gebhart/patrepeval huggingface dataset:
Delay budget partitioning to maximize network resource usage efficiency (2004)

Provisioning techniques for network flows with end-to-end QoS guarantees need to address the interpath and intrapath load balancing problems to maximize the resource utilization efficiency. This paper focuses on the intrapath load balancing problem: How to partition the end-to-end QoS requirement of a network flow along the links of a given path such that the deviation in the loads on these links is as small as possible? We propose a new algorithm to solve the end-to-end QoS partitioning problem for unicast and multicast flows that takes into account the loads on the constituent links of the chosen flow path. This algorithm can simultaneously partition multiple end-to-end QoS requirements such as the end-to-end delay and delay violation probability bound. The key concept in our proposal is the notion of slack, which quantifies the extent of flexibility available in partitioning the end-to-end delay requirement across the links of a selected path (or a multicast tree). We show that one can improve network resource usage efficiency by carefully selecting a slack partition that explicitly balances the loads on the underlying links. A detailed simulation study demonstrates that, compared with previous approaches, the proposed delay budget partitioning algorithm can increase the total number of long-term flows that can be provisioned along a network path by up to 1.2 times for deterministic and 2.8 times for statistical delay guarantees
Mobilization of natural killer cells inhibits development of collagen-induced arthritis (2011)

Although natural killer (NK) cells have been implicated in regulating immune responses, their ability to modulate disease development in autoimmune arthritis has not been analyzed. Here we investigate the contribution of NK cells to regulating collagen-induced arthritis, a well-characterized preclinical model of human rheumatoid arthritis. We find that the disease is induced by the combined action of two CD4(+) T helper (T(H)) subsets: follicular T(H) cells and T(H)17 cells. Both CD4(+) T(H) subsets are highly susceptible to lysis by NK cells after activation. Administration of antibody that activates NK cells through blockade of its inhibitory CD94/NKG2A receptor allows enhanced elimination of pathogenic follicular T(H) and T(H)17 cells and arrest of disease progression. These results suggest that antibody-dependent enhancement of NK activity may yield effective, previously undescribed therapeutic approaches to this autoimmune disorder.
Molecular cloning and characterization of a novel type of regulatory protein (GDI) for the rho proteins, ras p21-like small GTP-binding proteins. (1990)

We have recently purified to near homogeneity a novel type of regulatory protein for the rho proteins, ras p21-like small GTP-binding proteins, from bovine brain cytosol. This regulatory protein, named GDP dissociation inhibitor for the rho proteins (rho GDI), regulates the GDP/GTP exchange reaction of the rho proteins by inhibiting the dissociation of GDP from them, and the subsequent binding of GTP to them. In the present studies, we have isolated the cDNA of rho GDI from a bovine brain cDNA library using oligonucleotide probes designed from the partial amino acid sequences of the purified rho GDI and determined its complete nucleotide and deduced amino acid sequences. The cDNA contains an open reading frame encoding a protein of 204 amino acids with a calculated Mr value of 23,421. This Mr value is similar to those of the purified rho GDI estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and sucrose density gradient ultra-centrifugation, both of which are about 27,000. The rho GDI cDNA is expressed in Escherichia coli and COS7 cells and the encoded protein exhibits rho GDI activity. The 1.9-kilobase rho GDI mRNA corresponding to the isolated cDNA is detected in various rat tissues by Northern blot analysis. Hydropathy analysis indicates that rho GDI is overall hydrophilic except for one hydrophobic region. Computer homology search has revealed that rho GDI is a novel protein that does not share a high amino acid sequence homology with any known protein.
ZDOCK: An initial‐stage protein‐docking algorithm (2003)

The development of scoring functions is of great importance to protein docking. Here we present a new scoring function for the initial stage of unbound docking. It combines our recently developed pairwise shape complementarity with desolvation and electrostatics. We compare this scoring function with three other functions on a large benchmark of 49 nonredundant test cases and show its superior performance, especially for the antibody-antigen category of test cases. For 44 test cases (90% of the benchmark), we can retain at least one near-native structure within the top 2000 predictions at the 6 degrees rotational sampling density, with an average of 52 near-native structures per test case. The remaining five difficult test cases can be explained by a combination of poor binding affinity, large backbone conformational changes, and our algorithm's strong tendency for identifying large concave binding pockets. All four scoring functions have been integrated into our Fast Fourier Transform based docking algorithm ZDOCK, which is freely available to academic users at http://zlab.bu.edu/~ rong/dock.
Genetic Characterization of Escherichia coli Populations from Host Sources of Fecal Pollution by Using DNA Fingerprinting (2003)

Escherichia coli isolates were obtained from common host sources of fecal pollution and characterized by using repetitive extragenic palindromic (REP) PCR fingerprinting. The genetic relationship of strains within each host group was assessed as was the relationship of strains among different host groups. Multiple isolates from a single host animal (gull, human, or dog) were found to be identical; however, in some of the animals, additional strains occurred at a lower frequency. REP PCR fingerprint patterns of isolates from sewage (n = 180), gulls (n = 133), and dairy cattle (n = 121) were diverse; within a host group, pairwise comparison similarity indices ranged from 98% to as low as 15%. A composite dendrogram of E. coli fingerprint patterns did not cluster the isolates into distinct host groups but rather produced numerous subclusters (approximately >80% similarity scores calculated with the cosine coefficient) that were nearly exclusive for a host group. Approximately 65% of the isolates analyzed were arranged into host-specific groups. Comparable results were obtained by using enterobacterial repetitive intergenic consensus PCR and pulsed-field gel electrophoresis (PFGE), where PFGE gave a higher differentiation of closely related strains than both PCR techniques. These results demonstrate that environmental studies with genetic comparisons to detect sources of E. coli contamination will require extensive isolation of strains to encompass E. coli strain diversity found in host sources of contamination. These findings will assist in the development of approaches to determine sources of fecal pollution, an effort important for protecting water resources and public health.
Parallel-up structure evidences the molecular directionality during biosynthesis of bacterial cellulose (1997)

The "parallel-up" packing in cellulose Ialpha and Ibeta unit cells was experimentally demonstrated by a combination of direct-staining the reducing ends of cellulose chains and microdiffraction-tilting electron crystallographic analysis. Microdiffraction investigation of nascent bacterial cellulose microfibrils showed that the reducing end of the growing cellulose chains points away from the bacterium, and this provides direct evidence that polymerization by the cellulose synthase takes place at the nonreducing end of the growing cellulose chains. This mechanism is likely to be valid also for a number of processive glycosyltransferases such as chitin synthases, hyaluronan synthases, and proteins involved in the synthesis of nodulation factor backbones.
In Vivo Characterization of Coronary Atherosclerotic Plaque by Use of Optical Coherence Tomography (2005)

OCT is a safe and effective modality for characterizing coronary atherosclerotic plaques in vivo. Thin-cap fibroatheroma was more frequently observed in patients with AMI or ACS than SAP. This is the first study to compare detailed in vivo plaque morphology in patients with different clinical presentations.
Effect of Adrenalectomy on Weight Gain and Body Composition of Yellow Obese Mice (Ay/a) (1976)

It has been reported that the adrenal gland is essential to the development of obesity if Ay/a Yellow obese mice (Hausberger and Hausberger 1960). Since the actual body composition data to support this report has not been published, we attempted to duplicate this observation by adrenalectomy of the Yellow mice before the onset of obesity. Two groups of Yellow mice (Ay/a) and normal mice (a/a) were either sham operated or adrenalectomized at two months of age and at four months of age. Body weight was monitored until body gain had stopped. At that time the animals were sacrified and checked for completeness of adrenal removal. Body composition of dry matter, fat, protein, and ash was determined. Adrenalectomy caused a reduction of body fat of 33% and 30% in both the a/a Control and the Ay/a Yellow mice, respectively. The adrenalectomized Yellow mice were still fatter than adrenalectomized Controls (25.3% fat vs. 10.6% fat). Yellow and control adrenalectomized mice showed similar depression in growth rate. These data suggest that while the adrenal gland is essential for complete expression of the genetic potential for fat deposition, it may not be necessary for partial expression indicating a secondary role in the development of obesity in the Ay/a Yellow mouse.
Tolerance and Resistance of Pseudomonas aeruginosa Biofilms to Antimicrobial Agents—How P. aeruginosa Can Escape Antibiotics (2019)

<i>Pseudomonas aeruginosa</i> is one of the six bacterial pathogens, <i>Enterococcus faecium</i>, <i>Staphylococcus aureus</i>, <i>Klebsiella pneumoniae</i>, <i>Acinetobacter baumannii</i>, <i>Pseudomonas aeruginosa,</i> and <i>Enterobacter</i> spp., which are commonly associated with antimicrobial resistance, and denoted by their acronym ESKAPE. <i>P. aeruginosa</i> is also recognized as an important cause of chronic infections due to its ability to form biofilms, where the bacteria are present in aggregates encased in a self-produced extracellular matrix and are difficult or impossible to eradicate with antibiotic treatment. <i>P. aeruginosa</i> causes chronic infections in the lungs of patients with cystic fibrosis and chronic obstructive lung disease, as well as chronic urinary tract infections in patients with permanent bladder catheter, and ventilator-associated pneumonia in intubated patients, and is also an important pathogen in chronic wounds. Antibiotic treatment cannot eradicate these biofilm infections due to their intrinsic antibiotic tolerance and the development of mutational antibiotic resistance. The tolerance of biofilms to antibiotics is multifactorial involving physical, physiological, and genetic determinants, whereas the antibiotic resistance of bacteria in biofilms is caused by mutations and driven by the repeated exposure of the bacteria to high levels of antibiotics. In this review, both the antimicrobial tolerance and the development of resistance to antibiotics in <i>P. aeruginosa</i> biofilms are discussed. Possible therapeutic approaches based on the understanding of the mechanisms involved in the tolerance and resistances of biofilms to antibiotics are also addressed.
Simple, Highly Active Palladium Catalysts for Ketone and Malonate Arylation:  Dissecting the Importance of Chelation and Steric Hindrance (1999)

A remarkably active catalyst system for α-arylation of ketones and malonates was developed by proposing that sterically hindered alkylphosphines would accelerate the catalytic reaction rates. We initially tested the bisphosphine ligand DtBPF (1,1‘-bis-(di-tert-butylphosphino)ferrocene) for this palladium-catalyzed chemistry. This catalyst system led to fast reaction rates for reactions of aryl bromides with ketones, including room temperature chemistry in many cases. In some cases turnover numbers were 20 000. The catalyst also gave mild reactions with aryl chlorides with yields that were similar to the chemistry with aryl bromides. Independent synthesis of the arylpalladium enolate complexes with isobutyrophenone enolate showed that only one phosphorus of the bisphosphine ligand DtBPF was coordinated in the enolate complex. Thus, we tested sterically hindered alkylphosphine ligands for the ketone and malonate arylation process and found that P(t-Bu)3 gave exceptionally fast rates and high turnover numbers for these reactions. These results demonstrate several principles for the catalytic chemistry that we did not anticipate: palladium complexes of monophosphine ligands can activate aryl chlorides under mild conditions, and palladium enolates coordinated by certain monophosphines can undergo C−C bond-forming reductive elimination much faster than β-hydrogen elimination.
Discovery of Sequence-Selective Peptide Binding by Synthetic Receptors Using Encoded Combinatorial Libraries (1996)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDiscovery of Sequence-Selective Peptide Binding by Synthetic Receptors Using Encoded Combinatorial LibrariesW. Clark StillView Author Information Department of Chemistry, Columbia University, New York, New York 10027Cite this: Acc. Chem. Res. 1996, 29, 3, 155–163Publication Date (Web):March 13, 1996Publication History Received21 September 1995Published online13 March 1996Published inissue 13 March 1996https://pubs.acs.org/doi/10.1021/ar950166ihttps://doi.org/10.1021/ar950166iresearch-articleACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views980Altmetric-Citations280LEARN 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 SUBJECTS:Molecules,Peptides and proteins,Receptors,Selectivity,Surface interactions Get e-Alerts
The biocatalytic approach to the preparation of enantiomerically pure chiral building blocks (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleThe biocatalytic approach to the preparation of enantiomerically pure chiral building blocksEnzo Santaniello, Patrizia Ferraboschi, Paride Grisenti, and Ada ManzocchiCite this: Chem. Rev. 1992, 92, 5, 1071–1140Publication Date (Print):July 1, 1992Publication History Published online1 May 2002Published inissue 1 July 1992https://doi.org/10.1021/cr00013a016Request reuse permissionsArticle Views2120Altmetric-Citations472LEARN 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 InReddit PDF (7 MB) Get e-Alertsclose Get e-Alerts
A Discrete Site Modulates Activation of I Domains (1996)

A central characteristic of integrin adhesion receptors is their capacity to become activated, thereby enhancing their affinity for ligands. Here, we report the identification of a discrete site within the I domain of integrin alphaMbeta2, which modulates the adhesive activity of this receptor. Based upon the crystal structure, this region is composed of two short and spatially proximal loops, E162QLKKSKTL and Q190NNPNPRS. Mutations in these loops yield receptors which support spontaneous cell adhesion to fibrinogen, whereas mutation of an adjacent region and wild-type receptors require activation to adhere to this substrate. An activating monoclonal antibody enhanced the adhesive activity of one but not the other loop mutants, suggesting that the activation states of these two mutant receptors were not identical. Given that similar I domains exist in several other integrin alpha subunits and non-integrin proteins, and possibly in all integrin beta subunits, these two loop segments may represent a universal target for controlling integrin activation and the function of other I domain-containing proteins. In support of this hypothesis, several naturally occurring mutations that activate von Willebrand factor map to the same loops of its I(A) domain.
Interferon-α and Interleukin-12 Are Induced Differentially by Toll-like Receptor 7 Ligands in Human Blood Dendritic Cell Subsets (2002)

Dendritic cells (DCs) play a crucial role in the immune responses against infections by sensing microbial invasion through toll-like receptors (TLRs). In humans, two distinct DC subsets, CD11c(-) plasmacytoid DCs (PDCs) and CD11c(+) myeloid DCs (MDCs), have been identified and can respond to different TLR ligands, depending on the differential expression of cognate TLRs. In this study, we have examined the effect of TLR-7 ligands on human DC subsets. Both subsets expressed TLR-7 and could respond to TLR-7 ligands, which enhanced the survival of the subsets and upregulated the surface expression of costimulatory molecules such as CD40, CD80, and CD86. However, the cytokine induction pattern was distinct in that PDCs and MDCs produced interferon (IFN)-alpha and interleukin (IL)-12, respectively. In response to TLR-7 ligands, the Th1 cell supporting ability of both DC subsets was enhanced, depending on the cytokines the respective subsets produced. This study demonstrates that TLR-7 exerts its biological effect in a DC subset-specific manner.
An analog wavelet transform chip (2002)

The theory and implementation in subthreshold analog CMOS technology of a circuit which performs continuous wavelet decompositions of a one-dimensional (e.g., audio) input are described. The analog wavelet outputs are the output of a logarithmically scaled bank of bandpass filters; each band is sampled at a rate proportional to the Nyquist rate of the highest frequency content of that band. The result is a matrix of discrete points describing the input signal as a function of both frequency and time. The filter function of each band is Gaussian shaped in order to best resolve the uncertainty relation between time and frequency at each sampled point.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Alcohol Hypersensitivity, Increased Locomotion, and Spontaneous Myoclonus in Mice Lacking the Potassium Channels Kv3.1 and Kv3.3 (2001)

The Shaw-like potassium (K(+)) channels Kv3.1 and Kv3.3 are widely coexpressed in distinct neuronal populations in the CNS, possibly explaining the relatively "mild" phenotypes of the Kv3.1 and the Kv3.3 single mutant. Kv3.1-deficient mice show increased cortical gamma- and decreased delta-oscillations (Joho et al., 1997, 1999); otherwise, the Kv3.1-mutant phenotype is relatively subtle (Ho et al., 1997; Sánchez et al., 2000). Kv3.3-deficient mice display no overt phenotype (Chan, 1997). To investigate whether Kv3.1 and Kv3.3 K(+) channels are functionally redundant, we generated the Kv3.1/Kv3.3 double mutant. Kv3.1/Kv3.3-deficient mice were born at the expected Mendelian frequencies indicating that neither Kv3.1 nor Kv3.3 K(+) channels are essential for embryonic development. Although there are no obvious changes in gross brain anatomy, adult Kv3.1/Kv3.3-deficient mice display severe ataxia, tremulous movements, myoclonus, and hypersensitivity to ethanol. Mice appear unbalanced when moving, whereas at rest they exhibit whole-body jerks every few seconds. In spite of the severe motor impairment, Kv3.1/Kv3.3-deficient mice are hyperactive, show increased exploratory activity, and display no obvious learning or memory deficit. Myoclonus, tremor, and ethanol hypersensitivity are only seen in the double-homozygous Kv3.1/Kv3.3-deficient mice, whereas increased locomotor and exploratory activity are also present in double-heterozygous mice. The graded penetrance of mutant traits appears to depend on the number of null alleles, suggesting that some of the distinct phenotypic traits visible in the absence of Kv3.1 and Kv3.3 K(+) channels are unrelated and may be caused by localized dysfunction in different brain regions.
Energy transfer mechanism for downconversion in the (Pr3+,Yb3+) couple (2010)

Downconversion of one visible photon into two infrared photons has been reported for the lanthanide ion couple (${\text{Pr}}^{3+}$, ${\text{Yb}}^{3+}$) in a variety of host lattices. The mechanism responsible for downconversion is controversial and has been reported to be either a two-step energy transfer process (via two first-order transfer steps, the first being cross relaxation) or cooperative energy transfer from ${\text{Pr}}^{3+}$ to two ${\text{Yb}}^{3+}$ ions (a second-order process). Here we report experiments on downconversion for the (${\text{Pr}}^{3+}$, ${\text{Yb}}^{3+}$) in ${\text{LiYF}}_{4}$. Luminescence decay curves of the ${\text{Pr}}^{3+}$ emission are recorded as a function of the ${\text{Yb}}^{3+}$ concentration and analyzed using Monte Carlo simulations for both cooperative energy transfer and energy transfer through cross relaxation. We obtain a good agreement between experiment and simulations for energy transfer by cross relaxation but not for cooperative energy transfer. The observation that cross relaxation is more efficient than cooperative energy transfer is consistent with Judd-Ofelt calculations for the transition probabilities involved in the two energy transfer processes and the lower probability for the second-order cooperative transfer.
DNA binding induces active site conformational change in the human TREX2 3'-exonuclease (2009)

The TREX enzymes process DNA as the major 3'-->5' exonuclease activity in mammalian cells. TREX2 and TREX1 are members of the DnaQ family of exonucleases and utilize a two metal ion catalytic mechanism of hydrolysis. The structure of the dimeric TREX2 enzyme in complex with single-stranded DNA has revealed binding properties that are distinct from the TREX1 protein. The TREX2 protein undergoes a conformational change in the active site upon DNA binding including ordering of active site residues and a shift of an active site helix. Surprisingly, even when a single monomer binds DNA, both monomers in the dimer undergo the structural rearrangement. From this we have proposed a model for DNA binding and 3' hydrolysis for the TREX2 dimer. The structure also shows how TREX proteins potentially interact with double-stranded DNA and suggest features that might be involved in strand denaturation to provide a single-stranded substrate for the active site.