gebhart/patrepeval huggingface dataset:
Polysaccharide Vaccines for Enteric Pathogens: The Next Generation Multivalent Diarrhea Vaccine (2016)

Diarrheal disease due to enteric pathogens is a global health problem and three major contributors are enterotoxigenic Escherichia coli (ETEC), Shigella flexneri and Campylobacter jejuni. The effects of some gastric infections also go beyond the intestinal tract, such as C. jejuni and its link to Guillain-Barré Syndrome, and the autism associated pathogen, Clostridium bolteae. The first section of this thesis is an extension of my MSc research, in which I discovered the capsule polysaccharide of the autism associated bacteria, C. bolteae. Here, I show the conjugation of the C. bolteae polysaccharide to a carrier protein in preparation for upcoming immunological testing. More significantly, I also divulge the chemical synthesis of the C. bolteae capsule polysaccharide non-reducing end terminus with an aminopentyl linker at the reducing end: α-D-Manp-(1→4)-b-D-Rhap-(1→O(CH2)5NH2. The capsule polysaccharide of a key representative strain of C. jejuni serotype complex HS:5 was fully characterized in this work. C. jejuni HS:5 capsule polysaccharide was determined to be highly complex composed of 3,6-dideoxy-α-D-ribo-heptopyranose, glucitol, α-D-glycero-D-manno-heptopyranose, MeOPN, and diester phosphate:. Another interesting structural finding came from the analysis of an isogenic mutant of C. jejuni serotype HS:23/36 (PG3718), in which one of the two genes responsible for the addition of O-methyl-phosphoramidate (MeOPN) to the capsule polysaccharide was deactivated. In this case, the MeOPN was not connected to position 2 or 6 of galactose as in the wild-type strain, but to the 4 position of the said galactose. This isogenic strain was found to be more resistant to complement killing than the wild-type strain. Two other classes of polysaccharide conjugate vaccines are also described in this work; those composed of (i) C. jejuni polysaccharides (from serotypes HS:4AB and HS:53) and diphtheria toxoid (CRM197), and (ii) S. flexneri polysaccharide and the ETEC protein CfaEB. These polysaccharide conjugate vaccines were made using a scheme developed in the Monteiro laboratory, where the polysaccharides were first stoichiometric oxidized at primary hydroxyls with 2,2,6,6-tetramethylpiperidin-1-oxyl (TEMPO) and bleach and then conjugated to the immunostimulatory protein. These polysaccharide conjugate vaccines were shown to be highly immunogenic (high IgG levels) in a mouse model and represent a next generation multivalent diarrhea vaccine.
A Classification Framework for Software Component Models (2010)

In the last decade, a large number of different software component models have been developed, with different aims and using different principles and technologies. This has resulted in a number of models which have many similarities, but also principal differences, and in many cases unclear concepts. Component-based development has not succeeded in providing standard principles, as has, for example, object-oriented development. In order to increase the understanding of the concepts and to differentiate component models more easily, this paper identifies, discusses, and characterizes fundamental principles of component models and provides a Component Model Classification Framework based on these principles. Further, the paper classifies a large number of component models using this framework.
An mTERF domain protein functions in group II intron splicing in maize chloroplasts (2014)

The mitochondrial transcription termination factor (mTERF) proteins are nucleic acid binding proteins characterized by degenerate helical repeats of ∼30 amino acids. Metazoan genomes encode a small family of mTERF proteins whose members influence mitochondrial gene expression and DNA replication. The mTERF family in higher plants consists of roughly 30 members, which localize to mitochondria or chloroplasts. Effects of several mTERF proteins on plant development and physiology have been described, but molecular functions of mTERF proteins in plants are unknown. We show that a maize mTERF protein, Zm-mTERF4, promotes the splicing of group II introns in chloroplasts. Zm-mTERF4 coimmunoprecipitates with many chloroplast introns and the splicing of some of these introns is disrupted even in hypomorphic Zm-mterf4 mutants. Furthermore, Zm-mTERF4 is found in high molecular weight complexes that include known chloroplast splicing factors. The splicing of two transfer RNAs (trnI-GAU and trnA-UGC) and one ribosomal protein messenger RNA (rpl2) is particularly sensitive to the loss of Zm-mTERF4, accounting for the loss of plastid ribosomes in Zm-mTERF4 mutants. These findings extend the known functional repertoire of the mTERF family to include group II intron splicing and suggest that a conserved role in chloroplast RNA splicing underlies the physiological defects described for mutations in BSM/Rugosa2, the Zm-mTERF4 ortholog in Arabidopsis.
Rituximab efficacy and safety in adult splenectomy candidates with chronic immune thrombocytopenic purpura: results of a prospective multicenter phase 2 study (2008)

Whether rituximab could effectively and safely avoid splenectomy for adults with chronic immune thrombocytopenic purpura (ITP) remains unresolved. A multicenter, prospective, open-label, single-arm, phase 2 trial was conducted to assess rituximab safety and efficacy in adult splenectomy candidates with chronic ITP. Sixty patients with chronic (>or= 6 months) ITP and platelet counts less than 30 x 10(9)/L received a weekly intravenous infusion of rituximab (375 mg/m(2)) for 4 weeks. All other ITP treatments were stopped. A good response was defined as a platelet count 50 x 10(9)/L or more, with at least a doubling of the initial value at 1 and 2 years after the first rituximab infusion. Patients who required another treatment during follow up were considered nonresponders. Sixteen patients experienced transient side effects that necessitated treatment discontinuation for only 1. Good 1-year responses were obtained in 40% of the patients (24/60 [95% confidence interval: 28%-52%]). At 2 years, 33.3% (20/60 patients) had good responses and 6.7% (4/60) had sustained platelet counts of 30 x 10(9)/L or more without treatment. Thirty-six (60%) patients failed to respond; 25 underwent splenectomy. Based on these results, rituximab was an apparently safe and effective splenectomy-avoiding option in some adults with chronic ITP. This trial is registered at http://clinicaltrials.gov as NCT00225875.
Multiple sclerosis and occupational exposure to chemicals: a co-twin control study of a nationwide series of twins. (1989)

From the Finnish Twin Cohort (n = 27,100 pairs with known zygosity) all cases of diagnosed multiple sclerosis (MS) were reviewed and those with clinically verified MS were invited for further examinations at the Institute of Occupational Health, Helsinki, with their co-twins. Twenty one cases (19 pairs, of which 17 were discordant) fulfilled the strict criteria of MS. Detailed occupational history showed exposure to a mixture of solvents in six subjects, to lead in one, and to trichloroethylene in one. Of these seven, two monozygotic twins had MS whereas the other five cases were healthy co-twins. These results do not support a causal association between occupational exposure to chemicals and the aetiopathogenesis of MS.
Growth and doping of GaAsSb via metalorganic chemical vapor deposition for InP heterojunction bipolar transistors (1996)

GaAsSb is a low band gap, lattice matched to InP, alternative to GaInAs. Growth and doping using diethyltellurium and carbon tetrachloride were investigated. Hole concentrations up to 1.3×1020 cm−3 have been achieved in as-grown carbon-doped GaAsSb [i.e., no postgrowth annealing was necessary for dopant activation, a key requirement for n-p-n heterojunction bipolar transistor (HBT) structures]. This is a sevenfold improvement over the best carbon-doped InGaAs reported by metalorganic chemical vapor deposition. Hall measurements indicate that GaAsSb’s hole mobility is 55%–60% of GaInAs’s, for a given carrier concentration. InP HBTs with carbon-doped GaAsSb base are demonstrated.
The Development of Subretinal Microphotodiodes for Replacement of Degenerated Photoreceptors (1997)

There are presently several concepts to restore vision in blind or highly visually handicapped persons by implanting electronic devices into the eye in order to partially restore vision. Here, the approach to replace retinal photoreceptors by a subretinally implanted microphotodiode array (MPDA) is summarized. A survey is given on the present state of the development of MPDAs, the possibility of in vitro and in vivo tests as well as first results on biocompatibility and histology. Additionally, electrophysiological recordings in rabbits and rats are presented which have received such subretinal implants.
Conversion of amorphous tricalcium phosphate into apatitic tricalcium phosphate. (1982)

Precipitated calcium orthophosphate, rapidly prepared in highly supersaturated solutions at pH 9-11, is an amorphous tricalcium orthophosphate (atomic ratio Ca/P = 3/2) of formula Ca9(PO4)6, nH2O. Kept wet at room temperature, this phosphate is hydrolyzed according to the reaction PO4(3-) + H2O leads to HPO4(2-) + OH-; a tricalcium orthophosphate series is then formed, its general formula is Ca9 (HPO4)x (PO4)6-x (OH)x, O less than or equal to x less than or equal to 1. Moreover, the amorphous phosphate is converted into apatitic phosphate at half hydrolysis (x approximately equal to 0.5). The hydrolysis occurs simultaneously with an endothermic effect [delta H = 12.0 +/- 2.0 kJ/mol Ca9(PO4)6], and the conversion with an exothermic effect [delta H = -5.9 +/- 1.0 kJ/mol Ca9(PO4)6].
A single-nucleotide mutation in a gene encoding S-adenosylmethionine synthetase is associated with methionine over-accumulation phenotype in Arabidopsis thaliana. (2002)

Met-overaccumulating mutants provide a powerful genetic tool for examining both the regulation of the Met biosynthetic pathway and in vivo developmental responses of gene expression to altered Met levels. We have previously reported the identification of two Arabidopsis thaliana Met over-accumulation (mto) mutants, mto1-1 and mto2-1, that carry mutations in the genes encoding cystathionine gamma-synthase (CGS) and threonine synthase (TS), respectively. A third mutant, mto3-1, has recently been reported to carry a mutation in the gene encoding S-adenosylmethionine synthetase 3 (SAMS3). Here, we report the isolation of a new ethionine-resistant A. thaliana mutant that over-accumulates soluble Met approximately 20-fold in young rosettes. The causal mutation was determined to be a single, recessive mutation that was mapped to chromosome 3. Sequence analysis identified a single nucleotide change in the gene encoding SAMS3 that was distinct from the mto3-1 mutation and altered the amino acid sequence of the enzyme active site. This mutation was therefore referred to as mto3-2. Although Met over-accumulation in the mto3-2 mutant was similar to that in the mto2-1 mutant, CGS mRNA levels did not respond to the mto3-2 mutation and were similar to that in equivalent wild-type plants.
A self-powered damage detection sensor (2003)

All existing methods of embedded damage-detecting sensors require an external power source and a means of transmitting the data to a central processor. This paper presents a novel self-powered strain sensor capable of transmitting data wirelessly to a remote receiver. This paper illustrates the performance of the sensor through the theoretical and experimental analysis of a simple damaged beam. The results show that a sensor powered through the conversion of mechanical to electrical energy is viable for detecting damage. The potential benefits of this sensor include ease of implementation during manufacture of the structure, and the use of an environmentally safe and renewable power source.
Evidence for local production of acute phase response apolipoprotein serum amyloid A in Alzheimer's disease brain (1997)

Acute phase serum amyloid A (A-apoSAA), but not constitutive apoSAA (C-apoSAA), was identified by Western blotting experiments in brain protein extracts from eight of nine patients with Alzheimer's disease (AD), one with a brain tumor and one with multiple sclerosis. A-apoSAA was not detected in six subjects with Pick's or Lewy Body disease or three other non-AD brain specimens. Apolipoprotein A-I and albumin were not found in any of the brain protein extracts. A-apoSAA mRNA was detected in AD brain by reverse transcription-polymerase chain reaction (RT-PCR). These data suggest that apoSAA is locally produced in AD brain and that investigation of the neuroinflammatory effects of this injury specific apolipoprotein is warranted.
Detection of Tyrosine Phosphorylated Peptides by Precursor Ion Scanning Quadrupole TOF Mass Spectrometry in Positive Ion Mode (2001)

Phosphorylation is a common form of protein modification. To understand its biological role, the site of phosphorylation has to be determined. Generally, only limited amounts of phosphorylated proteins are present in a cell, thus demanding highly sensitive procedures for phosphorylation site determination. Here, a novel method is introduced which enables the localization of tyrosine phosphorylation in gel-separated proteins in the femtomol range. The method utilizes the immonium ion of phosphotyrosine at m/z 216.043 for positive ion mode precursor ion scanning combined with the recently introduced Q2-pulsing function on quadrupole TOF mass spectrometers. The high resolving power of the quadrupole TOF instrument enables the selective detection of phosphotyrosine immonium ions without interference from other peptide fragments of the same nominal mass. Performing precursor ion scans in the positive ion mode facilitates sequencing, because there is a no need for polarity switching or changing pH of the spraying solvent. Similar limits of detection were obtained in this approach when compared to triple-quadrupole mass spectrometers but with significantly better selectivity, owing to the high accuracy of the fragment ion selection. Synthetic phosphopeptides could be detected at 1 fmol/microL, and 100 fmol of a tyrosine phosphorylated protein in gel was sufficient for the detection of the phosphorylated peptide in the unseparated digestion mixture and for unambiguous phosphorylation site determination. The new method can be applied to unknown protein samples, because the identification and localization of the modification is performed on the same sample.
BN 80933, a dual inhibitor of neuronal nitric oxide synthase and lipid peroxidation: A promising neuroprotective strategy (1999)

Nitric oxide (NO) and reactive oxygen species (ROS) act independently as well as cooperatively to induce neuronal death in acute neurological disorders. Inhibition of neuronal nitric oxide synthase (nNOS) and inhibition of lipid peroxidation induced by ROS have both been proposed as neuroprotective strategies in stroke and trauma. Recently, in our laboratory, the combination of the two strategies was found to be synergistic in reducing neuronal damage. Here, we report that BN 80933 [(S)-N-[4-[4-[(3,4-dihydro-6-hydroxy-2, 5,7, 8-tetramethyl-2H-1-benzopyran-2-yl)carbonyl]-1-piperazinyl]phenyl]-2- thiophenecarboximidamide], a compound that combines potent antioxidant and selective nNOS inhibitory properties in vitro, affords remarkable neuronal protection in vivo. Intravenous administration of BN 80933 significantly reduced brain damage induced by head trauma in mice, global ischemia in gerbils, and transient focal ischemia in rats. Treatment with BN 80933 (0.3-10 mg/kg) significantly reduced infarct volume (>60% protection) and enhanced behavioral recovery in rats subjected to transient (2-h) middle cerebral artery occlusion and 48-h or 7-day reperfusion. Furthermore, treatment with BN 80933 commencing up to 8 h after the onset of ischemia resulted in a significant improvement of neurological outcome. All these results indicate that BN 80933 represents a class of potentially useful therapeutic agents for the treatment of stroke or trauma and possibly neurodegenerative disorders that involve both NO and ROS.
Fast algorithms for sorting and searching strings (1997)

We present theoretical algorithms for sorting and searching multikey data, and derive from them practical C implementations for applications in which keys are character strings. The sorting algorithm blends Quicksort and radix sort; it is competitive with the best known C sort codes. The searching algorithm blends tries and binary search trees; it is faster than hashing and other commonly used search methods. The basic ideas behind the algorithms date back at least to the 1960s, but their practical utility has been overlooked. We also present extensions to more complex string problems, such as partial-match searching.
The Role of Tec Family Kinases in Mononuclear Phagocytes (2009)

Mononuclear phagocytes, including monocytcs, macrophages, and dendritic cells, play an important role in innate and adaptive immune responses and are important regulators of the inflammatory response. Among these, monocytes/macrophages are involved in virtually all aspects of inflammation, ranging from the detection and phagocytosis of pathogens up to the resolution of inflammation and repair of tissue damage. The stimulation of cell surface receptors, such as Toll-like receptors, leads to the initiation of intracellular signal transduction pathways regulating macrophagc activation and effector functions. One group of signaling molecules stimulated on macrophage activation is formed by the Tec kinasc family, which consists of five members (Bmx, Btk, Itk, Rlk, and Tec) and constitutes the second-largest family of nonreceptor protein tyrosine kinases in the immune system. Some Tec kinases have been shown to be major regulators of antigen receptor signaling in lymphocytes, and deficiencies in Tec family kinases cause several immunological defects in humans and mice. Much less is known about the role of Tec family kinases in the myeloid branch of the hematopoietic system. In this review, we discuss the current knowledge about the role of Tec family kinases in monocytes/macrophages, in dendritic cells, and in osteoclasts.
Clinical Experience With the Dynesys Semirigid Fixation System for the Lumbar Spine (2005)

The results of the present study indicate that both back and leg pain are, on average, still moderately high 2 years after instrumentation with the Dynesys system. Only half of the patients declared that the operation had helped and had improved their overall quality of life; less than half reported improvements in functional capacity. The reoperation rate after Dynesys was relatively high. The results provide no support for the notion that semirigid fixation of the lumbar spine results in better patient-oriented outcomes than those typical of fusion.
The Synthesis of Substituted 2-Aryl 4(3H)-Quinazolinones using Nahso3/Dma. Steric Effect upon the Cyclisation-Dehydrogenation Step (2000)

A number of 2-aryl substituted 6-pyrrolidino-4(3H)-quinazolinones are reported. They were synthesised in four steps starting from commercially available 5-chloro-2-nitrobenzoic acid. The key cyclisation-dehydrogenation step between 2-amino-pyrrolidinobenzamide 5 and different benzaldehydes employs NaHSO 3 as the dehydrogenating agent in hot DMA. This last reaction shows a strong dependence on the position of the substituent at the aromatic ring of the benzaldehyde used. Thus, the 2-substituted benzaldehydes, in contrast to 3- and 4-substituted compounds give a poor yield of desired products or a mixture.
Gene expression in papillary thyroid carcinoma reveals highly consistent profiles (2001)

Papillary thyroid carcinoma (PTC) is clinically heterogeneous. Apart from an association with ionizing radiation, the etiology and molecular biology of PTC is poorly understood. We used oligo-based DNA arrays to study the expression profiles of eight matched pairs of normal thyroid and PTC tissues. Additional PTC tumors and other tissues were studied by reverse transcriptase-PCR and immunohistochemistry. The PTCs showed concordant expression of many genes and distinct clustered profiles. Genes with increased expression in PTC included many encoding adhesion and extracellular matrix proteins. Expression was increased in 8/8 tumors for 24 genes and in 7/8 tumors for 22 genes. Among these genes were several previously known to be overexpressed in PTC, such as MET, LGALS3, KRT19, DPP4, MDK, TIMP1, and FN1. The numerous additional genes include CITED1, CHI3L1, ODZ1, N33, SFTPB, and SCEL. Reverse transcriptase-PCR showed high expression of CITED1, CHI3L1, ODZ1, and SCEL in 6/6 additional PTCs. Immunohistochemical analysis detected CITED1 and SFTPB in 49/52 and 39/52 PTCs, respectively, but not in follicular thyroid carcinoma and normal thyroid tissue. Genes underexpressed in PTC included tumor suppressors, thyroid function-related proteins, and fatty acid binding proteins. Expression was decreased in 7/8 tumors for eight genes and decreased in 6/8 tumors for 19 genes. We conclude that, despite its clinical heterogeneity, PTC is characterized by consistent and specific molecular changes. These findings reveal clues to the molecular pathways involved in PTC and may provide biomarkers for clinical use.
Colicin Biology (2007)

Colicins are proteins produced by and toxic for some strains of Escherichia coli. They are produced by strains of E. coli carrying a colicinogenic plasmid that bears the genetic determinants for colicin synthesis, immunity, and release. Insights gained into each fundamental aspect of their biology are presented: their synthesis, which is under SOS regulation; their release into the extracellular medium, which involves the colicin lysis protein; and their uptake mechanisms and modes of action. Colicins are organized into three domains, each one involved in a different step of the process of killing sensitive bacteria. The structures of some colicins are known at the atomic level and are discussed. Colicins exert their lethal action by first binding to specific receptors, which are outer membrane proteins used for the entry of specific nutrients. They are then translocated through the outer membrane and transit through the periplasm by either the Tol or the TonB system. The components of each system are known, and their implication in the functioning of the system is described. Colicins then reach their lethal target and act either by forming a voltage-dependent channel into the inner membrane or by using their endonuclease activity on DNA, rRNA, or tRNA. The mechanisms of inhibition by specific and cognate immunity proteins are presented. Finally, the use of colicins as laboratory or biotechnological tools and their mode of evolution are discussed.
Proteomic identification of MYC2-dependent jasmonate-regulated proteins in Arabidopsis thaliana (2012)

We have identified MYC2-dependent jasmonate-regulated proteins in Arabidopsis thaliana by performing two-dimensional gel electrophoresis and MALDI-TOF/TOF MS analysis. The observed pattern of protein expression suggests that MYC2 has opposite effects on the biosynthetic enzymes of indolic and aliphatic glucosinolate pathways and positively regulates JA-mediated carbohydrate metabolism and oxidative stress tolerance-related proteins. Furthermore, it is very interesting to note that MYC2 plays opposite roles in the modulation of a subset of JA-regulated photosynthetic proteins during short-term and long-term JA signaling. This study will enhance our understanding of the function of MYC2 in JA signaling in Arabidopsis thaliana.