gebhart/patrepeval huggingface dataset:
Construction of a cysteineless variant of the E. coli pyruvate dehydrogenase E1 subunit (2006)

The crystal structure of the E1 subunit of the pyruvate dehydrogenase complex from E. coli (PDHc‐E1) revealed three regions of low electron density, spanning residues 1–55, 401–413 and 541–557 (Arjunan et al., Biochemistry 2002 , 41, 5213–5221). Region 1–55 has been shown to interact with the PDHc‐E2 subunit (Park et al , Biochemistry 2004 , 43, 14037–14046) while region 401–413 has a role in reductive acetylation of the lipoamide of the PDHc‐E2 subunit (Nemeria et al., Biochemistry 2002 , 41, 15459–15467). Studies using site specific labeling (SSL) with thiol‐directed probes sensitive to their local environment has immense potential to characterize the dynamics of these important regions. For this purpose five of six cysteine residues in parental PDHc‐E1 (120, 259, 575, 610, 654 and 770) were converted to alanines, the sixth C259 to asparagine, by site directed mutagenesis. This PDHc‐E1 variant without cysteines showed ~4‐fold reduction in activity compared to parental PDHc‐E1 in subunit‐specific as well as overall complex activity assays. These results confirm our previous observations (Nemeria et al, Biochemistry 1998 , 37, 911–922) where none of the cysteines in singly‐substituted PDHc‐E1 were found important for activity. Moreover, reintroduction of cysteine for SSL studies in regions 1–55 (I11C) and 401–413 (Q408C) did not result in significant reduction in PDHc‐E1 activity, retaining ~40% and 80% overall activity, respectively, compared to the cysteineless PDHc‐E1 variant. These results will facilitate SSL and functional characterization of these important regions in PDHc‐E1. Supported by NIH grants GM62330 and GM53080.
Experimental demonstration of all-optical 2R regeneration based on nonlinear birefringence in a LOA (2003)

A novel all-optical 2R regenerator has been demonstrated using nonlinear polarization rotation in a single linear semiconductor optical amplifier (LOA). The features of simple configuration, stable operation and high regenerative capabilities make this new scheme a promising technique for all-optical regeneration in future optical networks.
New sequences for asynchronous frequency-hopping multiplex (1986)

A new method for generating large sets of sequences for frequency-hopping multiplex, when arbitrary or bounded mutual asynchronity is present, is presented. The sequences are of length Q, with elements from GF(Q); Q is prime. The maximal number of sequences in the sets is very close to the theoretical bounds.
The Management of Cryptorchidism (1939)

No AccessJournal of Urology1 Aug 1939The Management of Cryptorchidism1 Robert E. Cone Robert E. ConeRobert E. Cone More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)71512-1AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail © 1939 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 42Issue 2August 1939Page: 240-248 Advertisement Copyright & Permissions© 1939 by The American Urological Association Education and Research, Inc.MetricsAuthor Information Robert E. Cone More articles by this author Expand All Advertisement PDF DownloadLoading ...
Proteases (1999)

Apoptosis, a prominent form of physiologic cell death, is assuming increased importance in human physiology and pathology (reviewed in ref. 1). Unlike necrosis, an uncontrolled process in which acute cellular injury leads to rapid cell swelling and lysis, apoptosis follows an ordered and stereotyped sequence, which results in cell shrinkage, fragmentation into membrane-bound bodies, and rapid phagocytosis by surrounding cells (2,3). Although the morphologic characteristics of apoptosis are readily recognizable, and internucleosomal DNA degradation is a frequent feature of apoptotic death (4), the actual apoptotic mechanism has been difficult to define (5).
EFFECT OF METHOD OF DETERMINATION ON DIGESTIBLE ENERGY AND NITROGEN AND ON METABOLIZABLE ENERGY VALUES OF RAPESEED MEAL AND SOYBEAN MEALS FED TO GROWING PIGS (1971)

Commercial samples of solvent-extracted rapeseed meal (RM), 44% crude protein soybean meal (SM) and 50% crude protein SM were evaluated for digestible energy (DE), metabolizable energy (ME), nitrogen-corrected ME (ME n ) and digestible nitrogen (DN), using two methods of evaluation. A comparison of results from feeding the test meals for two different lengths of time prior to conducting the determinations was also made. Sixteen castrate male pigs were allotted to each of the two evaluation methods, with four pigs assigned to each of three treatment groups, and four pigs assigned to the basal control group for each method. The two SM samples had higher DE, ME, ME n and DN than the RM sample. The DE, ME and ME n values in kcal/g dry matter for RM were 3.37, 3.13 and 2.76, and for SM they we’re 4.42, 4.21 and 3.71, respectively. The overall mean coefficient for DN was 79.2% for RM and 92.8% for SM. There were no significant differences observed between methods or between the two time periods. The values for the basal diets were uniform throughout the trial, as indicated by low standard errors.
Sustainability Science and Engineering:  The Emergence of a New Metadiscipline (2003)

A case is made for growth of a new metadiscipline of sustainability science and engineering. This new field integrates industrial, social, and environmental processes in a global context. The skills required for this higher level discipline represent a metadisciplinary endeavor, combining information and insights across multiple disciplines and perspectives with the common goal of achieving a desired balance among economic, environmental, and societal objectives. Skills and capabilities that are required to support the new metadiscipline are summarized. Examples of integrative projects are discussed in the areas of sustainability metrics and integration of industrial, societal, and environmental impacts. It is clear that a focus on green engineering that employs pollution prevention and industrial ecology alone are not sufficient to achieve sustainability, because even systems with efficient material and energy use can overwhelm the carrying capacity of a region or lead to other socially unacceptable outcomes. To meet the educational and human resource needs required for this new discipline, the technological and environmental awareness of society must be elevated and a sufficient and diverse pool of human talent must be attracted to this discipline.
Phosphoenolpyruvate Phosphotransferase System Components Modulate Gene Transcription and Virulence of Borrelia burgdorferi (2015)

The phosphoenolpyruvate phosphotransferase system (PEP-PTS) and adenylate cyclase (AC) IV (encoded by BB0723 [cyaB]) are well conserved in different species of Borrelia. However, the functional roles of PEP-PTS and AC in the infectious cycle of Borrelia have not been characterized previously. We examined 12 PEP-PTS transporter component mutants by needle inoculation of mice to assess their ability to cause mouse infection. Transposon mutants with mutations in the EIIBC components (ptsG) (BB0645, thought to be involved in glucose-specific transport) were unable to cause infection in mice, while all other tested PEP-PTS mutants retained infectivity. Infectivity was partially restored in an in trans-complemented strain of the ptsG mutant. While the ptsG mutant survived normally in unfed as well as fed ticks, it was unable to cause infection in mice by tick transmission, suggesting that the function of ptsG is essential to establish infection by either needle inoculation or tick transmission. In Gram-negative organisms, the regulatory effects of the PEP-PTS are mediated by adenylate cyclase and cyclic AMP (cAMP) levels. A recombinant protein encoded by B. burgdorferi BB0723 (a putative cyaB homolog) was shown to have adenylate cyclase activity in vitro; however, mutants with mutations in this gene were fully infectious in the tick-mouse infection cycle, indicating that its function is not required in this process. By transcriptome analysis, we demonstrated that the ptsG gene may directly or indirectly modulate gene expression of Borrelia burgdorferi. Overall, the PEP-PTS glucose transporter PtsG appears to play important roles in the pathogenesis of B. burgdorferi that extend beyond its transport functions.
One‐Pot Synthesis of Oxime Derivatives of 1,3‐Diphenylpyrazole‐4‐carboxaldehydes from Acetophenone Phenylhydrazones Using Vilsmeier—Haack Reagent. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Thermal Neutron Irradiation of Cotton' (1961)

Purified cotton samples were irradiated in a "pure" source of thermal neutrons in the dosage range of 5 × 10 14 through 1 X 10 17 neutrons per cm. 2 Neutron irradiation produced chain cleavage, carboxyl groups, and reducing groups in the cotton cellulose. The water solubility of the cotton was not appreciably affected in this dosage range. The wet and dry strengths and the elongation of the cotton were decreased by neutron irradiation. The uniformity of strength along the fiber length was only slightly lowered. The reducing groups produced in the neutron-irradiated cotton were shown to be markedly different in degree of reaction with sodium chlorite, copper equivalence, and influence on alkali sensitivity from the reducing aldehyde groups produced by periodate oxidation of cotton cellulose. A close similarity between the effects of thermal neutron and gamma ray irradiation on cotton was observed.
Cycle-cut decomposition and Log-based reconciliation (2004)

Optimistic reconciliation allows, multiple update of shared data without synchronization. The assumption is that the vast majority of the actions will not conflict. In those systems, write availability is raised in the presence of network failures, high latencies or parallel development. However, in order to remain consistent, optimistic systems repair divergences. To produce a new consistent state, they use the logs of each user in a process called log-based reconciliation. The purpose of an efficient reconciliation engine is then to compute a new consistent state which preserves the maximum of previous actions.
Effects of Imidacloprid on Development, Mobility, and Survival of First Instars of Diaprepes abbreviatus (Coleoptera: Curculionidae) (1997)

The effect of imidacloprid on mortality and ecdysis of 1st instars of Diaprepes abbreviatus L. was determined using contact and oral exposure bioassays. The effect of contact exposure to imidacloprid on 1st-instar mobility was determined with and without a soil substrate. Greenhouse studies were conducted to determine possible systemic effects of different rates of imidacloprid applied as a soil drench on larval mortality and on root protection of container-grown citrus seedlings. When larvae were fed treated carrot or artificial diet at doses of ≥12.5 ppm, imidacloprid reduced feeding, which contributed to slower larval development and reduced ecdysis. Imidacloprid also affected larval mobility and development by contact exposure at doses >100 ppm. Larval mobility was impaired significantly in soil treated with imidacloprid at doses >6 μg/g of soil. In moistened soil, larval movement was significantly impaired at 6 μg/g of soil. Mortality caused by imidacloprid was slow for either mode of entry but was 6 times faster by oral than by contact exposure. When exposure to doses of imidacloprid was followed by periods without exposure to the chemical, larvae were able to recover. When imidacloprid was applied as a soil drench to container-grown citrus trees at 200 ppm, no larvae survived in the soil, suggesting death from starvation before reaching plant roots or death after feeding, on roots containing imidacloprid.
Compressed Suffix Arrays and Suffix Trees with Applications to Text Indexing and String Matching Read More: http://epubs.siam.org/doi/abs/10.1137/S0097539702402354 (2005)

The proliferation of online text, such as found on the World Wide Web and in online databases, motivates the need for space-efficient text indexing methods that support fast string searching. We model this scenario as follows: Consider a text T consisting of n symbols drawn from a fixed alphabet $\Sigma$. The text T can be represented in $n \lg |\Sigma|$ bits by encoding each symbol with $\lg |\Sigma|$ bits. The goal is to support fast online queries for searching any string pattern P of m symbols, with T being fully scanned only once, namely, when the index is created at preprocessing time. The text indexing schemes published in the literature are greedy in terms of space usage: they require $\Omega(n \lg n)$ additional bits of space in the worst case. For example, in the standard unit cost RAM, suffix trees and suffix arrays need $\Omega(n)$ memory words, each of $\Omega(\lg n)$ bits. These indexes are larger than the text itself by a multiplicative factor of $\Omega(\smash{\lg_{|\Sigma|} n})$, which is significant when $\Sigma$ is of constant size, such as in \textsc{ascii} or \textsc{unicode}. On the other hand, these indexes support fast searching, either in $O(m \lg |\Sigma|)$ time or in $O(m +\lg n)$ time, plus an output-sensitive cost $O(\mathit{occ})$ for listing the $\mathit{occ}$ pattern occurrences. We present a new text index that is based upon compressed representations of suffix arrays and suffix trees. It achieves a fast $\smash{O(m /\lg_{|\Sigma|} n + \lg_{|\Sigma|}^\epsilon n)}$ search time in the worst case, for any constant $0 < \epsilon \leq 1$, using at most $\smash{\bigl(\epsilon^{-1} + O(1)\bigr) \, n \lg |\Sigma|}$ bits of storage. Our result thus presents for the first time an efficient index whose size is provably linear in the size of the text in the worst case, and for many scenarios, the space is actually sublinear in practice. As a concrete example, the compressed suffix array for a typical 100 MB \textsc{ascii} file can require 30--40 MB or less, while the raw suffix array requires 500 MB. Our theoretical bounds improve \emph{both} time and space of previous indexing schemes. Listing the pattern occurrences introduces a sublogarithmic slowdown factor in the output-sensitive cost, giving $O(\mathit{occ} \, \smash{\lg_{|\Sigma|}^\epsilon n})$ time as a result. When the patterns are sufficiently long, we can use auxiliary data structures in $O(n \lg |\Sigma|)$ bits to obtain a total search bound of $O(m /\lg_{|\Sigma|} n + \mathit{occ})$ time, which is optimal.
Synthesis of block copolymers by oligomer‐coupling reactions in the bulk: Bisimidazoline/cooh and bisoxazolinone/nh<sub>2</sub> reactions (1997)

Abstract The polyaddition reaction of bisimidazolines with α, ω‐dicarboxy polyamide‐12 in the bulk at 200–240°C (oligomer coupling reaction) produces high MW polymers, while degradation reactions were observed with aliphatic polyesters. The chain extension of a α, ω‐dicarboxy polyamide‐polyoxytetramethylene‐polyamide oligomer with 2, 2'‐tetramethylene‐bis(imidazoline) yielded a poly(poly‐ether‐block‐polyamide). 4‐substituted and 4, 4‐disubstituted bis(5(4H)oxazolinones) are efficient coupling agents for amino‐terminated oligomers, allowing the rapid synthesis of copolymers containing polyether and polyamide blocks. The chemistry of these chain‐coupling reactions has been studied by NMR. DSC shows the phase separation between the hard (polyamide) and the soft (polyether) blocks.
A semiclassical approach to concerted proton transfer in condensed media (1982)

Rate expressions are provided for proton transfer reactions in which a proton is transferred from a donor site to a catalyst molecule “in concert with” proton transfer from a different site on the catalyst to a proton acceptor (bifunctional catalysis). The basis of the description is a semiclassical approach according to which the process is represented by three-well potential energy surfaces spanned by low-frequency nuclear co-ordinates. The minima correspond to localization of a proton on the donor, the catalyst and the acceptor. Each vibrational state of the proton causes a vertical shift of the appropriate surface, and within the semiclassical approach both weak and strong intermolecular interactions are covered.For strong catalysts, corresponding to low energies of the intermediate state, the two protons are transferred separately. In such cases Brønsted relation and kinetic isotope effect variation with pKa of the catalyst do not differ fundamentally from those of step-wise individual proton transfers. For weak catalysts the two protons are transferred in a “synchronous” motion. The effect of the catalyst is then reflected in the pre-exponential factor of the rate expressions and gives a small Brønsted coefficient and slow variation of the kinetic isotope effect with pKa of the catalyst.
A non‐empirical molecular orbital study of valence tautomers of C<sub>2</sub>H<sub>3</sub>N (1977)

Abstract The valence tautomers of C 2 H 3 N have been examined by non‐empirical molecular orbital calculations using two split‐valence shell basis sets. All geometries were fully optimized using the 4–31G basis set and these structures were then used in 6–31G basis set calculations. The order of stability of the three possible cyclic isomers is 1‐azirine > cyclic carbene > 2‐azirine. The profiles for conversion of vinylmethylene into cyclopropene, vinylnitrene into 1‐arizine, and iminomethylene into 2‐azirine have all been shown to have barriers.
Characterization of the major immediate-early polypeptides encoded by murine cytomegalovirus (1985)

The immediate-early (IE) infected cell proteins induced by the murine cytomegalovirus (Smith strain) were studied. These polypeptides were identified as IE proteins by their synthesis in the presence of actinomycin D after removal from a protein synthesis block mediated by cycloheximide. By using a murine antiserum against murine cytomegalovirus, three abundant polypeptides of 89, 84, and 76 kilodaltons (kd) were immunoprecipitated. The three major proteins are phosphorylated but not glycosylated and share antigenic determinants recognized by monoclonal antibodies. The 84 and 76-kd polypeptides represent post-translational modification products of the 89-kd protein. Accordingly, in vitro translation of IE infected cell RNA revealed only the 89-kd polypeptide. The viral origin of the RNA species directing the synthesis of the major 89-kd IE polypeptide was verified by hybrid selection of IE RNA with DNA fragments representing the region from 0.769 to 0.815 map units of the murine cytomegalovirus genome. IE polypeptides were found to be located in the nuclei and the cytoplasm of infected cells. Studies on the kinetics of IE polypeptide synthesis revealed negative regulatory effects on IE gene expression correlated with the synthesis of early proteins.
Image retrieval based on similarity learning (2002)

We explore the use of various learning algorithms to predict the user's measure of similarity between a given query image and images in a database. Our aim is to obtain a similarity coefficient, for use in image retrieval, that more accurately reflects that of the user. The performance of a variety of learning machines was evaluated using statistical resampling to estimate the prediction error and retrieval effectiveness. The proposed approach was demonstrated using synthetic shape and texture examples. The results of the study are very promising, especially those obtained by the general regression neural network and the support vector machine/radial basis function method.
Cerebro-cerebellar Interactions Underlying Temporal Information Processing (2010)

The neural basis of temporal information processing remains unclear, but it is proposed that the cerebellum plays an important role through its internal clock or feed-forward computation functions. In this study, fMRI was used to investigate the brain networks engaged in perceptual and motor aspects of subsecond temporal processing without accompanying coprocessing of spatial information. Direct comparison between perceptual and motor aspects of time processing was made with a categorical-design analysis. The right lateral cerebellum (lobule VI) was active during a time discrimination task, whereas the left cerebellar lobule VI was activated during a timed movement generation task. These findings were consistent with the idea that the cerebellum contributed to subsecond time processing in both perceptual and motor aspects. The feed-forward computational theory of the cerebellum predicted increased cerebro-cerebellar interactions during time information processing. In fact, a psychophysiological interaction analysis identified the supplementary motor and dorsal premotor areas, which had a significant functional connectivity with the right cerebellar region during a time discrimination task and with the left lateral cerebellum during a timed movement generation task. The involvement of cerebro-cerebellar interactions may provide supportive evidence that temporal information processing relies on the simulation of timing information through feed-forward computation in the cerebellum.
Real-time eye tracking using a smart camera (2011)

Real-time eye and iris tracking is important for handsoff gaze-based password entry, instrument control by paraplegic patients, Internet user studies, as well as homeland security applications. In this project, a smart camera, LabVIEW and vision software tools are utilized to generate eye detection and tracking algorithms. The algorithms are uploaded to the smart camera for on-board image processing. Eye detection refers to finding eye features in a single frame. Eye tracking is achieved by detecting the same eye features across multiple image frames and correlating them to a particular eye. The algorithms are tested for eye detection and tracking under different conditions including different angles of the face, head motion speed, and eye occlusions to determine their usability for the proposed applications. This paper presents the implemented algorithms and performance results of these algorithms on the smart camera.
Occupational Status, Cortisol Secretory Pattern, and Visceral Obesity in Middle‐aged Men (2000)

It was concluded that a low socioeconomic status is associated with perturbed cortisol secretion, which is elevated in relation to perceived stress. When the hypothalamic-pituitary-adrenal axis is subjected to prolonged increases in cortisol elicited by chronic stress, the regulation of cortisol secretion is affected, indicating neuroendocrine dysregulations. These observations may provide a means for understanding the association of socioeconomic impairments with visceral obesity and the social inequality in risk for prevalent and serious diseases.