetic patients. These next-generation whole-cell biosensors with improved computing and amplification capacity could meet clinical requirements and should enable new approaches for medical diagnosis.
Sequence and expression of a human type II mesothelial keratin. (1985)

Using mRNA from cultured human mesothelial cells, we constructed bacterial plasmids and lambda phage vectors that contained cDNA sequences specific for the keratins expressed in these cells. A cloned cDNA encoding keratin K7 (55 kD) was identified by positive hybrid selection. Southern Blot analysis indicated that this sequence is represented only once in the human genome, and Northern Blot analysis demonstrated that the gene encoding K7 is expressed in abundance in cultured bronchial and mesothelial cells, but only weakly in cultured epidermal cells and not at all in liver, colon, or exocervical tissue. The predicted amino acid sequence of this keratin has revealed a striking difference between this keratin and the type II keratins expressed in epidermal cells: whereas all of the epidermal type II keratins thus far sequenced have long nonhelical termini rich in glycine and serine, this mesothelial type II keratin has amino and carboxy terminal regions that are unusually short and lack the inexact repeats of glycine and serine residues.
The Amino Acid Sequence of the Qβ Coat Protein (1971)

Abstract The amino acid sequence of the coat protein from the RNA bacteriophage Qβ has been determined. Tryptic peptides which were obtained from the oxidized protein accounted for all of the amino acid residues in the protein. The sequence of the tryptic peptides was established by a combination of enzymatic fragmentation and Edman degradation. The tryptic peptides were ordered on the basis of overlap peptides obtained from chymotrypsin and thermolysin digests of the protein. The Qβ coat protein contains 131 residues, 2 more than the f2 or R17 coat proteins. The f2 and Qβ coat proteins have only 30 residues in common, even if five insertions and five deletions are allowed in the comparison. The regions of identity are clustered in intermittent stretches 3 to 5 residues in length near the middle of the sequence.
Micromachining applications of a high resolution ultrathick photoresist (1995)

This article describes a new negative-tone photoresist, SU-8, for ultrathick layer applications. An aspect ratio of 10:1 has been achieved using near-ultraviolet lithography in a 200-μm-thick layer. The use of this resist for building tall micromechanical structures by deep silicon reactive-ion etching and electroplating is demonstrated. Using SU-8 stencils, etched depths of ≳200 μm in Si and electroplated 130-μm-thick Au structures with near-vertical sidewalls have been achieved.
Protection of a Decapeptide from Proteolytic Cleavage by Lipidation and Self-Assembly into High-Axial-Ratio Microstructures:  A Kinetic and Structural Study (1999)

We report on the synthesis, kinetics of proteolysis by trypsin, and morphological characterization of a novel lipidated decapeptide that spontaneously self-assembles in aqueous solutions into 0.5 μm diameter hollow tubules and helices that range in length from tens to hundreds of micrometers depending on formation conditions. We also report on an improved method for the tritioacetylation of peptides. Tight molecular packing of the peptide−amphiphile into a crystalline bilayer array forces tight packing between peptide headgroups, which was found to significantly protect the peptides from proteolysis by trypsin. Relief of this steric hindrance between peptide headgroups caused by solubilization of the bilayer into detergent micelles accelerated the rate of trypsin hydrolysis by 32,000-fold. Raman spectroscopy and circular dichroism spectropolarimetry were used to gain molecular-level insight into the difference between hydrolysis rates. Results obtained from these studies suggest that differences in molecular packing and conformation of the peptide headgroups in crystalline tubular and dispersed micellar phases determine the extent of proteolytic protection. Protection from proteolysis is considered a useful feature of lipidated peptide tubules for their potential use as a depot of bioactive peptides and other labile prodrugs at defined biological sites for sustained release.
The Incomplete Bucindolol Evaluation in Acute Myocardial Infarction Trial (BEAT) (2002)

Due to early closure it is unknown whether bucindolol changes mortality in high-risk post myocardial infarct patients when added to best medical therapy. The frequency of reinfarction was significantly reduced.
RULE-BASED DETECTION OF INCONSISTENCY IN UML MODELS (2002)

Abstract. Software design inconsistency can be hard to trace manually. Computer assistance in detecting and resolving inconsistency issues can help improve the quality of sophisticated software designs. This paper describes a rule-based (or production system) solution to the aforementioned problem. We characterize classes of inconsistency that occur in software design. We define a production system language and rules specific to software designs modeled in UML. Using this approach, we are able to detect inconsistencies, notify the users, recommend resolutions, and automatically fix the inconsistency during the design process. 1
Effect of supplementing a fibre basal diet with different nitrogen forms on ruminal fermentation and microbial growth in an in vitro semi-continuous culture system (RUSITEC) (1999)

Incubation trials were carried out with the rumen simulation technique (RUSITEC) to study the effects of four forms of N on the growth of ruminal micro-organisms and the fermentation variables when an all-fibre basal diet was incubated. The basal diet consisted of 10 g neutral-detergent fibre (NDF) from grass hay plus 2 g NDF from sugarbeet pulp. N forms were isolated soyabean protein, soyabean peptides, amino acids blended to profile soyabean protein and NH3 as NH4Cl. Half of the daily N supply was infused as NH4Cl and the other half was infused as each of the four treatments described. Non-NH3 N (NAN) forms increased NDF (P = 0.006), acid-detergent fibre (P = 0.003) and cellulose (P = 0.015) disappearance after 48 h incubation, CO2 (P < 0.001), CH4 (P = 0.002) and total volatile fatty acids production (P < 0.001), as well as the molar percentages of isobutyrate, isovalerate and valerate, which reflected the fermentation of amino acid C skeletons. NAN treatments also increased microbial N flow (P < 0.001) compared with NH3, with peptides and protein supporting more (P = 0.036) than amino acids. The proportion of microbial N derived from NH3 decreased successively (P < 0.05) with NH3 > amino acids > peptides > protein treatments, indicating preferential uptake of peptides without passage through the NH3 pool. Microbial efficiency (g microbial N/kg organic matter apparent disappearance) was greater (P = 0.002) for the NAN forms than for the NH3 treatment, with peptides and protein treatments supporting higher (P = 0.009) values than amino acid treatment. These results indicate that N forms other than NH3 are required for optimal fibre digestion and microbial growth.
Identification of three human renin mRNA isoforms from alternative tissue-specific transcriptional initiation (2000)

We have reported that mice transgenic for 140- and 160-kb P1 phage artificial chromosomes (PACs) containing the human renin gene express the gene in a highly tissue-restricted and regulated manner. Herein, we demonstrate that the transgene is also expressed appropriately throughout development. In the course of this investigation, we identified the existence of three transcriptional isoforms of human renin mRNA derived from the utilization of alternative transcription start sites. The first isoform is the kidney-specific isoform, which utilizes the classic renin promoter. The second is a brain-specific isoform, which when previously identified in rats and mice was due to a transcription initiation site within intron A. However, the start site in the human gene resides approximately 1,325 bp upstream of the classic promoter and encodes a new exon 1 (termed exon 1b) that splices directly to exon 2. The third isoform is lung specific and is due to transcriptional initiation 79 bp directly upstream of exon 2, fusing additional DNA within intron A (termed exon 1c) directly to exon 2 without splicing. Importantly, the alternative first exons observed in the PAC transgenic mice were identical to those used to transcribe renin in human fetal kidney, brain, and lung, suggesting these sites are bona fide isoforms of human renin mRNA and not artifacts of transgenesis. Moreover, the subtle differences in tissue-specific transcriptional initiation observed in the renin gene of rats and humans can be faithfully and accurately emulated in a transgenic model.
Formation of a Tetra-σ-Bonded Intermediate in Acetylethyne Binding on Si(100)-2 × 1 (2005)

The covalent binding of acetylethyne on Si(100)-2 x 1 has been investigated using high-resolution electron energy loss spectroscopy (HREELS) and X-ray photoelectron spectroscopy (XPS). The HREELS spectra of chemisorbed monolayers show the absence of the C=O, C[triple bond]C, and C(sp)-H stretching modes coupled with the appearance of C=C (at 1580 cm(-1)) and C(sp2)-H (at 3067 cm(-1)) stretching modes. This demonstrates that both of the C=O and CC groups of acetylethyne directly participate in binding with silicon surfaces to form C-O and C=C bonds, respectively, which is further confirmed by the XPS studies. A tetra-sigma-binding configuration through two [2 + 2]-like cycloaddition reactions in acetylethyne binding on Si(100) is proposed to account for the experimental observation. The cycloadduct containing a C=C double bond may be employed as an intermediate for further in situ chemical syntheses of multilayer organic thin films or surface functionalization.
Ultra-compact G-band 16way power splitter/combiner module fabricated through a new method of 3D-copper additive manufacturing (2015)

A new design and fabrication methodology for mmw and sub-mmw components is defined. The 3D copper additive manufacturing process is described with a full 3D volumetric 16 way splitter-combiner demonstration at G-band frequency range. The WR4 combiner is folded through design compaction and then sliced through its Z-direction and fabricated as slices to form a final 23 slice stack. The stack was then measured at 200-270 GHz using a WR4 test-through waveguide that traverses through the entire stack. The insertion loss measured at only 0.03 dB/mm showcasing its low loss characteristics. The 16 way splitter -combiner back to back was also tested using micro-machined WR4 through lines, fabricated and measured at an overall insertion loss of 4dB. The results highlight the success of the volumetric design in which a 16 way combiner measures <; 2dB insertion loss and occupies no more than 3.6 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> volume.
RETRACTED ARTICLE: Pericyte loss influences Alzheimer-like neurodegeneration in mice (2013)

Pericytes are cells in the blood-brain barrier that degenerate in Alzheimer's disease (AD), a neurological disorder associated with neurovascular dysfunction, abnormal elevation of amyloid β-peptide (Aβ), tau pathology and neuronal loss. Whether pericyte degeneration can influence AD-like neurodegeneration and contribute to disease pathogenesis remains, however, unknown. Here we show that in mice overexpressing Aβ-precursor protein, pericyte loss elevates brain Aβ40 and Aβ42 levels and accelerates amyloid angiopathy and cerebral β-amyloidosis by diminishing clearance of soluble Aβ40 and Aβ42 from brain interstitial fluid prior to Aβ deposition. We further show that pericyte deficiency leads to the development of tau pathology and an early neuronal loss that is normally absent in Aβ-precursor protein transgenic mice, resulting in cognitive decline. Our data suggest that pericytes control multiple steps of AD-like neurodegeneration pathogenic cascade in Aβ-precursor protein-overexpressing mice. Therefore, pericytes may represent a novel therapeutic target to modify disease progression in AD.
Covid-19: WHO declares pandemic because of “alarming levels” of spread, severity, and inaction (2020)

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Cardiac Hypertrophy and Impaired Relaxation in Transgenic Mice Overexpressing Triadin 1 (2001)

Triadin 1 is a major transmembrane protein in cardiac junctional sarcoplasmic reticulum (SR), which forms a quaternary complex with the ryanodine receptor (Ca(2+) release channel), junctin, and calsequestrin. To better understand the role of triadin 1 in excitation-contraction coupling in the heart, we generated transgenic mice with targeted overexpression of triadin 1 to mouse atrium and ventricle, employing the alpha-myosin heavy chain promoter to drive protein expression. The protein was overexpressed 5-fold in mouse ventricles, and overexpression was accompanied by cardiac hypertrophy. The levels of two other junctional SR proteins, the ryanodine receptor and junctin, were reduced by 55% and 73%, respectively, in association with triadin 1 overexpression, whereas the levels of calsequestrin, the Ca(2+)-binding protein of junctional SR, and of phospholamban and SERCA2a, Ca(2+)-handling proteins of the free SR, were unchanged. Cardiac myocytes from triadin 1-overexpressing mice exhibited depressed contractility; Ca(2+) transients decayed at a slower rate, and cell shortening and relengthening were diminished. The extent of depression of cell shortening of triadin 1-overexpressing cardiomyocytes was rate-dependent, being more depressed under low stimulation frequencies (0.5 Hz), but reaching comparable levels at higher frequencies of stimulation (5 Hz). Spontaneously beating, isolated work-performing heart preparations overexpressing triadin 1 also relaxed at a slower rate than control hearts, and failed to adapt to increased afterload appropriately. The fast time inactivation constant, tau(1), of the l-type Ca(2+) channel was prolonged in transgenic cardiomyocytes. Our results provide evidence for the coordinated regulation of junctional SR protein expression in heart independent of free SR protein expression, and furthermore suggest an important role for triadin 1 in regulating the contractile properties of the heart during excitation-contraction coupling.
Cloning and characterization of rod opsin cDNA from the Old World monkey, Macaca fascicularis. (1995)

The opsins of man and Old World monkeys have diverged little from the time they shared a common ancestor. Comparison of opsins from diverse phyla, however, shows that only 34 residues have been conserved. These conserved residues are likely to be important in the structure and function of rhodopsin.
The AeAct‐4 gene is expressed in the developing flight muscles of female Aedes aegypti (2004)

Population reduction of mosquitoes is an effective method for controlling dengue fever and malaria transmission. Recent developments in control techniques include proposals to construct transgenic strains of mosquitoes carrying dominant, conditional-lethal genes under the control of sex- and stage-specific promoters. In order to identify such promoters, subtractive cDNA libraries derived from male and female pupal mRNA of the yellow fever mosquito, Aedes aegypti, were constructed and screened. A cDNA clone, F49, corresponds to a gene expressed specifically in female pupae. Sequence analyses revealed that this gene belongs to the actin gene family, and therefore was designated Aedes Actin-4 (AeAct-4). Transcription analyses demonstrated that this gene is expressed predominantly in the indirect flight muscles and, to a lesser extent, the legs of developing female mosquitoes. The promoter of this gene may be a useful tool for developing conditional lethal strains of mosquitoes.