gebhart/patrepeval huggingface dataset:
Prdm9, a Major Determinant of Meiotic Recombination Hotspots, Is Not Functional in Dogs and Their Wild Relatives, Wolves and Coyotes (2011)

Meiotic recombination is a fundamental process needed for the correct segregation of chromosomes during meiosis in sexually reproducing organisms. In humans, 80% of crossovers are estimated to occur at specific areas of the genome called recombination hotspots. Recently, a protein called PRDM9 was identified as a major player in determining the location of genome-wide meiotic recombination hotspots in humans and mice. The origin of this protein seems to be ancient in evolutionary time, as reflected by its fairly conserved structure in lineages that diverged over 700 million years ago. Despite its important role, there are many animal groups in which Prdm9 is absent (e.g. birds, reptiles, amphibians, diptera) and it has been suggested to have disruptive mutations and thus to be a pseudogene in dogs. Because of the dog's history through domestication and artificial selection, we wanted to confirm the presence of a disrupted Prdm9 gene in dogs and determine whether this was exclusive of this species or whether it also occurred in its wild ancestor, the wolf, and in a close relative, the coyote. We sequenced the region in the dog genome that aligned to the last exon of the human Prdm9, containing the entire zinc finger domain, in 4 dogs, 17 wolves and 2 coyotes. Our results show that the three canid species possess mutations that likely make this gene non functional. Because these mutations are shared across the three species, they must have appeared prior to the split of the wolf and the coyote, millions of years ago, and are not related to domestication. In addition, our results suggest that in these three canid species recombination does not occur at hotspots or hotspot location is controlled through a mechanism yet to be determined.
Inhibition of premature death by isothiocyanates through immune restoration in LP-BM5 leukemia retrovirus-infected C57BL/6 mice (2011)

The purpose of this study was to determine the effect of isothiocyanates (ITCs) in delaying the progression of the murine immunodeficiency virus to murine AIDS, resulting in increased life span. Furthermore, we investigated the role of ITCs in modulating immune dysfunction caused by LP-BM5 retrovirus infection. Among the tested ITCs, oral administration of sulforaphane (SUL), benzyl isothiocyante (BITC), and phenethyl isothiocyanate (PEITC) showed the inhibition of premature death caused by LP-BM5 retrovirus infection, while indolo[3,2-b] carbazole (ICZ) and indole-3-carbinol (I3C) did not delay the progress of the LP-BM5 retrovirus to murine AIDS. Inhibition of premature death by BITC, PEITC, and SUL could be explained by restoration of the immune system and down regulation of free radicals. Dysfunction of T and B cell mitogenesis caused by retrovirus infection in primary cultured splenocytes has been partially recovered with administration of BITC, PEITC, and SUL. There was a shift from imbalanced cytokine production (increased Th2 and decreased Th1 cell cytokine production) into balanced Th1/Th2 cell secretion of cytokines under administration of these ITCs during the development of murine AIDS. Hepatic vitamin E level was significantly restored by administration of these ITCs, in accordance with reduced hepatic lipid peroxidation levels. This study suggests that certain types of ITCs have beneficial effects in preventing premature death during progression to murine AIDS by restoration of immune dysfunction and removal of excessive free radicals, implying that selective usage of ITCs would be helpful in retarding the progression from HIV infection to AIDS.
Widespread and early myocardial gene expression by adeno-associated virus vector type 6 with a β-actin hybrid promoter (2005)

Gene therapy for acute cardiac events such as myocardial infarction requires early gene expression over an entire region of myocardium, which has not been possible using adeno-associated virus (AAV) vectors to date. Here we demonstrate marked improvement in the distribution and rapidity of gene expression in myocardium using the AAV pseudotype 6 (AAV6) vector, compared to the standard serotype 2 (AAV2) vector. An alkaline phosphatase (AP) reporter construct driven by the chicken beta-actin promoter was packaged in either AAV6 or AAV2 capsids and delivered to rat hearts in vivo by direct injection. AP expression was evident in both AAV6 and AAV2 vector-treated hearts as early as 1 day after injection, but increased rapidly in AAV6 vector-treated hearts during the first 7 days. The amplitude of AP activity produced by the AAV6 vector was 5-fold greater than that produced by the equivalent AAV2 vector at both 3 and 7 days postinjection. Additionally, the AAV6 vector transduced a myocardial volume that was 10-fold larger than the AAV2 vector. These results indicate the significant potential of AAV6 serotype vectors for early gene expression and widespread regional transduction of myocardium, both auspicious results for in vivo applications in acute cardiac disease.
O-GlcNAcase Catalyzes Cleavage of Thioglycosides without General Acid Catalysis (2005)

O-GlcNAcase catalyzes the removal of N-acetylglucosamine residues from serine and threonine residues of post-translationally modified proteins using a catalytic mechanism involving substrate-assisted catalysis and general acid/base catalysis. Since thioglycosides are widely perceived as resistant to hydrolysis by glycosidases, it was surprising to find that O-GlcNAcase also catalyzes the efficient hydrolysis of S-glycosides. Brønsted analyses and pH-activity studies of the O-GlcNAcase-catalyzed hydrolysis of a series of aryl S- and O-glycosides reveal that O-GlcNAcase effects hydrolysis of thioglycosides without the assistance of general acid catalysis. alpha-Deuterium kinetic isotope effects for O- and S-glycosides, as well as Taft-like analyses using N-fluoroacetyl-beta-glycosides, suggest that O-GlcNAcase accomplishes hydrolysis of thioglycosides by stabilizing late transition states. For S-glycosides this transition state shows greater nucleophilic participation from the 2-acetamido group than for O-glycosides. The rate constants governing the O-GlcNAcase-catalyzed hydrolysis of O- and S-glycosides as compared to those previously determined for the spontaneous hydrolysis of structurally similar O,O- and O,S-acetals show a similar ratio. O-GlcNAcase therefore demonstrates similar catalytic proficiency toward both O- and S-glycosides. We conclude that O-GlcNAcase is a bifunctional catalyst capable of efficiently cleaving thioglycosides without general acid catalysis, an observation that may have biological implications.
High-Performance Accumulated Back-Interface Dynamic Threshold SOI MOSFET (AB-DTMOS) with Large Body Effect at Low Supply Voltage (1999)

A high-performance accumulated back-interface dynamic threshold silicon-on-insulator metal-oxide-semiconductor field effect transistor (AB-DTMOS) with a large body effect at low supply voltage ( V dd &lt; 0.5 V) is proposed for low-power applications. In AB-DTMOS, the back interface between the non-doped thin SOI and the buried oxide is accumulated by a large negative substrate bias, and the gate electrode is connected to this electrically induced body. AB-DTMOS realizes an ideal low/ultrahigh step channel profile electrically and achieves the maximum body effect. At fixed V th , the body effect factor (γ) of AB-DTMOS is twice as large as that of the conventional uniformly doped channel DTMOS, because the channel depletion layer width of AB-DTMOS is half that of the conventional DTMOS. Experimental results show a steep subthreshold slope, a high current drive due to a large V th shift, and a suppressed short channel effect.
Development of a Microfluidic Device for Detection of Pathogens in Oral Samples Using Upconverting Phosphor Technology (UPT) (2007)

Abstract : Confirmatory detection of diseases, such as HIV and HIV‐associated pathogens in a rapid point‐of‐care (POC) diagnostic remains a goal for disease control, prevention, and therapy. If a sample could be analyzed onsite with a verified result, the individual could be counseled immediately and appropriate therapy initiated. Our group is focused on developing a microfluidic “lab‐on‐a‐chip” that will simultaneously identify antigens, antibodies, RNA, and DNA using a single oral sample. The approach has been to design individual modules for each assay that uses similar components (e.g., valves, heaters, metering chambers, mixers) installed on a polycarbonate base with a common reporter system. Assay miniaturization reduces the overall analysis time, increases accuracy by simultaneously identifying multiple targets, and enhances detector sensitivity by upconverting phosphor technology (UPT). Our microfluidic approach employs four interrelated components: (1) sample acquisition–OraSure UP link ™ collectors that pick‐up and release bacteria, soluble analytes, and viruses from an oral sample; (2) microfluidic processing–movement of microliter volumes of analyte, target analyte extraction and amplification; (3) detection of analytes using UPT particles in a lateral flow system; and (4) software for processing the results. Ultimately, the oral‐based microscale diagnostic system will detect viruses and bacteria, associated pathogen antigens and nucleic acids, and antibodies to these pathogens.
Melphalan and its role in the management of patients with multiple myeloma (2007)

Melphalan is an alkylating agent approved for the treatment of multiple myeloma and ovarian cancer. The combination of oral melphalan and prednisone was first introduced in the 1960s and remains the standard therapy for elderly multiple myeloma patients. High-dose melphalan followed by autologous stem cell support became the standard treatment for younger patients since the 1990s. The occurrence of drug resistance is the major limiting factor for the long-term success of this therapy, and relapse always occurs. In recent years, advances in the understanding of the pathogenesis of myeloma and the mechanism of drug resistance have led to the development of novel targeted therapies that are able to overcome resistance and show additive or synergistic effects with melphalan. Thalidomide, its immunomodulatory derivative lenalidomide and the proteasome inhibitor bortezomib, in combination with oral melphalan in the elderly and with intravenous melphalan in younger patients, are changing the traditional treatment paradigm of multiple myeloma.
Enrichment of microsatellites from the citrus genome using biotinylated oligonucleotide sequences bound to streptavidin-coated magnetic particles. (1994)

A method is described for the rapid isolation of microsatellite sequences using a biotin-labeled oligonucleotide attached to streptavidin-coated magnetic particles. The oligonucleotide "hook" in solution hybridizes to complementary single-stranded lengths of genomic DNA onto which have been engineered specific PCR priming sites. The final product is an enriched library of microsatellites of defined sequences. The method is applicable to any genome and in principle is adaptable to the rapid isolation of both repetitive as well as genic sequences. It is illustrated by the isolation of trinucleotide repeat (TAA)n sequences from the citrus genome.
Analysis of myo-inositol hexakisphosphate hydrolysis by Bacillus phytase: indication of a novel reaction mechanism (2000)

Phytic acid (myo-inositol hexakisphosphate, InsP6) hydrolysis by Bacillus phytase (PhyC) was studied. The enzyme hydrolyses only three phosphates from phytic acid. Moreover, the enzyme seems to prefer the hydrolysis of every second phosphate over that of adjacent ones. Furthermore, it is very likely that the enzyme has two alternative pathways for the hydrolysis of phytic acid, resulting in two different myo-inositol trisphosphate end products: Ins(2,4,6)P3 and Ins(1,3,5)P3. These results, together with inhibition studies with fluoride, vanadate, substrate and a substrate analogue, indicate a reaction mechanism different from that of other phytases. By combining the data presented in this study with (1) structural information obtained from the crystal structure of Bacillus amyloliquefaciens phytase [Ha, Oh, Shin, Kim, Oh, Kim, Choi and Oh (2000) Nat. Struct. Biol. 7, 147Ő153], and (2) computer-modelling analyses of enzymeŐsubstrate complexes, a novel mode of phytic acid hydrolysis is proposed.
An investigation of the neuroprotective properties of fenamate NSAIDs, against experimental models of ischemic stroke (2007)

Stroke is a devastating neurological disease with limited treatment opportunities. Recent advances in understanding the underlying pathogenesis of cerebral ischemia support the involvement of multiple biochemical pathways in the development of the ischemic injury. The work reported in this thesis was undertaken to investigate the hypothesis that fenamate NSAIDs have neuroprotective properties against ischemic stroke and to explore the underlying mechanisms for any efficacy. Fenamates are non-selective inhibitors of cyclooxygenases. In addition, fenamates are antagonists of non-selective cation channels, subtype-selective modulators of GABA A receptors, weak inhibitors of glutamate receptors and activators of some potassium channels, all potentially important in the pathogenesis of ischemic stroke. Mefenamic acid, a prototype fenamate, administered by intracerebroventricular (ICV) infusion, reduced the ischemic brain damage and edema volume in the middle cerebral artery occlusion model in male rats. Consistent with these results, systemic administration of mefenamic acid, by multiple intravenous injections, also reduced the ischemic damage and edema volume measured by morphometric analysis and as a function of brain water content. These are the first set of experiments to demonstrate a significant neuroprotective effect of a fenamate against an in vivo model of ischemic stroke. In vitro , mefenamic acid was also shown to reduce glutamate-evoked cell death ( excitotoxicity ) in a concentration-dependent manner in cultured embryonic rat hippocampal neurons. Similarly, selected other fenamates also reduced excitotoxicity in the rank order (from highest): mefenamic acid > flufenamic acid ≥ meclofenamic acid > niflumic acid supporting the idea that this is a drug class action. Three pharmacological properties of fenamates, cyclooxygenase inhibition, GABA A receptor modulation and potassium channel activation were investigated as the potential mechanism(s) for the neuroprotective effects of mefenamic acid against excitotoxicity. The experimental results suggest that these are not the primary mechanisms for neuroprotective effects of mefenamic acid against glutamate-evoked cell death. Collectively, these data support the hypothesis that fenamate NSAIDs are neuroprotective against experimental models of cerebral ischemia and suggest they should be further investigated as potential pharmacological treatments for stroke.
Metabolic engineering of hydroxy fatty acid production in plants: RcDGAT2 drives dramatic increases in ricinoleate levels in seed oil (2008)

A central goal of green chemistry is to produce industrially useful fatty acids in oilseed crops. Although genes encoding suitable fatty acid-modifying enzymes are available from many wild species, progress has been limited because the expression of these genes in transgenic plants produces low yields of the desired products. For example, Ricinus communis fatty acid hydroxylase 12 (FAH12) produces a maximum of only 17% hydroxy fatty acids (HFAs) when expressed in Arabidopsis. cDNA clones encoding R. communis enzymes for additional steps in the seed oil biosynthetic pathway were identified. Expression of these cDNAs in FAH12 transgenic plants revealed that the R. communis type-2 acyl-coenzyme A:diacylglycerol acyltransferase (RcDGAT2) could increase HFAs from 17% to nearly 30%. Detailed comparisons of seed neutral lipids from the single- and double-transgenic lines indicated that RcDGAT2 substantially modified the triacylglycerol (TAG) pool, with significant increases in most of the major TAG species observed in native castor bean oil. These data suggest that RcDGAT2 prefers acyl-coenzyme A and diacylglycerol substrates containing HFAs, and biochemical analyses of RcDGAT2 expressed in yeast cells confirmed a strong preference for HFA-containing diacylglycerol substrates. Our results demonstrate that pathway engineering approaches can be used successfully to increase the yields of industrial feedstocks in plants, and that members of the DGAT2 gene family probably play a key role in this process.
Modulation of endotoxin-induced monokine release in human monocytes by lipid A partial structures that inhibit binding of 125I-lipopolysaccharide (1992)

We have previously shown that the synthetic tetraacyl precursor Ia (compound 406, LA-14-PP, or lipid IVa) was not able to induce the production of tumor necrosis factor, interleukin-1, and interleukin-6 in human monocytes but strongly antagonized lipopolysaccharide (LPS)-induced formation of these monokines. This inhibition was detectable at the level of mRNA production. To achieve a better understanding of molecular basis of this inhibition, we investigated whether lipid A precursor Ia (LA-14-PP), Escherichia coli-type lipid A (LA-15-PP), Chromobacterium violaceum-type lipid A (LA-22-PP), and synthetic lipid A partial structures and analogs (LA-23-PP, LA-24-PP, and PE-4) were able to influence the binding of 125I-LPS to human monocytes and compared this inhibitory activity with the agonistic and antagonistic action in the induction of monokines in human monocytes. 125I-LPS (20 ng per well) was added to human monocytes in the presence or absence of unlabeled rough Re mutant-derived LPS (Re-LPS) or lipid A compounds, and specific LPS binding was determined after 7 h. This binding was found to be dependent on CD14 as shown by the use of an anti-CD14 monoclonal antibody. Compound LA-14-PP was found to inhibit the binding of 125I-LPS to the cells in a similar dose-response to that of unlabeled LPS. This shows that the inhibitory capacity on LPS binding does not correlate with the monokine-inducing capacity because Re-LPS is active in inducing tumor necrosis factor, interleukin-1, and interleukin-6, while LA-14-PP is not. The strong capacity of LA-14-PP to inhibit 125I-LPS binding, however, correlates with the strong inhibitory capacity of this compound on LPS-induced monokine production. Compounds LA-15-PP, LA-23-PP, and LA-24-PP were active in the inhibition of 125I-LPS binding but were 5- to 10-fold weaker than Re-LPS and LA-14-PP. Of all lipid A structures tested, compound LA-22-PP expressed the weakest inhibitory capacity on LPS binding. These compounds showed again that the activity of binding inhibition does not correlate with the monokine-inducing capacity. We assume that the inhibitory effects of lipid A partial structures on LPS-induced monokine production have their origin in a competitive inhibition between LPS and the lipid A partial structures for the same binding site on the cell membrane.
Determining RF angle of arrival using COTS antenna arrays: A field evaluation (2012)

We are interested in estimating the angle of arrival of an RF signal by using commercial-off-the-shelf (COTS) software-defined radios (SDRs). The proposed COTS-based approach has the advantages of flexibility, low cost and ease of deployment, but-unlike traditional phased antenna arrays in which elements are already phase-aligned - we face the challenge of aligning individual SDRs during field deployment in order to ensure coherent phase detection. We propose a strategy to relax the requirement of tight phase synchronization between distributed oscillators by using a novel phase difference of arrival mechanism based on a field-deployable reference transmitter. This approach enables flexible and inexpensive COTS phased-array designs. We evaluate our method in an outdoor, 20m×20m open field and observe localization errors below 3m. We conclude that a COTS-based approach to RF source localization is amenable to rapid and low-cost deployment of sensing infrastructure and could potentially be of interest to the Intelligence, Surveillance and Reconnaissance (ISR) community at the tactical edge.
SystemT: An Algebraic Approach to Declarative Information Extraction (2010)

As information extraction (IE) becomes more central to enterprise applications, rule-based IE engines have become increasingly important. In this paper, we describe SystemT, a rule-based IE system whose basic design removes the expressivity and performance limitations of current systems based on cascading grammars. SystemT uses a declarative rule language, AQL, and an optimizer that generates high-performance algebraic execution plans for AQL rules. We compare SystemT’s approach against cascading grammars, both theoretically and with a thorough experimental evaluation. Our results show that SystemT can deliver result quality comparable to the state-of-theart and an order of magnitude higher annotation throughput. 1
Appearance of heparin-binding EGF-like growth factor in wound fluid as a response to injury. (1993)

Wound fluid was obtained from porcine partial-thickness excisional wounds and analyzed for heparin-binding growth factors. Two heparin-binding growth factor activities were detected, a relatively minor one that was eluted from a heparin affinity column with 0.65 M NaCl and a major one that was eluted with 1.1 M NaCl. These activities were not present in wound fluid 1 hr after injury but appeared 1 day after injury, were maximal 2-3 days after injury, and were not detectable by 8 days after injury. The heparin-binding growth factor eluted with 0.65 M NaCl was identified as a platelet-derived growth factor (PDGF)-like activity by the use of specific anti-PDGF neutralizing antibodies. The heparin-binding growth factor eluted with 1.1 M NaCl was shown to be structurally related to heparin-binding epidermal growth factor (EGF)-like growth factor (HB-EGF) by several criteria, including binding to heparin affinity columns and elution with 1.1 M NaCl, competition with the binding of 125I-EGF to the EGF receptor, triggering phosphorylation of the EGF receptor, immunodetection on a Western blot, and stimulation of fibroblast and keratinocyte growth. It was concluded that HB-EGF is a major growth factor component of wound fluid and, since it is mitogenic for fibroblasts and keratinocytes, that it might play an important role in wound healing.
Timing of Applying Electrical Stimulation Is an Important Factor Deciding the Success Rate and Maturity of Regenerating Rat Sciatic Nerves (2010)

A short delay in the onset of ES may improve the recovery of a severe peripheral nerve injury, which should be considered as a way of augmenting rehabilitative approaches.