gebhart/patrepeval huggingface dataset:
Serial Analysis of Gene Expression in Turkey Sperm Storage Tubules in the Presence and Absence of Resident Sperm (2003)

Turkey sperm lose viability within 8-18 h when stored as liquid semen using current methods and extenders. In contrast, turkey hens maintain viable, fertile sperm in their sperm storage tubules (SST) for 45 or more days following a single insemination. Our long-term objectives are to identify and characterize differentially expressed genes that may underlie this prolonged sperm storage and then use this information to develop improved methods for storing liquid turkey semen. We employed serial analysis of gene expression (SAGE) to compare gene expression patterns in turkey SST recovered from hens after artificial insemination (AI) with extended semen (sperm AI) or extender alone (control AI). We constructed two separate SAGE libraries with SST RNA obtained from sperm and control AI hens. We used these libraries to generate 95,325 ten-base pair SAGE tags. These 95,325 tags represented 27,430 unique genes. The sperm and control AI libraries contained 47,663 and 47,662 tags representing 18,030 and 19,101 putative unique transcripts, respectively. Approximately 1% of these putative unique genes were differentially expressed (P<0.05) between treatments. Tentative annotations were ascribed to the SAGE tag nucleotide sequences by comparing them against publicly available SAGE tag and cDNA sequence databases. Based on its SAGE tag nucleotide sequence, we cloned a partial turkey avidin cDNA and confirmed its up-regulation in the sperm AI SST. The bioinformatics and experimental procedures employed to clone turkey avidin and confirm its differential expression represent a useful paradigm for analyzing SAGE tag data from relatively uncharacterized model systems.
Automatic Fault Extraction in 3D Seismic Interpretation (2005)

F035 Automatic Fault Extraction in 3-D Seismic Interpretation Abstract 1 Fault interpretation remains one of the most tedious and time-consuming aspects of 3D seismic interpretation and geologic model building. Traditionally faults are manually picked from seismic data as discontinuities in seismic amplitude on sections slices or in volumes. There have been several attempts to automate fault interpretation in the past that have failed to deliver acceptable interpretations with less effort in less time than manual methods. In general these methods have required very high quality data sets with very simple fault geometries and significant user correction. The Automatic Fault Extraction
The planetary biology of cytochrome P450 aromatases (2004)

This combination of bioinformatics analysis, molecular evolution, paleontology, cladistics, global climatology, structural biology, and organic chemistry serves as a paradigm in planetary biology. As the geological, paleontological, and genomic records improve, this approach should become widely useful to make systems biology statements about high-level function for biomolecular systems.
Studies on Zinc Deficiency: Changes in Trace Elements and Enzyme Activities in Tissues of Zinc-deficient Rats * (1967)

Zinc content of testes, bones, esophagus, kidneys, and muscles was decreased, whereas iron content was increased in the testes of zinc-deficient rats compared to restrictedly fed control rats. Histochemical enzyme determinations revealed reduced activities of certain enzymes in the testes, bones, esophagus, and kidneys. In the testes, lactic dehydrogenase (LDH), malic dehydrogenase (MDH), alcohol dehydrogenase (ADH), and NADH diaphorase; in the bones, LDH, MDH, ADH, and alkaline phosphatase; in the esophagus, MDH, ADH, and NADH diaphorase; and in the kidneys, MDH and alkaline phosphatase were decreased in zinc-deficient rats compared to restrictedly fed controls. Succinic dehydrogenase (SDH) revealed no significant changes under the conditions of our experiments in various groups of rats that were investigated. In a "repleted" group of rats, content of zinc in testes and bones increased significantly, compared to the deficient group. The iron content of the testes decreased after repletion with zinc. In the testes, bones, esophagus, and kidneys, the activities of various enzymes increased after repletion with zinc. Inasmuch as the major manifestations of zinc deficiency syndrome in the rat include growth retardation, testicular atrophy, and esophageal parakeratosis, our results suggest that the content of zinc in the above tissues most likely controls the physiological processes through the formation of zinc-dependent enzymes.
The Chemokine Stromal Cell-Derived Factor-1α Modulates α4β7 Integrin-Mediated Lymphocyte Adhesion to Mucosal Addressin Cell Adhesion Molecule-1 and Fibronectin (2002)

The interaction between the integrin alpha(4)beta(7) and its ligand, mucosal addressin cell adhesion molecule-1, on high endothelial venules represents a key adhesion event during lymphocyte homing to secondary lymphoid tissue. Stromal cell-derived factor-1alpha (SDF-1alpha) is a chemokine that attracts T and B lymphocytes and has been hypothesized to be involved in lymphocyte homing. In this work we show that alpha(4)beta(7)-mediated adhesion of CD4(+) T lymphocytes and the RPMI 8866 cell line to mucosal addressin cell adhesion molecule-1 was up-regulated by SDF-1alpha in both static adhesion and cell detachment under shear stress assays. Both naive and memory phenotype CD4(+) T cells were targets of SDF-1alpha-triggered increased adhesion. In addition, SDF-1alpha augmented alpha(4)beta(7)-dependent adhesion of RPMI 8866 cells to connecting segment-1 of fibronectin. While pertussis toxin totally blocked chemotaxis of CD4(+) and RPMI 8866 cells to SDF-1alpha, enhanced alpha(4)beta(7)-dependent adhesion triggered by this chemokine was partially inhibited, indicating the participation of Galpha(i)-dependent as well as Galpha(i)-independent signaling. Accordingly, we show that SDF-1alpha induced a rapid and transient association between its receptor CXCR4 and Galpha(i), whereas association of pertussis toxin-insensitive Galpha(13) with CXCR4 was slower and of a lesser extent. SDF-1alpha also activated the small GTPases RhoA and Rac1, and inhibition of RhoA activation reduced the up-regulation of alpha(4)beta(7)-mediated lymphocyte adhesion in response to SDF-1alpha, suggesting that activation of RhoA could play an important role in the enhanced adhesion. These data indicate that up-regulation by SDF-1alpha of lymphocyte adhesion mediated by alpha(4)beta(7) could contribute to lymphocyte homing to secondary lymphoid tissues.
Compact post-compression system for peak power enhancement of an ultrafast diode-pumped laser (2010)

We report on a compact system based on post-compression of an ytterbium ultrafast laser, using Nitrogen-filled hollow fiber, delivering 60fs pulses with 330µJ energy at 2kHz and 200µJ at 5kHz.
Parvovirus B19 Infection in Human Immunodeficiency Virus Type 1-Infected Persons Failing or Intolerant to Zidovudine Therapy (1993)

To determine the incidence of B19 infection in patients with AIDS who were being treated with dideoxyinosine, serial sera (n = 28) taken over a 2-year period from 14 individuals were analyzed with respect to anti-B19 serology and the presence of B19 DNA. All 14 individuals were anti-B19 IgM negative. Nine of 14 had B19 viremia by Southern analysis of polymerase chain reaction product. Five of 9 with B19 viremia had > or = 1 anti-B19 IgG-positive sample; none of 5 without viremia had anti-B19 IgG. Four of 9 viremic individuals had serially positive samples. All 4 had severe anemia (hemoglobin < 8.5 g/dL) while taking zidovudine. A fifth individual whose severe anemia resolved after zidovudine was discontinued did not have B19 viremia. Therefore, a significant proportion of this group of patients with AIDS who developed severe anemia while receiving zidovudine had persistent B19 infection. These results suggest that B19 infection should be considered in anemic patients with AIDS.
Synthesis and characterization of main-chain NLO oligomers and polymer that contain 4-dialkylamino- 4?-(alkylsulfonyl)azobenzene chromophores (2000)

An ω-amino carboxylic acid monomer that contained a nonlinear optical (NLO) chromophore was prepared by a convergent synthesis. Strategies for selective protection/deprotection of the amino and carboxylic acid functionalities were developed. The protected monomer, 4-[N-(4-benzyloxycarbonyl)butyl-N-methylamino]-4′-[2″,5″-bis(decyloxy)-4″-(phthalimidomethyl)benzylsulfonyl]azobenzene, could be deprotected selectively or sequentially to give HOOC-monomer-N-phthaloyl, benzyl-OOC-monomer-NH2, or HOOC-monomer-NH2. Sequential synthesis was performed to yield main-chain NLO dimers and tetramers. This was accomplished by selective deprotection and dicyclohexylcarbodiimide coupling. The HOOC-monomer-NH2 was polymerized by treatment with diphenylphosphoryl azide to give a main-chain NLO polyamide. The monomer, dimer, tetramer, and polymer NLO materials were characterized by 1H, 13C, IR, and UV–visible spectroscopy as well as by gel permeation chromatography, differential scanning calorimetry, and elemental analysis. The NLO properties of these materials were measured. Thin films of the oligomers and polymer were prepared by spin casting on indium-tin oxide coated glass. The second-order NLO properties of the oligomers and polymer thin films were studied by in situ corona poling/second-harmonic generation and attenuated total reflection methods. The optimal poling temperatures were significantly lower than the melting temperatures or glass-transition temperatures of the oligomers and polymer. The poling efficiency increased in the following order: monomer, oligomers, and polymer. An electro-optic coefficient of 4 pm/V at 1.06 μm was obtained for the polymer. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 546–559, 2000
Thermally tunable integrated optical ring resonator with poly-Si thermistor (1996)

Doped polysilicon is applied as a thermo-optic heating element to temperature tune the ring resonator based on silicon nitride rib waveguides on silicon. The ring diameter is 2 mm allowing a large free spectral range of 26 GHz. For the first time, a poly-Si resistor is used as a thermistor to measure waveguide temperature. The temperature coefficient of the poly-Si thermistor is 9.5/spl times/10/sup -4///spl deg/C. The reproducibility of the temperature measurement is 0.3/spl deg/C. The finesse of the ring resonator is 77. The propagation loss of silicon nitride rib waveguide is 0.5 dB/cm at the wavelength of 1.312 /spl mu/m. The temperature tuning of the ring resonator and the in situ supervision of the temperature on chip based on the same poly-Si fabrication process may find use especially in optical sensor applications.
Crystal structure of a translation termination complex formed with release factor RF2 (2008)

We report the crystal structure of a translation termination complex formed by the Thermus thermophilus 70S ribosome bound with release factor RF2, in response to a UAA stop codon, solved at 3 A resolution. The backbone of helix alpha5 and the side chain of serine of the conserved SPF motif of RF2 recognize U1 and A2 of the stop codon, respectively. A3 is unstacked from the first 2 bases, contacting Thr-216 and Val-203 of RF2 and stacking on G530 of 16S rRNA. The structure of the RF2 complex supports our previous proposal that conformational changes in the ribosome in response to recognition of the stop codon stabilize rearrangement of the switch loop of the release factor, resulting in docking of the universally conserved GGQ motif in the PTC of the 50S subunit. As seen for the RF1 complex, the main-chain amide nitrogen of glutamine in the GGQ motif is positioned to contribute directly to catalysis of peptidyl-tRNA hydrolysis, consistent with mutational studies, which show that most side-chain substitutions of the conserved glutamine have little effect. We show that when the H-bonding capability of the main-chain N-H of the conserved glutamine is eliminated by substitution with proline, peptidyl-tRNA esterase activity is abolished, consistent with its proposed role in catalysis.
Music, language, and the origins of modernity (2007)

The contrast between two notional kinds of ‘metaphysics’ adumbrated in the previous chapter can be understood as another way of characterising the tension between a ‘positivist’, science-oriented, conception of modern philosophy, and a ‘Romantic’ conception which is oriented towards what the arts reveal that the sciences cannot. This tension is too often seen in rigid terms, and I want to develop a more nuanced version of it via the issue of music. In the last chapter I employed the notion of metaphysics to suggest ways of rehabilitating the claim that philosophy should be concerned with the idea of what constitutes a meaningful world, without falling back into no longer defensible, ‘dogmatic’ theological or metaphysical conceptions of meaning. Part of this rehabilitation relies, though, precisely on the possibility that it is when the limits of philosophy become apparent that other means of revealing meaning in the world, like music, may become most significant. The resistance of what is manifest in terms of metaphysics to the terms of metaphysics suggests both new possibilities and instructive difficulties. The initial difficulty is that any positive explanatory assertion about these kinds of meaning has to take one in the direction of metaphysics, even though metaphysics does not offer resources for meaning of the kind that form the focus of metaphysics. This also implies, however, that the discursive demands of many kinds of philosophy cannot be fulfilled by the resources of metaphysics.
Mapping 3′ mRNA Isoforms on a Genomic Scale (2015)

Most eukaryotic genes are transcribed into mRNAs with alternative poly(A) sites. Emerging evidence suggests that mRNA isoforms with alternative poly(A) sites can perform critical regulatory functions in numerous biological processes. In recent years, a number of strategies utilizing high-throughput sequencing technologies have been developed to aid in the identification of genome-wide poly(A) sites. This unit describes a modified protocol for a recently published 3'READS (3' region extraction and deep sequencing) method that accurately identifies genome-wide poly(A) sites and that can be used to quantify the relative abundance of the resulting 3' mRNA isoforms. This approach minimizes nonspecific sequence reads due to internal priming and typically yields a high percentage of sequence reads that are ideally suited for accurate poly(A) identification.
Optical pulse-burst position modulation for antenna beam forming (2009)

We present a realization of an optically controlled pulse-burst position modulator to be used for a radio-frequency photonic circuit aiming to produce beam forming for a Radar-transmitting antenna. The configuration uses a set of fiber ring resonators that contain erbium-doped fiber amplifiers. By controlling the pumping in each loop, the gain of the doped fibers is changed, which results with a change in the resonators" finesses. In the end of each optical path, the optical signal is sampled and converted to an electronic signal while an electronic subtraction is performed between the outputs of the two resonators. Because each resonator has different and controlled finesse, the subtraction results in an output pulse burst with varied position.
Vaptans: A Potential New Approach for Treating Chronic Hyponatremia in Psychotic Patients (2012)

Chronic hyponatremia is known to have deleterious effects on the quality of life for many patient groups. These preliminary results suggest that oral tolvaptan provides rapid, effective, and safe treatment of chronic hyponatremia in patients with psychotic disorders and that the effect is safely sustained over long periods of time. These findings represent an important step forward in treating a significant unmet need in psychotic populations.
Structures of the heat-treatment centers<i>NL</i>8 and<i>NL</i>10 in silicon (1989)

An electron-spin-resonance investigation on n-type (P-doped) and an electron-nuclear double-resonance (ENDOR) investigation on p-type (B- and Al-doped) Czochralski-grown oxygen-rich Si was performed after annealing at 460 \ifmmode^\circ\else\textdegree\fi{}C and formation of the heat-treatment centers Si-NL8 and Si-NL10. The NL10 defects have different structures influenced by the silicon dopants in contrast to NL8. It is shown that a recent suggestion that NL10 could be an acceptor state of NL8 is not convincing.
Rheumatoid arthritis and sterile corneal ulceration (1984)

Tissue immune effector cells and epithelial surface antigens present in eye tissue of rheumatoid arthritis (RA) patients with sterile corneal ulceration were studied using a large panel of monoclonal antibodies. During periods of active corneal ulceration, conjunctivae and corneas of all RA patients studied contained numerous immune-associated (Ia) antigen-positive tissue macrophages. In 4 of 6 patients, conjunctival or corneal T cell infiltrations were present. In 2 patients, a T cell vasculitis was seen in conjunctival tissue. Conjunctival epithelial cells of all 6 RA patients expressed Ia antigens during active corneal ulceration. These data provide evidence for immune-mediated mechanisms in the pathophysiology of corneal ulceration in RA. Moreover, the expression of Ia antigens by conjunctival epithelial cells may be a useful indicator of disease activity in RA patients with sterile corneal ulceration.
Dispiro(fluorene-9,4'-[1,3]dithiolane-5',9''-fluorene) (1995)

The crystal structure of dispiro(fluorene-9,4'-[1,3]dithiolane-5',9-fluorene), C 27 H 18 S 2 , is reported. The C4-C5 bond connecting the two fluorenyl groups is 1.580 (4) A which is slightly longer than the C-C bond lengths [1.36-1.49 A] in other 1,3-dithiolanes.
O3‐10‐03: SEX AND APOE EFFECTS ON MEMORY PERFORMANCE, NEURODEGENERATION, AND B‐AMYLOID ACROSS THE ADULT LIFESPAN (2014)

To examine sex and APOE effects on memory, brain structure (adjusted hippocampal volume or HVa) and β-amyloid as a function of age over the adult life span (age 30 - 90 plus) in cognitively normal individuals. We studied 970 cognitively normal subjects cross-sectionally; 934 participants aged 51-96 enrolled in a population-based study of cognitive aging; and 36 aged 30-50 who were self-selected volunteers. All subjects underwent the same memory testing, MRI, and amyloid PET protocols. Participants were grouped by sex and APOEε4 (carrier vs. non-carrier). We used quantile regression to estimate the median amyloid PET, HVa or memory value as a function of age. We fit a single model that included age, sex, and APOEε4 status along with all two-way interactions. Overall, memory performance worsened gradually from 30 to 70 years and more steeply above 70. HVa was relatively steady from 30 to 60 years but worsened noticeably above age 60. Median amyloid PET was low through approximately age 65 and increased beyond that age in all groups. Men performed worse than women from age 40-50 onward on memory. HVa was lower in men than women beyond age 60. There was no sex difference in amyloid PET at any age. Within each sex, memory and HVa were not different by APOE at any age, except for worse memory among women carriers beyond their 70s. APOE ε4 increased the proportion of abnormal amyloid PET values in those above age 65, but had no impact prior to that age. Individuals with abnormal amyloid PET values first appeared around age 65 years in both APOE ε4 carriers and non-carriers. Advancing age and male sex had more substantial impacts on memory and HVa than APOEε4 in cognitively normal individuals across the adult lifespan (most from a population based sample). In addition, worsening memory and HVa preceded abnormal b -amyloidosis at the population level. We conclude that the onset of b -amyloidosis typically arises on a background of preexisting functional decline and structural degeneration that are unrelated to fibrillar b -amyloid deposition; therefore the onset of b -amyloidosis in late life likely accelerates rather than initiates memory dysfunction and brain atrophy.
VLSI hardware architecture for complex fuzzy systems (1999)

This paper presents the design of a VLSI fuzzy processor, which is capable of dealing with complex fuzzy inference systems, i.e., fuzzy inferences that include rule chaining. The architecture of the processor is based on a computational model whose main features are: the capability to cope effectively with complex fuzzy inference systems; a detection phase of the rule with a positive degree of activation to reduce the number of rules to be processed per inference; parallel computation of the degree of activation of active rules; and representation of membership functions based on /spl alpha/-level sets. As the fuzzy inference can be divided into different processing phases, the processor is made up of a number of stages which are pipelined. In each stage several inference processing phases are performed parallelly. Its performance is in the order of 2 MFLIPS with 256 rules, eight inputs, two chained variables, and four outputs and 5.2 MFLIPS with 32 rules, three inputs, and one output with a clock frequency of 66 MHz.
[Indication for prosthesis in pertrochanteric fractures]. (1978)

Trochanteric fractures with concomitant osteoarthrosis of the hip joint present a clear indication for total hip replacement there by treating both the fracture and the joint disease. Trochanteric fractures with an otherwise normal hip joint are usually treated by internal fixation. Under certain conditions (old patient, simple fracture) femoral head or total hip replacement may, however, be preferable. As a rule, duration and technical difficulty of such an operation should not exceed that of any classical method of internal fixation.
The mechanism of the colour shift of astaxanthin in α-crustacyanin as investigated by 13C MAS NMR and specific isotope enrichment (1997)

Abstract
Detection of Chemokines in Nasal Secretion Using Filter Paper (2006)

It is widely assumed that cytokines and chemokines play a significant role in the pathogenesis of inflammatory diseases such as allergic rhinitis. Much of the data supporting this concept has been generated under in vitro experimental conditions; a definitive proof of the involvement of these factors in inflammation would require the recovery of factors from inflammatory sites. Although washing and lavage of inflammatory sites is routinely done to detect factors at the site, relatively high concentrations of factors are only measurable by conventional methods. We attempted to detect chemokines in nasal secretion by filter paper and to determine possible mechanisms of chemokines in the development of allergic rhinitis. Small filter strips (7×30mm) were placed on nasal turbinates for 1min. After being air-dried strips were cut into small pieces and factors were extracted by rocking for 12h at 4°C. The eluate was collected and assayed for eotaxin and RANTES by ELISA. The eluate from normal control subjects contained detectable levels of both eotaxin and RANTES. These factor levels were significantly increased in patients with pollinosis. Levels of eotaxin, but not of RANTES, correlate closely with the presence of eosinophils in nasal mucosa. These results suggest that eotaxin is an important factor in nasal mucosal eosinophilia in pollinosis.
A MagDot-Nanoconveyor Assay Detects and Isolates Molecular Biomarkers. (2012)

The ability to quickly analyze, separate, and manipulate multiple types of biomarkers from small sample volumes is a significant step toward personalized medicine.
2-Methylpentadienyl- and 2,4-dimethylpentadienylpotassium: first examples of U-shaped, though open-chain, organometallics (1978)

The U-shaped structures of the title compds. I (R = H, Me) were elucidated by the dimethoxyboration-oxidn. procedure to II (R = H, R1 = Me; R = Me, R1 = H, and R = R1 = Me). [on SciFinder (R)]