gebhart/patrepeval huggingface dataset:
Magnetic characterization using elements of a PRML channel (1991)

The authors examine several magnetic characterization techniques which are easily implemented using elements of a partial-response maximum-likelihood (PRML) channel. These techniques are applicable over a broad range of topics. The use of the PRML digital samples with specialized data patterns to detect defective media sites is discussed. A sensitive and calibrated method for measuring fly height variations is outlined. A statistical measurement scheme that provides a figure of merit for magnetic performance is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Association between Gene Expression Profiles and Clinical Outcome of Pemetrexed-Based Treatment in Patients with Advanced Non-Squamous Non-Small Cell Lung Cancer: Exploratory Results from a Phase II Study (2014)

These exploratory gene-expression profiling results describe genes potentially linked to low TS-expression. Nine genes were significantly associated with PFS/OS but could not be differentiated as prognostic or predictive as this was a single-arm study. Although these hypotheses-generating results are interesting, they provide no evidence to change the current histology-based treatment approach with pemetrexed.
Discharge Profiles of Ventral Tegmental Area GABA Neurons during Movement, Anesthesia, and the Sleep–Wake Cycle (2001)

Although mesolimbic dopamine (DA) transmission has been implicated in behavioral and cortical arousal, DA neurons in the ventral tegmental area (VTA) and substantia nigra pars compacta (SNc) are not significantly modulated by anesthetics or the sleep-wake cycle. However, VTA and SN non-DA neurons evince increased firing rates during active wakefulness (AW) and rapid eye movement (REM) sleep, relative to quiet wakefulness. Here we describe the effects of movement, select anesthetics, and the sleep-wake cycle on the activity of a homogeneous population of VTA GABA-containing neurons during normal sleep and after 24 hr sleep deprivation. In freely behaving rats, VTA GABA neurons were relatively fast firing (29 +/- 6 Hz during AW), nonbursting neurons that exhibited markedly increased activity during the onset of discrete movements. Adequate anesthesia produced by administration of chloral hydrate, ketamine, or halothane significantly reduced VTA GABA neuron firing rate and converted their activity into phasic 0.5-2.0 sec ON/OFF periods. VTA GABA neuron firing rate decreased 53% during slow-wave sleep (SWS) and increased 79% during REM, relative to AW; however, the discharging was not synchronous with electrocortical alpha wave activity during AW, delta wave activity during SWS, or gamma wave activity during REM. During deprived SWS, there was a direct correlation between increased VTA GABA neuron slowing and increased delta wave power. These findings indicate that the discharging of VTA GABA neurons correlates with psychomotor behavior and that these neurons may be an integral part of the extrathalamic cortical activating system.
64-Tb/s, 8 b/s/Hz, PDM-36QAM Transmission Over 320 km Using Both Pre- and Post-Transmission Digital Signal Processing (2011)

We report the successful transmission of 64 Tb/s capacity (640 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\,\times\,$</tex></formula> 107 Gb/s with 12.5 GHz channel spacing) over 320 km reach utilizing 8-THz of spectrum in the <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">${\rm C}+{\rm L}$</tex> </formula> -bands at a net spectral efficiency of 8 bit/s/Hz. Such a result is accomplished by the use of raised-cosine pulse-shaped PDM-36QAM modulation, intradyne detection, both pre- and post-transmission digital equalization, and ultra-large-area fiber. We discuss in detail the digital modulation technology and signal processing algorithms used in the experiment, including a new two-stage, blind frequency-search-based frequency-offset estimation algorithm and a more computationally efficient carrier-phase recovery algorithm.
A simple method for 3'-labeling of RNA (1996)

We describe a simple method for 3'-end labeling RNAs of known sequence. A short DNA template is designed to anneal to the 3'-end of the RNA, with a two nucleotide 5' overhang of 3'-TA-5', 3'-TG-5' or 3'-TC-5'. The Klenow fragment of DNA polymerase I can then cleanly and efficiently extend the 3'-end of the RNA by the incorporation of a single alpha-32P-labeled dATP residue. This method can be used to label one RNA in a mixture of RNAs, or to label 5'-blocked RNAs such as mRNA.
Human mesenchymal stem cells reduce the severity of acute lung injury in a sheep model of bacterial pneumonia (2014)

NCT01775774 for Phase 1. NCT02097641 for Phase 2.
Engineering the Diiron Site of Escherichia coli Ribonucleotide Reductase Protein R2 to Accumulate an Intermediate Similar to Hperoxo, the Putative Peroxodiiron(III) Complex from the Methane Monooxygenase Catalytic Cycle (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTEngineering the Diiron Site of Escherichia coli Ribonucleotide Reductase Protein R2 to Accumulate an Intermediate Similar to Hperoxo, the Putative Peroxodiiron(III) Complex from the Methane Monooxygenase Catalytic CycleJ. Martin Bollinger,, Carsten Krebs, Armeria Vicol, Shuxian Chen, Brenda A. Ley, Dale E. Edmondson, and Boi Hanh HuynhView Author Information Department of Biochemistry and Molecular Biology The Pennsylvania State University University Park, Pennsylvania 16802 Departments of Physics, Biochemistry, and Chemistry Emory University, Atlanta, Georgia 30322 Cite this: J. Am. Chem. Soc. 1998, 120, 5, 1094–1095Publication Date (Web):February 11, 1998Publication History Received21 October 1997Published online11 February 1998Published inissue 1 February 1998https://pubs.acs.org/doi/10.1021/ja973651chttps://doi.org/10.1021/ja973651crapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views620Altmetric-Citations125LEARN 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:Absorption,Adducts,Cluster chemistry,Diirons,Peptides and proteins Get e-Alerts
A 3-Dimensional Trimeric β-Barrel Model for Chlamydia MOMP Contains Conserved and Novel Elements of Gram-Negative Bacterial Porins (2013)

Chlamydia trachomatis is the most prevalent cause of bacterial sexually transmitted diseases and the leading cause of preventable blindness worldwide. Global control of Chlamydia will best be achieved with a vaccine, a primary target for which is the major outer membrane protein, MOMP, which comprises ~60% of the outer membrane protein mass of this bacterium. In the absence of experimental structural information on MOMP, three previously published topology models presumed a16-stranded barrel architecture. Here, we use the latest β-barrel prediction algorithms, previous 2D topology modeling results, and comparative modeling methodology to build a 3D model based on the 16-stranded, trimeric assumption. We find that while a 3D MOMP model captures many structural hallmarks of a trimeric 16-stranded β-barrel porin, and is consistent with most of the experimental evidence for MOMP, MOMP residues 320-334 cannot be modeled as β-strands that span the entire membrane, as is consistently observed in published 16-stranded β-barrel crystal structures. Given the ambiguous results for β-strand delineation found in this study, recent publications of membrane β-barrel structures breaking with the canonical rule for an even number of β-strands, findings of β-barrels with strand-exchanged oligomeric conformations, and alternate folds dependent upon the lifecycle of the bacterium, we suggest that although the MOMP porin structure incorporates canonical 16-stranded conformations, it may have novel oligomeric or dynamic structural changes accounting for the discrepancies observed.
Cloning, Sequencing, and Expression of the Leukotoxin Gene fromFusobacterium necrophorum (2001)

Fusobacterium necrophorum is a gram-negative, rod-shaped, anaerobic bacterium that is a primary or secondary etiological agent in a variety of necrotic purulent infections in animals and humans. Included are diseases of cattle such as liver abscesses and foot rot, which have economically important consequences for the cattle industry. The major virulence factor of this bacterium is leukotoxin, a secreted protein of high molecular weight active against leukocytes from ruminants. The screening of a genomic DNA library with polyclonal antisera raised against native affinity-purified leukotoxin and further extension of the sequence using inverse PCR led to the cloning of the entire leukotoxin gene. The leukotoxin gene open reading frame (ORF; lktA) consists of 9,726 bp and encodes a protein of 3,241 amino acids with an overall molecular weight of 335,956. The leukotoxin does not have sequence similarity with any other bacterial leukotoxin. Five truncated overlapping polypeptides covering the whole lktA ORF were used to immunize rabbits. In Western blot assays, polyclonal antisera raised against all five truncated polypeptides recognized affinity-purified leukotoxin from F. necrophorum culture supernatant in a Western blot assay. Antisera directed against two of the five polypeptides had neutralizing activity against the toxin. The entire leukotoxin ORF was expressed in Escherichia coli. Flow-cytometric analysis showed that the recombinant leukotoxin was active against bovine polymorphonuclear leukocytes and was inhibited with antiserum raised against the F. necrophorum leukotoxin. Southern blot hybridization analysis revealed different patterns of lktA hybridizing bands between isolates of the two subspecies of F. necrophorum.
The nucleotide sequence of the serA gene of Escherichia coli and the amino acid sequence of the encoded protein, D-3-phosphoglycerate dehydrogenase. (1986)

The nucleotide sequence of serA, the structural gene of Escherichia coli which codes for D-3-phosphoglycerate dehydrogenase, has been determined. The structural gene contains 1233 nucleotides which code for the 409 amino acids of the subunit of the tetrameric enzyme, as well as the initiator methionine, which is cleaved from the mature protein, and the termination codon. The majority of the primary structure of the enzyme has been confirmed by automated Edman degradation of peptide fragments produced by a variety of cleavage agents. Comparison of the amino acid sequence of phosphoglycerate dehydrogenase with other NAD-dependent oxidoreductases reveals less than 20% homology, although conservation of certain specific residues in the coenzyme binding domain appears to be evident.
NF-κB as a therapeutic target in chronic lymphocytic leukemia (2010)

NF-kappaB is a relevant target in CLL and inhibitors of this prosurvival pathway, alone or in combination, represent a novel therapeutic strategy for the treatment of CLL patients.
Stability of HER-2/neu Expression Over Time and at Multiple Metastatic Sites (1993)

The fact that p185 immunoreactivity is rarely heterogeneous is encouraging, both for the potential use of HER-2/neu-related proteins as serum tumor markers and for innovative therapies targeted at p185 expression.
Epileptic Seizures and Epilepsy: Definitions Proposed by the International League Against Epilepsy (ILAE) and the International Bureau for Epilepsy (IBE) (2005)

The International League Against Epilepsy (ILAE) and the International Bureau for Epilepsy (IBE) have come to consensus definitions for the terms epileptic seizure and epilepsy. An epileptic seizure is a transient occurrence of signs and/or symptoms due to abnormal excessive or synchronous neuronal activity in the brain. Epilepsy is a disorder of the brain characterized by an enduring predisposition to generate epileptic seizures and by the neurobiologic, cognitive, psychological, and social consequences of this condition. The definition of epilepsy requires the occurrence of at least one epileptic seizure.
14th International Headache Congress: Basic Science Highlights (2010)

During the 14th International Headache Congress the results of several innovative studies that contribute to our understanding of headache pathophysiology and treatment were presented. Here we summarize work expected to contribute substantially to understanding headache mechanisms, while an accompanying manuscript summarizes presentations regarding the treatment of headache. This manuscript highlights research on mechanisms of photophobia and phonophobia, pharmacologic inhibition of cortical spreading depression, a proposed mechanism by which oxygen effectively treats cluster headache, identification of functional and structural aberrations in people with hypnic headache, and research on functional imaging markers of a migraine attack.
Fusion of Magnetic and Visual Sensors for Indoor Localization: Infrastructure-Free and More Effective (2016)

Accurate and infrastructure-free indoor positioning can be very useful in a variety of applications. However, most existing approaches (e.g., WiFi and infrared-based methods) for indoor localization heavily rely on infrastructure, which is neither scalable nor pervasively available. In this paper, we propose a novel indoor localization and tracking approach, termed VMag, that does not require any infrastructure assistance. The user can be localized while simply holding a smartphone. To the best of our knowledge, the proposed method is the first exploration of fusing geomagnetic and visual sensing for indoor localization. More specifically, we conduct an in-depth study on both the advantageous properties and the challenges in leveraging the geomagnetic field and visual images for indoor localization. Based on these studies, we design a context-aware particle filtering framework to track the user with the goal of maximizing the positioning accuracy. We also introduce a neural-network-based method to extract deep features for the purpose of indoor positioning. We have conducted extensive experiments on four different indoor settings including a laboratory, a garage, a canteen, and an office building. Experimental results demonstrate the superior performance of VMag over the state of the art with these four indoor settings.
Short chain fatty acids in human large intestine, portal, hepatic and venous blood. (1987)

Evidence for the occurrence of microbial breakdown of carbohydrate in the human colon has been sought by measuring short chain fatty acid (SCFA) concentrations in the contents of all regions of the large intestine and in portal, hepatic and peripheral venous blood obtained at autopsy of sudden death victims within four hours of death. Total SCFA concentration (mmol/kg) was low in the terminal ileum at 13 +/- 6 but high in all regions of the colon ranging from 131 +/- 9 in the caecum to 80 +/- 11 in the descending colon. The presence of branched chain fatty acids was also noted. A significant trend from high to low concentrations was found on passing distally from caecum to descending colon. pH also changed with region from 5.6 +/- 0.2 in the caecum to 6.6 +/- 0.1 in the descending colon. pH and SCFA concentrations were inversely related. Total SCFA (mumol/l) in blood was, portal 375 +/- 70, hepatic 148 +/- 42 and peripheral 79 +/- 22. In all samples acetate was the principal anion but molar ratios of the three principal SCFA changed on going from colonic contents to portal blood to hepatic vein indicating greater uptake of butyrate by the colonic epithelium and propionate by the liver. These data indicate that substantial carbohydrate, and possibly protein, fermentation is occurring in the human large intestine, principally in the caecum and ascending colon and that the large bowel may have a greater role to play in digestion than has previously been ascribed to it.
Phase II trial of aflibercept (VEGF Trap) in previously treated patients with metastatic colorectal cancer (MCRC): A PMH phase II consortium trial (2008)

4027 Background: Vascular endothelial growth factor (VEGF) is an important target in MCRC. Aflibercept (VEGF Trap) is a recombinant fusion protein of the human VEGFR1 and R2 extracellular domains and the Fc portion of human IgG1. Methods: This is an open-label, multi-centre, 2-stage phase II trial in pts with MCRC. Eligibility criteria: >1 prior systemic therapy for MCRC, ECOG < 2. Exclusion criteria: prior treatment with a VEGF or VEGFR inhibitor other than bevacizumab (BEV). IV VEGF Trap (4 mg/kg) was administered every 2 weeks (1 cycle). The primary endpoint was RR and 4-month PFS. Pts were enrolled in two cohorts: BEV naïve and prior BEV. Planned sample size in each cohort was 40 pts. Results: In total, 51 pts were enrolled (BEV naive = 24 pts; prior BEV = 27; median age=59, range 39–80; M:F = 30:21; ECOG 0:1:2 = 21:27:3; median # prior regimens for MCRC = 2, range 1–6). After 287 cycles of therapy, most common treatment adverse events (TAEs) of any grade were (#pts): fatigue (40), hypertension (28), proteinuria (25), headache (22), voice alteration (16), anorexia (12), and joint pain (9). Grade 3+ TAEs in > 1 pt were (#pts): hypertension (4), proteinuria (4), fatigue (3), headache (3). One pt died on treatment due to PD. In the BEV naïve cohort (n=24), 4 pts were inevaluable: 7 pts maintained 4-mo PFS, disease control rate (PR + SD > 16 wks) = 29% [95% CI 13–51%], and median PFS was 2.0 mo [95% CI 1.7- not reached (NR)]. In the prior BEV cohort (n=27), 1 pt was inevaluable. There was 1 confirmed PR and 7 pts maintained 4-mo PFS, disease control rate 30% [95% CI 14–50%], and median PFS was 3.4 mo [95% CI 1.9-NR]. Conclusions: Aflibercept (VEGF Trap) is well tolerated in pretreated pts with MCRC. Single agent activity has been observed in the prior BEV cohort, and accrual is ongoing in this stratum. Based on the study results, studies of aflibercept as single agent or in combination should be explored. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration Johnson & Johnson, Pfizer Oncology
Low-magnesium, trans-cleavage activity by type III, tertiary stabilized hammerhead ribozymes with stem 1 discontinuities (2005)

Hammerhead ribozymes with the "type III" topology can be converted to a tertiary, trans-cleavage design. Separating the stabilization and substrate recognition functions of stem 1 increases cleavage activity at physiological concentrations of divalent magnesium while retaining recognition of exogenous targets. Trans-cleaving ribozymes that exploit the tertiary stabilizing motifs of all natural hammerhead topologies can therefore be used in intracellular applications.
Choroid plexus: Target for polypeptides and site of their synthesis (2000)

Choroid plexus (CP) is an important target organ for polypeptides. The fenestrated phenotype of choroidal endothelium facilitates the penetration of blood-borne polypeptides across the capillary walls. Thus, both circulating and cerebrospinal fluid (CSF)-borne polypeptides can reach their receptors on choroidal epithelium. Several polypeptides have been demonstrated to regulate CSF formation by controlling blood flow to choroid plexus and/or the activity of ion transport in choroidal epithelium. However, many ligand-receptor interactions occurring in the CP are not involved in the regulation of fluid secretion. Increasing evidence suggests that the choroidal epithelium plays an important role in hormonal signaling via a receptor-mediated transport into the brain (e.g., leptin) and helps to clear certain CSF-borne polypeptides (e.g., soluble amyloid beta-protein). Thus, impaired choroidal transport or insufficient clearance of polypeptides may contribute to pathogenesis of systemic or central nervous system (CNS) disorders, such as obesity or Alzheimer's disease. CP epithelium is not only a target but is also a source of neuropeptides, growth factors, and cytokines in the CNS. These polypeptides following their release into the CSF may exert distal, endocrine-like effects on target cells in the brain due to bulk flow of this fluid. Distinct temporal patterns of choroidal expression of several polypeptides are observed during brain development and in various CNS disorders, including traumatic brain injury and ischemia. Therefore, it is proposed that the CP plays an integral role not only in normal brain functioning, but also in the recovery from the injury. This review attempts to critically analyze the available data to support the above hypothesis.
A Cancer Specific Cell-Penetrating Peptide, BR2, for the Efficient Delivery of an scFv into Cancer Cells (2013)

Cell-penetrating peptides (CPPs) have proven very effective as intracellular delivery vehicles for various therapeutics. However, there are some concerns about non-specific penetration and cytotoxicity of CPPs for effective cancer treatments. Herein, based on the cell-penetrating motif of an anticancer peptide, buforin IIb, we designed several CPP derivatives with cancer cell specificity. Among the derivatives, a 17-amino acid peptide (BR2) was found to have cancer-specificity without toxicity to normal cells. After specifically targeting cancer cells through interaction with gangliosides, BR2 entered cells via lipid-mediated macropinocytosis. Moreover, BR2 showed higher membrane translocation efficiency than the well-known CPP Tat (49-57). The capability of BR2 as a cancer-specific drug carrier was demonstrated by fusion of BR2 to a single-chain variable fragment (scFv) directed toward a mutated K-ras (G12V). BR2-fused scFv induced a higher degree of apoptosis than Tat-fused scFv in K-ras mutated HCT116 cells. These results suggest that the novel cell-penetrating peptide BR2 has great potential as a useful drug delivery carrier with cancer cell specificity.
METABOLIC ENGINEERING WITH RECOMBINANT ADENOVIRUSES (1999)

Fuel homeostasis in mammals is accomplished by the interplay between tissues and organs with distinct metabolic roles. These regulatory mechanisms are disrupted in obesity and diabetes, leading to a renewed emphasis on discovery of molecular and pharmacologic methods for reversing metabolic disorders. In this chapter, we review the use of recombinant adenoviral vectors as tools for delivering metabolic regulatory genes to cells in culture and to tissues of intact animals. Included are studies on the use of these vectors for gaining insights into the biochemical mechanisms that regulate glucose-stimulated insulin secretion from pancreatic islet beta-cells. We also highlight their use for understanding the function of newly discovered genes that regulate glycogen metabolism in liver and other tissues, and for evaluating "candidate" genes such as glucose-6-phosphatase, which may contribute to development of metabolic dysfunction in pancreatic islets and liver. Finally, we discuss the use of adenoviral and related vectors for causing chronic increases in the levels of circulating hormones. These examples serve to highlight the power of viral gene transfer vectors as tools for understanding metabolic regulatory mechanisms.