gebhart/patrepeval huggingface dataset:
The lipopolysaccharide of the mastitis isolate Escherichia coli strain 1303 comprises a novel O-antigen and the rare K-12 core type (2011)

Mastitis represents one of the most significant health problems of dairy herds. The two major causative agents of this disease are Escherichia coli and Staphylococcus aureus. Of the first, its lipopolysaccharide (LPS) is thought to play a prominent role during infection. Here, we report the O-antigen (OPS, O-specific polysaccharide) structure of the LPS from bovine mastitis isolate E. coli 1303. The structure was determined utilizing chemical analyses, mass spectrometry, and 1D and 2D NMR spectroscopy methods. The O-repeating unit was characterized as -[→4)-β-D-Quip3NAc-(1→3)-α-L-Fucp2OAc-(1→4)-β-D-Galp-(1→3)-α-D-GalpNAc-(1→]- in which the O-acetyl substitution was non-stoichiometric. The nucleotide sequence of the O-antigen gene cluster of E. coli 1303 was also determined. This cluster, located between the gnd and galF genes, contains 13 putative open reading frames, most of which represent unknown nucleotide sequences that have not been described before. The O-antigen of E. coli 1303 was shown to substitute O-7 of the terminal LD-heptose of the K-12 core oligosaccharide. Interestingly, the non-OPS-substituted core oligosaccharide represented a truncated version of the K-12 outer core - namely terminal LD-heptose and glucose were missing; however, it possessed a third Kdo residue in the inner core. On the basis of structural and genetic data we show that the mastitis isolate E. coli 1303 represents a new serotype and possesses the K-12 core type, which is rather uncommon among human and bovine isolates.
Beyond routing: an algebraic approach to network coding (2003)

We consider the issue of network capacity. Recent work by Li and Yeung examined the network capacity of multicast networks and related capacity to cutsets. Capacity is achieved by coding over a network. We present a new framework for studying networks and their capacity. Our framework, based on algebraic methods, is surprisingly simple and effective. For networks which are restricted to using linear codes (we make the meaning of linear codes precise, since the codes are not bit-wise linear), we find necessary and sufficient conditions for any given set of connections to be achievable over a given network. For multicast connections, linear codes are not a restrictive assumption, since all achievable connections can be achieved using linear codes. Moreover, coding can be used to maintain connections after permanent failures, such as the removal of an edge from the network. We show necessary and sufficient conditions for a set of connections to be robust to a set of permanent failures. For multicast connections, we show the rather surprising result that, if a multicast connection is achievable under different failure scenarios, a single static code can ensure robustness of the connection under all of those failure scenarios.
Independence of Path and All That (1996)

(1996). Independence of Path and All That. The College Mathematics Journal: Vol. 27, No. 4, pp. 272-277.
Epigenetic profiling reveals etiologically distinct patterns of DNA methylation in head and neck squamous cell carcinoma (2009)

Head and neck squamous cell carcinomas (HNSCCs) represent clinically and etiologically heterogeneous tumors affecting >40 000 patients per year in the USA. Previous research has identified individual epigenetic alterations and, in some cases, the relationship of these alterations with carcinogen exposure or patient outcomes, suggesting that specific exposures give rise to specific types of molecular alterations in HNSCCs. Here, we describe how different etiologic factors are reflected in the molecular character and clinical outcome of these tumors. In a case series of primary, incident HNSCC (n = 68), we examined the DNA methylation profile of 1413 autosomal CpG loci in 773 genes, in relation to exposures and etiologic factors. The overall pattern of epigenetic alteration could significantly distinguish tumor from normal head and neck epithelial tissues (P < 0.0001) more effectively than specific gene methylation events. Among tumors, there were significant associations between specific DNA methylation profile classes and tobacco smoking and alcohol exposures. Although there was a significant association between methylation profile and tumor stage (P < 0.01), we did not observe an association between these profiles and overall patient survival after adjustment for stage; although methylation of a number of specific loci falling in different cellular pathways was associated with overall patient survival. We found that the etiologic heterogeneity of HNSCC is reflected in specific patterns of molecular epigenetic alterations within the tumors and that the DNA methylation profiles may hold clinical promise worthy of further study.
Clinicopathologic Effects of a 21‐Aminosteroid Compound (U74389G) and High‐Dose Methylprednisolone on Spinal Cord Function After Simulated Spinal Cord Trauma (1995)

A model simulating acute-compressive spinal cord trauma at the second lumbar spinal cord segment (100 g, 300 seconds) was used to evaluate the efficacy of a vehicle control, methylprednisolone sodium succinate (MPSS), and a 21-aminosteroid compound (U74389G). Dogs were allocated into one of five treatment groups (A to E) using ultrasonographic determination of spinal cord diameters to ensure even distribution of spinal cord diameters among the treatment groups. Initial dosages of the vehicle control (A), methylprednisolone (30 mg/kg of body weight) (B), or U74389G (30 mg/kg, 3 mg/kg, or 10 mg/kg of body weight) (C, D, or E, respectively) were administered intravenously 30 minutes after trauma. Dosages were reduced by one-half for 2 and 6 hour treatments. Then every 4 hours for 42 hours, dosages were reduced one-third and one-sixth from the original dose of methylprednisolone and U74389G, respectively. Neurological examinations were performed daily for 21 days. Histopathological examination of the traumatized spinal cord showed malacic and degenerative lesions. Although significant differences in some portions of the neurological and histopathologic examinations were observed, clinical efficacy for MPSS and U74389G could not be established in this model.
The Role of T H 1 and T H 2 Cells in a Rodent Malaria Infection (1993)

CD4+ T cells play a major role in protective immunity against the blood stage of malaria, but the mechanism of protection is unclear. By adoptive transfer of cloned T cell lines, direct evidence is provided that both TH1 and TH2 subsets of CD4+ T cells can protect mice against Plasmodium chabaudi chabaudi infection. TH1 cells protect by a nitric oxide-dependent mechanism, whereas TH2 cells protect by the enhancement and accelerated production of specific immunoglobulin G1 antibody.
Group 4 Salalen Complexes and Their Application for the Ring-Opening Polymerization of rac-Lactide (2010)

In this paper, we report the preparation and characterization of a series of unsymmetrical group 4 metal complexes based on ONNO salalen-type ligands. In these examples, the ligand is unsymmetrical with an amine and an imine nitrogen center. All complexes {except Hf(3)(O(i)Pr)(2)} adopt a beta-cis configuration in the solid state, which is also in agreement with solution-state NMR spectroscopic measurements. The complexes have been tested for the ROP of rac-lactide (both in solution and under melt conditions). Narrow polydispersities have been seen (1.07-1.82). The Ti(IV) complexes produce atactic PLA, whereas the Zr(IV) complexes form PLA with a heterotactic bias. Hf(IV) complexes have been shown to produce isotactic PLA with a P(m) of 0.75. The kinetics for all initiators have been investigated and are discussed.
Thiazolidinediones Stimulate Uncoupling Protein-2 Expression in Cell Lines Representing White and Brown Adipose Tissues and Skeletal Muscle (1998)

Thiazolidinediones (TZD) are PPAR gamma ligands that sensitize tissues to insulin. A cDNA encoding a mitochondrial protein likely to act as uncoupler (uncoupling protein 2, UCP2) has been recently cloned. Since TZD have been reported to increase energy expenditure in animals, we have examined the effects of these drugs on the expression of UCP2 mRNA in cell lines representing white (3T3-L1 and 3T3-F442A) and brown (HIB-1B) adipose tissues and skeletal muscle (L6). Northern blots probed with a mouse UCP2 full-length cDNA showed a mRNA of 1.6 kb both in tissues and the aforementioned cells lines. Within 4 h of exposing these cells to 30 microM darglitazone, there was an increase in UCP2 mRNA which reached a plateau of 5-10 times the basal in about 8 h. In all cells TZDs (darglitazone, troglitazone) were more active than the predominantly PPAR alpha ligands WY-14,613 and clofibrate, or the non-selective ligand linoleic acid. These results indicate that TZDs can stimulate the expression of UCP2 gene probably via PPAR gamma and hence have the potential to increase energy expenditure in adult humans, in whom UCP2 is expressed ubiquitously.
Isolation and functional characterization of murine prostate stem cells (2006)

The ability to isolate prostate stem cells is essential to explore their role in prostate development and disease. In vitro prostate colony- and sphere-forming assays were used to quantitatively measure murine prostate stem/progenitor cell enrichment and self-renewal. Cell surface markers were screened for their ability to positively or negatively enrich for cells with enhanced growth potential in these assays. Immunohistochemical and FACS analyses demonstrate that specific cell surface markers can be used to discriminate prostate stromal (CD34(+)), luminal epithelial (CD24(+)CD49f(-)), basal epithelial (CD24(+)CD49f(+)), hematopoietic (CD45(+), Ter119(+)), and endothelial (CD31(+)) lineages. Sorting for cells with a CD45(-)CD31(-)Ter119(-)Sca-1(+)CD49f(+) antigenic profile results in a 60-fold enrichment for colony- and sphere-forming cells. These cells can self-renew and expand to form spheres for many generations and can differentiate to produce prostatic tubule structures containing both basal and luminal cells in vivo. These cells also localize to the basal cell layer within the region of the gland that is proximal to the urethra, which has been identified as the prostate stem cell niche. Prostate stem cells can be isolated to a purity of up to 1 in 35 by using this antigenic profile. The remarkable similarity in cell surface profile between prostate and mammary gland stem cells suggests these markers may be conserved among epithelial stem cell populations.
Theoretical analysis of perfect quantum state transfer with superconducting qubits (2008)

Superconducting quantum circuits, fabricated with multiple layers, are proposed to implement perfect quantum state transfer between nodes of a hypercube network. For tunable devices such as the phase qubit, each node can transmit quantum information to any other node at a constant rate independent of the distance between qubits. The physical limits of quantum state transfer in this network are theoretically analyzed, including the effects of disorder, decoherence, and higher-order couplings.
Kinetics of p56lck and p60src Src homology 2 domain binding to tyrosine-phosphorylated peptides determined by a competition assay or surface plasmon resonance. (1993)

Src homology 2 (SH2) domains are phosphotyrosine-binding modules found within various signal-transducing proteins. We have determined by 125I competition assay and surface plasmon resonance that the SH2 domains of Src and Lck bind to a variety of phosphopeptides with similar affinity and specificity. Both bound with highest affinity [Kd(app) approximately 3.7 nM; ka = 2.4 x 10(5) M-1 x s-1; kd = 1.2 x 10(-3) s-1] a phosphopeptide having a Tyr(P)-Glu-Glu-Ile motif found in the hamster polyomavirus middle-sized tumor antigen. Intermediate affinity (5- to 40-fold lower) was observed with phosphopeptides corresponding to the regulatory domains of Src and Lck, containing Tyr527 and Tyr505, respectively. Lowest affinity (80- to 300-fold lower) was observed with phosphopeptides corresponding to phosphorylated tyrosines of GTPase-activating protein, insulin receptor substrate 1, and SH2 domain-containing protein-tyrosine-phosphatase 1.
In vivo measurement of 5‐aminolaevulinic acid‐induced protoporphyrin IX photobleaching: a comparison of red and blue light of various intensities (2004)

Comparison of the photobleaching rates suggests that a blue light intensity of 5 mW/cm(2) gives the same rate of photobleaching as the typical red light PDT intensity of 100 mW/cm(2). Further investigation of the correlation between PpIX photobleaching and PDT effect would be beneficial in interpreting the clinical significance of our findings.
Mutations in the Yellow Fever Virus Nonstructural Protein NS2A Selectively Block Production of Infectious Particles (2002)

Little is known about the function of flavivirus nonstructural protein NS2A. Two forms of NS2A are found in yellow fever virus-infected cells. Full-length NS2A (224 amino acids) is the product of cleavage at the NS1/2A and NS2A/2B sites. NS2Aalpha, a C-terminally truncated form of 190 amino acids, results from partial cleavage by the viral NS2B-3 serine protease at the sequence QK /T within NS2A. Exchange of serine for lysine at this site (QKT-->QST) blocks the production of both NS2Aalpha and infectious virus. The present study reveals that this defect is not at the level of RNA replication. Despite normal structural region processing, infectious particles containing genome RNA and capsid protein were not released from cells transfected with the mutant RNA. Nevertheless, production of subviral prM/M- and E-containing particles was unimpaired. The NS2A defect could be complemented in trans by providing NS1-2A or NS1-2Aalpha. However, trans complementation was not observed when the C-terminal lysine of NS1-2Aalpha was replaced with serine. In addition to true reversions, NS2Aalpha cleavage site mutations could be suppressed by two classes of second-site changes. The first class consisted of insertions at the NS2Aalpha cleavage site that restored its basic character and cleavability. A second class of suppressors occurred in the NS3 helicase domain, in which NS3 aspartate 343 was replaced with an uncharged residue (either valine, alanine, or glycine). These mutations in NS3 restored infectious-virus production in the absence of cleavage at the mutant NS2Aalpha site. Taken together, our results reveal an unexpected role for NS2A and NS3 in the assembly and/or release of infectious flavivirus particles.
Osteoconductive Composite Grouts for Orthopedic Use (1988)

A composite of HA particulate and calcium sulfate hemihydrate has been developed. When this dry material is mixed with either sterile saline or water, the resulting mixture begins to gel. While in the gel or dough state, the composite can be manually inserted or injected under pressure into a bone defect where it sets in situ. The calcium sulfate acts as a binder to hold the HA particles in place. The subsequent resorption of the calcium sulfate leaves controlled porosity for bone ingrowth and attachment to the nonresorbable HA particulate. The combination of calcium sulfate and HA results in a composite with handling properties superior to those of HA alone. Calcium sulfate has a long history of medical use as an implant material. The biocompatibility of the material has been clearly established. The combination of HA and calcium sulfate is likewise extremely compatible as demonstrated in the present studies. Bone ingrowth concomitant with resorption occurs rapidly with efficient conduction of bone from particle to particle. Based on the experiments presented herein, the composite of HA and calcium sulfate may be a useful alternative or adjunct to autogenous bone grafting. Many questions, however, remain regarding long-term tissue response and bone remodeling as well as the efficacy of this material relative to bone grafting.
Cloning, Characterization and Heterologous Expression of a Polyketide Synthase and P-450 Oxidase Involved in the Biosynthesis of the Antibiotic Oleandomycin. (2000)

The gene cluster encoding the deoxyoleandolide polyketide synthase (OlePKS) was isolated from the oleandomycin producing strain Streptomnyces antibioticus. Sequencing of the first two genes encoding OlePKS, together with the previously identified third gene revealed an overall genetic and protein architecture similar to that of the erythromycin gene cluster encoding the 6-deoxyerythronolide B synthase (DEBS) from Saccharopolyspora erythraea. When the entire OlePKS (10,487 amino acids) was expressed in the heterologous host Streptomyces lividans, it produced 8,8a-deoxyoleandolide, an aglycone precursor of oleandomycin. The role of the P-450 monooxygenase, OleP, in oleandomycin biosynthesis was also examined in vivo by co-expression with DEBS in S. lividans. The production of 8,8a-dihydroxy-6-deoxyerythronolide B and other derivatives indicates that OleP is involved in the epoxidation pathway of oleandomycin biosynthesis. Since there are currently no genetic systems available for manipulation of the natural oleandomycin producing strain, the heterologous expression system reported here provides a useful tool for studying this important macrolide antibiotic.
Strong intrinsic mixing in vortex magnetic fields (2009)

We report a method of magnetic mixing wherein a "vortex" magnetic field applied to a suspension of magnetic particles creates strong homogeneous mixing throughout the fluid volume. Experiments designed to elucidate the microscopic mechanism of mixing show that the torque is quadratic in the field, decreases with field frequency, and is optimized at a vortex field angle of approximately 55 degrees . Theory and simulations indicate that the field-induced formation of volatile particle chains is responsible for these phenomena. This technique has applications in microfluidic devices and is ideally suited to applications such as accelerating the binding of target biomolecules to biofunctionalized magnetic microbeads.
The History of Pyrosequencing<sup>®</sup> (2007)

One late afternoon in the beginning of January 1986, bicycling from the lab over the hill to the small village of Fulbourn, the idea for an alternative DNA sequencing technique came to my mind. The basic concept was to follow the activity of DNA polymerase during nucleotide incorporation into a DNA strand by analyzing the pyrophosphate released during the process. Today, the technique is used in multidisciplinary fields in academic, clinical, and industrial settings all over the word. This technique can be used for both single-base sequencing and whole-genome sequencing, depending on the format used.In this chapter, I give my personal account of the development of Pyrosequencing(®)-beginning on a winter day in 1986, when I first envisioned the method-until today, nearly 30 years later.
Time reversal with MISO for ultra-wideband communications: experimental results (2006)

Time reversal (TR) communications marks a paradigm shift in UWB communications. The system complexity can be shifted from the receiver to the transmitter, which is ideal to UWB sensors. UWB multiple input single output (MISO) is enabled by the use of the TR scheme. Two basic problems are investigated experimentally using short UWB radio pulses (nanosecond duration). Temporal focusing and SNR increase with the number of antennas are verified. Also, reciprocity of realistic channels, the foundation of TR, is demonstrated for the first time in electromagnetics.
The Gene yjcG , Cotranscribed with the Gene acs , Encodes an Acetate Permease in Escherichia coli (2003)

We isolated an Escherichia coli mutant strain that suppresses the glycolate-negative phenotype of a strain deficient in both GlcA and LldP transporters of this compound. This suppressing phenotype was assigned to yjcG, a gene whose function was previously unknown, which was found to encode a membrane protein able to transport glycolate. On the basis of sequence similarity, the yjcG gene product was classified as a member of the sodium:solute symporter family. Northern experiments revealed that yjcG is cotranscribed with its neighbor, acs, encoding acetyl coenzyme A synthetase, which is involved in the scavenging acetate. The fortuitous presence of an IS2 element in acs, which impaired yjcG expression by polarity in our parental strain, allowed us to conclude that the alternative glycolate carrier became active after precise excision of IS2 in the suppressed strain. The finding that yjcG encodes a putative membrane carrier for glycolate and the cotranscription of yjcG with acs suggested that the primary function of the yjcG gene product (proposed gene name, actP) could be acetate transport and allowed us to define an operon involved in acetate metabolism. The time course of [1,2-(14)C]acetate uptake and the results of a concentration kinetics analysis performed with cells expressing ActP or cells deficient in ActP supported the the hypothesis that this carrier is an acetate transporter and suggested that there may be another transport system for this monocarboxylate.
Affine invariant model-based object recognition (1990)

New techniques are described for model-based recognition of the objects in 3-D space. The recognition is performed from single gray-scale images taken from unknown viewpoints. The objects in the scene may be overlapping and partially occluded. An efficient matching algorithm, which assumes affine approximation to the prospective viewing transformation, is proposed. The algorithm has an offline model preprocessing (shape representation) phase which is independent of the scene information and a recognition phase based on efficient indexing. It has a straightforward parallel implementation. The algorithm was successfully tested in recognition of industrial objects appearing in composite occluded scenes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
What Counterfactuals Can Be Tested (2012)

Counterfactual statements, e.g., "my headache would be gone had I taken an aspirin" are central to scientific discourse, and are formally interpreted as statements derived from "alternative worlds". However, since they invoke hypothetical states of affairs, often incompatible with what is actually known or observed, testing counterfactuals is fraught with conceptual and practical difficulties. In this paper, we provide a complete characterization of "testable counterfactuals," namely, counterfactual statements whose probabilities can be inferred from physical experiments. We provide complete procedures for discerning whether a given counterfactual is testable and, if so, expressing its probability in terms of experimental data.
Synthesis and Antimicrobial Activities of Some Novel Quinoxalinone Derivatives (2000)

Condensation of 4-benzoyl-1,2-phenylenediamine with sodium pyruvate in acetic acid furnished two products which were identified as 6-benzoyl and 7-benzoyl-3-methyl-2(1H)quinoxalinones (1a,b). Fusion of 1a with aromatic aldehydes furnished the styryl derivatives 2a-c. Alkylation of 1a,b with dimethyl sulphate or ethyl chloroacetate produced the N-alkyl derivatives 3a,b and 4a,b. Hydrazinolysis of the ester derivative 4a with hydrazine hydrate afforded the hydrazide derivative 5 which underwent condensation with aldehydes to give the corresponding hydrazone derivatives 6a,b. In addition, chlorination of 1a with thionyl chloride afforded the 2-chloro derivative 7 which was subjected to reaction with sodium azide and n-butylamine to yield the corresponding tetrazolo (8) and n-butylamino (9) derivatives, respectively. The structures of the compounds prepared were confirmed by analytical and spectral data. Also, some of the synthesized compounds were screened for antimicrobial activity.