gebhart/patrepeval huggingface dataset:
Allelic forms of rat κ chain genes: Evidence for strong selection at the level of nucleotide sequence (1981)

The genes that code for two allotypic forms of the rat kappa light chain constant region (C(kappa)) have been cloned and the nucleotide sequence of 1172 base pairs of coding and flanking sequence has been determined for both alleles. These sequences have been compared to each other and to the corresponding sequences found in the mouse and human. Comparison of the LEW allele with mouse C(kappa) reveals two surprising features: (i) There is an unusually large number of amino acid substitutions (21) relative to the total number of nucleotide changes (37) in the coding region. Comparision among several other mammalian genes reveals a larger proportion of "silent" changes. (ii) The rate of accumulation of base substitutions is the same within the coding region as it is in some 870 base pairs of noncoding sequence (including 3' untranslated, 3' flanking, and 5' intervening sequences). Comparison of the two allelic forms of rat C(kappa) shows the same unusual features in more extreme form. (i) Twelve base substitutions in the coding region determine 11 amino acid differences-only one "silent" change exists. (ii) There are 12 base substitutions in the 318 base pairs of coding sequence (3.7% difference) and only 9 in the remaining 854 base pairs of noncoding DNA (1.1%), a highly significant difference. This degree of conservation of noncoding sequences and of "silent" sites within the coding region is unique among the mammalian genes studied thus far. These patterns suggest that there has been strong selection for conservation of nucleotide sequences, both inside and outside the coding region, independent of the selection required to maintain the function and characteristic structure of the immunoglobulin domain itself. The functions of the nucleotide sequences that account for this selective pressure are unclear at the present time.
The Modified National Institutes of Health Stroke Scale: its Time has Come (2009)

The National Institutes of Health Stroke Scale (NIHSS) is a well known, reliable and valid stroke deficit scale. The NIHSS is simple, quick, and has shown significant reliability in diverse groups, settings, and languages. The NIHSS also contains items with poor reliability and redundancy. Recent investigations (include assessing a new training DVD, analyzing webbased or videotape certifications, and testing foreign language versions) have further detailed reliability issues. Items recurrently shown to have poor reliability include Level of Consciousness, Facial Palsy, Limb Ataxia, and Dysarthria. The modified NIHSS (mNIHSS) minimizes redundancy and eliminates poorly reliable items. The mNIHSS shows greater reliability in multiple settings and cohorts, including scores abstracted from records, when used via telemedicine, and when used in clinical trials. In a validation of the mNIHSS against the NIHSS, the number of elements with excellent agreement increased from 54% to 71%, while poor agreement decreased from 12% to 5%. Overall, 45% of NIHSS items had less than excellent reliability vs. only 29% for the mNIHSS. The mNIHSS is not the ideal stroke scale, but it is a significant improvement over the NIHSS. The mNIHSS has shown reliability at bedside, with record abstraction, with telemedicine, and in clinical trials. Since the mNIHSS is more reliable, it may allow for improved practitioner communication, improved medical care, and refinement of trial enrollments. The mNIHSS should now serve as the primary stroke clinical deficit scale for clinical and research aims. When it comes to the mNIHSS, its time has come!
Increase in Mechanical Strength of Al&ndash;Y&ndash;Ni Amorphous Alloys by Dispersion of Nanoscale fcc-Al Particles (1991)

Al-base amorphous alloys in which nanoscale fcc-Al particles are uniformly dispersed have been produced over the composition range of 0 to 10% Y and 0 to 10% Ni. The alloys exhibit tensile fracture strength (σf) and hardness (Hv) higher than those of amorphous single phase alloys with the same compositions, retaining a good bending ductility. The particle size of the fcc-Al phase increases in the range of 3 to 50 nm with a decrease of cooling rate. The Hv and Young’s modulus (E) increase monotonically with increasing volume fraction of the fcc phase (Vf) while the σf shows a maximum value in the Vf range of 10 to 20%. The increase of σf in the Vf range below 20% is presumably due to an enhancement of the resistance to shear deformation caused by the nanoscale fcc particles which have higher mechanical strengths than the amorphous phase with the same compositions. On the other hand, the decrease of σf with further increasing Vf is due to an enhancement of embrittlement tendency. In addtion, the increase of σf, Hv and E with a decrease of Y/(Y+Ni) in the mixed Al88Y12−xNix alloys with a constant Vf (\simeq10%) seems to originate from an increase in the attractive bonding force among the constituent atoms.
Chemical Behavior of a Pair of (COD)CpRh and −Ir Complexes with Pendant Peripheral −B(C<sub>6</sub>F<sub>5</sub>)<sub>2</sub>Groups (2008)

Hydroboration of (COD)Rh(η5-C5H4-allyl) (7) with the strongly electrophilic reagent HB(C6F5)2 yields (COD)Rh[η5-C5H4-(CH2)3B(C6F5)2] (8). Nucleophilic N-heterocyclic reagents (1-methylimidazole or 1-methylbenzimidazole) add to the boron atom of the bifunctional complex to yield the respective adducts (9a, 9b). Both were characterized by X-ray diffraction. Addition of HB(C6F5)2 to the corresponding (COD)Ir(η5-C5H4-allyl) complex (10) eventually results in the formation and isolation of the cycloborylated zwitterionic (COD)(η5-C5H3-cyclo-(CH2)3B(C6F5)2]IrH product (13) (also characterized by X-ray crystal structure analysis). However, 13 seems to thermally equilibrate in a reverse electrophilic aromatic substitution reaction with the thermodynamically disfavored open-chain (COD)Ir[η5-C5H4-(CH2)3B(C6F5)2] isomer (11). This follows from reactions of 13 with 1-methylimidazole or 1-methylbenzimidazole, which rapidly yield the corresponding open-chain adducts 14a and 14b at room temperature (both characterized by X-ray diffraction). In a slow reaction complex 13 even eventually reacts with pyrrole by ring opening to yield the open-chain product 15, which features the 2H-pyrrole isomer coordinated to the strong −B(C6F5)2 Lewis acid at the end of the trimethylene tether. Complex 15 was also characterized by an X-ray crystal structure analysis.
Effect of DNA Scaffolding on Intramolecular Electron Transfer Quenching of a Photoexcited Ruthenium(II) Polypyridine Naphthalene Diimide (1999)

Intramolecular emission quenching of a photoexcited ruthenium(II) polypyridine by a covalently linked naphthalene diimide (NDI) has been measured in aqueous buffer both without and with calf thymus DNA. The complex consists of a Ru(2,2'-bipyridine)(2)(2,2'-bipyridine-5-carboxamide)(2+) electron donor covalently attached by way of a -CH(2)CH(2)CH(2)- linker to a 1,4,5,8-naphthalene diimide acceptor (Ru-NDI, 1). The NDI portion of the complex intercalates in calf thymus DNA, as indicated by the hypochromism of its optical absorbance bands and observation of an induced circular dichroism spectrum in the same region. Emission quenching in Ru-NDI has been measured relative to a Ru tris-bpy model lacking the NDI moiety by both lifetime and emission quantum yield techniques. Using lifetime averages, the relative emission quenching is, respectively, 99.1% and 97.9% in aqueous buffer solutions without and with DNA. The emission quenching is ascribed to intramolecular electron transfer within the Ru-NDI complex with an estimated driving force (-DeltaG degrees ) of 0.33 eV. In buffer, the emission decays of Ru-NDI alone are fit well with a triexponential model with lifetimes of 0.34 (0.88), 1.99 (0.11), and 12.6 (0.008) ns (relative amplitude). The emission decays of the DNA-intercalated Ru-NDI complex are also fit well with a triexponential model with lifetimes of 0.31 (0.79), 2.00 (0.13), and 11.8 (0.08) ns. Thus, the fractional amplitudes of the lifetimes change upon DNA intercalation of the complex, while the lifetimes themselves remain essentially the same. The average rates of electron transfer in aqueous buffer without and with DNA are, respectively, 1.6 x 10(9) and 6.8 x 10(8) s(-)(1). The striking result of this study is that the overall character of electron transfer quenching in Ru-NDI is very similar whether or not it is bound to DNA. Intercalation of the NDI in DNA apparently has negligible consequences for electron transfer, implying either that the activation energy and electronic coupling in Ru-NDI are largely unaffected by this, at first glance, seemingly significant environmental change or that changes in these parameters on DNA binding cancel fortuitously.
The Efficient Computation of Position-Specific Match Scores with the Fast Fourier Transform (2002)

Historically, in computational biology the fast Fourier transform (FFT) has been used almost exclusively to count the number of exact letter matches between two biosequences. This paper presents an FFT algorithm that can compute the match score of a sequence against a position-specific scoring matrix (PSSM). Our algorithm finds the PSSM score simultaneously over all offsets of the PSSM with the sequence, although like all previous FFT algorithms, it still disallows gaps. Although our algorithm is presented in the context of global matching, it can be adapted to local matching without gaps. As a benchmark, our PSSM-modified FFT algorithm computed pairwise match scores. In timing experiments, our most efficient FFT implementation for pairwise scoring appeared to be 10 to 26 times faster than a traditional FFT implementation, with only a factor of 2 in the acceleration attributable to a previously known compression scheme. Many important algorithms for detecting biosequence similarities, e.g., gapped BLAST or PSIBLAST, have a heuristic screening phase that disallows gaps. This paper demonstrates that FFT algorithms merit reconsideration in these screening applications.
Conversion of Mono- and Oligodeoxyribonucleotides to 5'-Triphosphates<sup>1</sup> (1965)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTConversion of Mono- and Oligodeoxyribonucleotides to 5'-Triphosphates1Donald E. Hoard and Donald G. OttCite this: J. Am. Chem. Soc. 1965, 87, 8, 1785–1788Publication Date (Print):April 1, 1965Publication History Published online1 May 2002Published inissue 1 April 1965https://pubs.acs.org/doi/10.1021/ja01086a031https://doi.org/10.1021/ja01086a031research-articleACS PublicationsRequest reuse permissionsArticle Views1517Altmetric-Citations317LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Soluble Epoxide Hydrolase as an Anti-inflammatory Target of the Thrombolytic Stroke Drug SMTP-7 (2014)

Although ischemic stroke is a major cause of death and disability worldwide, only a small fraction of patients benefit from the current thrombolytic therapy due to a risk of cerebral hemorrhage caused by inflammation. Thus, the development of a new strategy to combat inflammation during thrombolysis is an urgent demand. The small molecule thrombolytic SMTP-7 effectively treats ischemic stroke in several animal models with reducing cerebral hemorrhage. Here we revealed that SMTP-7 targeted soluble epoxide hydrolase (sEH) to suppress inflammation. SMTP-7 inhibited both of the two sEH enzyme activities: epoxide hydrolase (which inactivates anti-inflammatory epoxy-fatty acids) and lipid phosphate phosphatase. SMTP-7 suppressed epoxy-fatty acid hydrolysis in HepG2 cells in culture, implicating the sEH inhibition in the anti-inflammatory mechanism. The sEH inhibition by SMTP-7 was independent of its thrombolytic activity. The simultaneous targeting of thrombolysis and sEH by a single molecule is a promising strategy to revolutionize the current stroke therapy.
A phase I dose escalation trial of ispinesib (SB-715992) administered days 1–3 of a 21-day cycle in patients with advanced solid tumors (2006)

2026 Background: Ispinesib, a novel cytotoxic agent inhibiting the kinesin spindle protein (KSP) has demonstrated significant antitumor activity in multiple murine tumor models. The primary objectives of the study were to assess the safety and tolerability of SB-715992, to determine the dose limiting toxicity (DLT), and the maximum tolerated dose (MTD). Methods: Ispinesib was administered days 1–3 intravenously over 1 hour every 21 days, starting at a dose of 1 mg/m 2 /day. Traditional 3-patient cohort trial design was utilized with dose levels of 2, 4, 6, 8 mg/m 2 /day. Results: Twenty-seven patients (24 Caucasians, 3 African-Americans, 16 males, 11 females) with various tumor types were enrolled; colorectal (7), renal (5), bladder (2), lung (2), pharynx (2), pancreas (2), others (7). Grade 3/4 toxicities were noted starting at the 4 mg/m 2 dose level with two patients developing grade 4 neutropenia; one for < 5 days, one for > 5 days (with grade 3 leukopenia). At the 6 mg/m 2 dose level, grade 3 neutropenia and leukopenia were reported. At the 8 mg/m 2 dose level, 3 of 3 patients had grade 4 neutropenia and leukopenia. The 6 mg/m 2 dose level was declared the MTD. Toxicities seen in the additional 6 patients included grade 1 fatigue (1/6), grade 1 infusion- related flushing (1/6), grade 3 febrile neutropenia (1/6), and grade 4 neutropenia and leukopenia (1/6). The MTD cohort has been expanded to 10 evaluable patients for confirmation of tolerability and pharmacodynamic endpoints including phosphohistone 3 (PH3), cyclin E, and TUNEL assay on serial tumor biopsies. Preliminary pharmacokinetic data appear linear, but not dose proportional. As predicted, between days 1 and 3, accumulation ranged from 40 to 106%. Exposures appear comparable between cycles 1 and 2. Stable disease in 2 patients with renal cell carcinoma (4 and 5 cycles) and minor response in one patient with bladder cancer were seen. Conclusions: Treatment with ispinesib at the MTD of 6 mg/m 2 /day x 3 days in patients with advanced solid tumors was well tolerated with consistent dose limiting toxicity of myelosuppression. No significant financial relationships to disclose.
Excretion of three major prostatic secretory proteins in the urine of normal men and patients with benign prostatic hypertrophy or prostate cancer (1987)

We have studied the mode of excretion of three prostatic secretory proteins, namely acid phosphatase (PAP), prostate-specific antigen (PSA) and beta-inhibin, in the urine of normal adult men, and we have determined the urinary levels of these proteins in men with benign prostatic hypertrophy (BPH) or adenocarcinoma. The output of the three proteins was highly variable during the day. In order to minimize these variations, 24-hour urine samples were collected thereafter. Our study showed that PAP concentrations in 50% of men with or without symptomatic BPH were similar to those of normal young men. In the remaining 50%, PAP was undetectable. In contrast, average PSA and beta-inhibin concentrations were higher in patients with BPH than in young men (p less than 0.05). The three markers were decreased or nondetectable in about half of the patients with untreated prostatic cancer. This phenomenon was even more pronounced in patients receiving hormonal treatment (castration or diethylstilbestrol). However, some of these patients still excreted normal amounts of PAP, PSA, and beta-inhibin. Urinary and serum PAP levels showed no correlation. These results indicate that urinary prostatic markers provide an easy means to study the behavior of the primary prostatic tumor. This information may be of potential value since it is not obtained with serum markers which originate mostly from metastatic cells.
Automatic sushi classification from images using color histograms and shape properties (2014)

Self-service sushi vendors are becoming popular with Thai people. The cashier operation is usually a bottleneck in a purchase process and can cause long queues at the cashier counter. This paper proposes an automatic sushi point-of-sale system that captures sushi images from a webcam to identify types of sushi and calculate the total cost of that purchase. The system segments each piece of sushi from the background using color information. Histograms of color in RGB and HSV color spaces and shape properties of each piece of sushi are used as features for k-Nearest Neighbor classifier. Experimental results showed the accuracy of the proposed system at 93.7%.
Azo Dyes from Cashewnut Shell Liquid Derivatives. Part II. Azo Dyes from 5-Pentadecylresoreinol (1964)

5-Pentadecyl resorcinol, a hydrogenated derivative of a component of cashewnut shell liquid, has been coupled with p-methexybenzenediazonium chloride. Two monoaze and two disazo dyes have been obtained and their position isomerism has been thoroughly investigated. The structures of the monoazo and disazo dyes have been arrived at by comparing their absorption spectra and mode of formation of copper complexes with those of monoazo and disazo dyes of resorcinol.
Dorsoventral Extension of the Talairach Transformation and Its Automatic Calculation for Magnetic Resonance Neuroimages (2005)

The Talairach transformation (TT), the most prevalent method for brain normalization and atlas-to-data warping, is conceptually simple, fast and can be automated. Two problems with the TT in the clinical setting that are addressed in this article are reduced accuracy at the orbitofrontal cortex and upper corpus callosum (CC) and unsuitability for functional neurosurgery because of incomplete scanning. To increase dorsoventral accuracy, we introduce 2 additional landmarks: the top of the CC (SM) and the most ventral point of the orbitofrontal cortex on the midsagittal slab (IM). A method for their automatic calculation is proposed and validated against 55 diversified magnetic resonance (MR) imaging cases. The SM and IM landmarks are identified accurately and robustly in an automatic way. The average error of SM localization is 0.69 mm, and 91% of all cases have an error not greater than 1 mm. The average error of IM localization is 0.98 mm, approximately three quarters of cases have an error not greater than 1 mm, and 95% of all cases have an error not larger than 2 mm. The SM is correlated (R(2) = 0.72) with the most superior cortical landmark, whereas the IM is only loosely correlated (R(2) = 0.22) with the most inferior cortical landmark. On average, the original TT overlays the atlas axial plate at -24 on the orbitofrontal cortex as opposed to the correct plate at -28. Therefore, 1-dimensional ventral scaling in the original TT is insufficient to cope with variability in the orbitofrontal cortex. The key advantages of our approach are the preserved conceptual simplicity of the TT, fully automatic identification of the new landmarks, improved accuracy of the atlas-to-data match without compromising performance, and enabled TT use in functional neurosurgery when a dorsal part of the brain is not available in the scan.
Sterilization by gamma radiation impairs the tensile fatigue life of cortical bone by two orders of magnitude (2005)

Cortical bone grafts are utilized frequently for skeletal reconstruction, spinal fusion and tumor surgery. Due to its efficacy and convenience terminal sterilization by gamma radiation is often essential to minimize disease transmission and infection. However, the impairment in the material properties of bone tissue secondary to gamma radiation sterilization is a concern since the mechanical functionality of a bone graft is of primary importance. While the extent of this impairment is well investigated for monotonic loading conditions, there does not seem to exist any information on the effects of gamma radiation sterilization on cortical bone's fatigue properties, the physiologically relevant mode of loading. In this study we investigated the degradation in the high-cycle and low-cycle tensile fatigue lives of cortical bone tissue secondary to gamma radiation sterilization at a dose of 36.4 kGy which approximately falls in the higher end of the standard dose range used in tissue banking. The high-cycle and the low-cycle fatigue tests were conducted under load control at initial strain levels of 0.2% and 0.4%, respectively. Monotonic tensile tests were also conducted to compare the impairment of fatigue properties with the impairment of monotonic properties. Results demonstrated that the impairment in both the high-cycle and the low-cycle fatigue lives were two orders of magnitude following sterilization, a change much more pronounced than that observed for monotonic loading. In conclusion, the results suggest that the impairment of the mechanical function of gamma radiation sterilized allografts is even worse in fatigue than monotonically. Therefore, grafts should be designed to minimize functional strains and avoid stress raisers to prevent premature fatigue failures.
Direct continuous-wave measurement of n2 in various types of telecommunication fiber at 155 μm (1996)

A method for measuring the nonlinear refractive index of optical fibers with an error of less than 5% is demonstrated. The technique is based on measuring the nonlinear phase shift experienced by a dual-frequency beat signal, permitting a simple, highly sensitive, accurate, repeatable, and easily automated measurement procedure and sampling. Measurements of the nonlinear coefficient in standard telecommunication, dispersion-shifted, and a number of dispersion-compensated fibers are presented.
Morphological development of impact polypropylene produced in gas phase with a TiCl<sub>4</sub>/MgCl<sub>2</sub> catalyst (2001)

Abstract This article reports on a comprehensive study of the reaction kinetics, particle morphology development, and polymer properties of impact polypropylene produced in gas phase with a TiCl 4 /MgCl 2 catalyst. Experiments were conducted over a range of copolymerization times, temperatures, monomer compositions, and hydrogen levels. The catalyst was found to exhibit a decay‐type reaction rate for ethylene and propylene, but the presence of both monomers together caused an activation of the catalyst. Copolymer composition was constant over reaction time. Hydrogen was found to reversibly enhance the rate of propylene polymerization but to have no effect on ethylene. Microscopy provided evidence that the copolymer phase segregates from the homopolymer during polymerization. As copolymer content increased, product bulk density decreased because of the presence of sticky material on the particle surface. However, even at 70 wt % copolymer, enough pores were present in the particle to prevent monomer diffusion limitations. © 2001 John Wiley & Sons, Inc. J Appl Polym Sci 81: 3085–3106, 2001