gebhart/patrepeval huggingface dataset:
Stalking the wily hacker (1988)

An astronomer-turned-sleuth traces a German trespasser on our military networks, who slipped through operating system security holes and browsed through sensitive databases. Was it espionage?
Adaptive recovery techniques for real-time audio streams (2002)

There are a number of packet-loss recovery techniques proposed for streaming audio applications. However, there are few works that are able to exploit the tradeoff between the recovery quality and the computational complexity. We develop a recovery method, called DSPWR (Double Sided Pitch Waveform Replication) which is able to tolerate a much higher packet loss rate. In essence, DSPWR is composed of several procedures devised to improve the quality of the reconstructed speech. It is noted that a more sophisticated recovery scheme that can tolerate a higher degree of packet loss in general requires a larger computational cost. In view of this, we evaluate the quality of the reconstructed speech under different packet loss rates for various receiver-based recovery methods, and compare the computational complexity among these methods. Under the acceptable speech quality whose MOS (Mean Opinion Score) is above 3.5, we develop an adaptive mechanism that can select the recovery method with the minimal complexity in accordance with different packet loss rates encountered. To conduct real experiments in the networks, we implement these recovery methods and evaluate the performance of DSPWR devised and the adaptive recovery techniques empirically. As validated by our experimental results, the adaptive mechanism is able to strike a compromise between the computational overhead and the quality of the speech desired.
Molecular characterization of proprotein convertase subtilisin/kexin type 9-mediated degradation of the LDLR (2012)

Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a secreted protein that promotes degradation of cell surface LDL receptors (LDLRs) in selected cell types. Here we used genetic and pharmacological inhibitors to define the pathways involved in PCSK9-mediated LDLR degradation. Inactivating mutations in autosomal recessive hypercholesterolemia (ARH), an endocytic adaptor, blocked PCSK9-mediated LDLR degradation in lymphocytes but not in fibroblasts. Thus, ARH is not specifically required for PCSK9-mediated LDLR degradation. Knockdown of clathrin heavy chain with siRNAs prevented LDLR degradation. In contrast, prevention of ubiquitination of the LDLR cytoplasmic tail, inhibition of proteasomal activity, or disruption of proteins required for lysosomal targeting via macroautophagy (autophagy related 5 and 7) or the endosomal sorting complex required for trafficking (ESCRT) pathway (hepatocyte growth factor-regulated Tyr-kinase substrate and tumor suppressor gene 101) failed to block PCSK9-mediated LDLR degradation. These findings are consistent with a model in which the LDLR-PCSK9 complex is internalized via clathrin-mediated endocytosis and then routed to lysosomes via a mechanism that does not require ubiquitination and is distinct from the autophagy and proteosomal degradation pathways. Finally, the PCSK9-LDLR complex appears not to be transported by the canonical ESCRT pathway.
The RcsCDB Signaling System and Swarming Motility inSalmonella entericaSerovar Typhimurium: Dual Regulation of Flagellar and SPI-2 Virulence Genes (2007)

The Rcs phosphorelay is a multicomponent signaling system that positively regulates colanic acid synthesis and negatively regulates motility and virulence. We have exploited a spontaneously isolated mutant, IgaA(T191P), that is nearly maximally activated for the Rcs system to identify a vast set of genes that respond to the stimulation, and we report new regulatory properties of this signaling system in Salmonella enterica serovar Typhimurium. Microarray data show that the Rcs system normally functions as a positive regulator of SPI-2 and other genes important for the growth of Salmonella in macrophages, although when highly activated the system completely represses the SPI-1/SPI-2 virulence, flagellar, and fimbrial biogenesis pathways. The auxiliary protein RcsA, which works with RcsB to positively regulate colanic acid and other target genes, not only stimulates but also antagonizes the positive regulation of many genes in the igaA mutant. We show that RcsB represses motility through the RcsB box in the promoter region of the master operon flhDC and that RcsA is not required for this regulation. Curiously, RcsB selectively stimulates expression of the flagellar type 3 secretion genes fliPQR; an RcsAB box located downstream of fliR influences this regulation. We show that excess colanic acid impairs swimming and inhibits swarming motility, consistent with the inverse regulation of the two pathways by the Rcs system.
Differentiation of Human Embryonic Stem Cells to Neural Lineages in Adherent Culture by Blocking Bone Morphogenetic Protein Signaling (2005)

Human embryonic stem cells (hESCs) have extensive self-renewal capacity and are competent to differentiate into any cell type of the body. They are valuable not only for the study of early human development but also for regenerative medicine. However, how to direct differentiation of hESCs along a particular lineage pathway to a specific cell type remains a challenge. Although hESCs have been shown to differentiate in vitro into neural progenitors, the factors controlling their differentiation are poorly understood. In this study, we report the development of an in vitro adherent culture system to efficiently generate neural progenitors in which neither multicellular aggregates nor stromal cells are required. We show that inhibition of bone morphogenetic protein signaling by its antagonist noggin is sufficient to block extraembryonic cell fate, transiently sustain Oct4 gene expression, and result in robust production of neural progenitors. Our findings will provide a platform for studying the molecular mechanism controlling neural differentiation.
Galanin — a novel biologically active peptide from porcine intestine (1983)

The isolation of a novel biologically active peptide, designated galanin, is described. The peptide was discovered by the detection of its C-terminal amide structure in porcine intestinal extract using a chemical method. It was found that galanin consists of 29 amino acids and the complete amino acid sequence is: Gly-Trp-Thr-Leu-Asn-Ser-Ala-Gly-Tyr-Leu-Leu-Gly-Pro-His-Ala-Ile-Asp-Asn-His -Arg-Ser -Phe-His-Asp-Lys-Tyr-Gly-Leu-Ala-NH2. Galanin was found to contract smooth muscle preparations from the rat and to cause a mild and sustained hyperglycemia in dog.
Replacement of glycoprotein B gene in the herpes simplex virus type 1 strain ANGpath DNA by that originating from nonpathogenic strain KOS reduces the pathogenicity of recombinant virus. (1994)

Herpes simplex virus type-1 (HSV-1) strain ANGpath and its recombinants, in which the 8.1 kbp BamHI G restriction fragment (0.345-0.399) containing the glycoprotein B (gBpath) gene (UL27) or its subfragments-coding either for cytoplasmic or surface domains of gB-had been replaced with the corresponding fragments from nonpathogenic KOS virus DNA (gBKOS), were tested for their pathogenicity for DBA/2 mice and rabbits. The recombinant ANGpath/B6KOS prepared by transferring the 2.7 kbp SstI-SstI subfragment (0.351-0.368) of the BamHI GKOS fragment still had the original sequence of ANGpath DNA coding for the syn3 marker in the cytoplasmic domain of gB and was pathogenic for mice as well as for rabbits. Virological and immunohistological studies in DBA/2 mice infected with the latter pathogenic recombinant and with ANGpath showed the presence of infectious virus and viral antigen at inoculation site (epidermis, subcutaneous connective tissue and striated muscle in the area of right lip), in homolateral trigeminal nerve and ganglion, brain stem, midbrain, thalamic and hypothalamic nuclei. In contrast, nonpathogenic recombinants ANGpath/syn+B6KOS (prepared by transferring the whole BamHI GKOS fragment) and ANGpath/syn+KOS (prepared by transferring the 0.8 kbp BamHI-SstI subfragment of the BamHI GKOS fragment) showed limited haematogenous and neural spread, but no evidence of replication in CNS; thus, their behaviour resembled that of the wild type strain KOS. The recombinant ANGpath/syn+KOS, which was not pathogenic for mice, still remained pathogenic for rabbits, a phenomenon indicating the presence of an additional locus in the gB molecule participating on virulence. Sequencing the 1478 bp SstI-SstI subfragment of the BamHI G(path) fragment (nt 53,348-54,826 of UL segment) showed the presence of at least 3 mutations as compared to the KOS sequence, from which the change of cytosine to thymine at nt 54,251 altered the codon for arginine to that for histidine (amino acid 515) in the gB polypeptide chain.
The New Neurobiology of Autism (2007)

This review covers a fraction of the new research developments in autism but establishes the basic elements of the new neurobiologic understanding of autism. Autism is a polygenetic developmental neurobiologic disorder with multiorgan system involvement, though it predominantly involves central nervous system dysfunction. The evidence supports autism as a disorder of the association cortex, both its neurons and their projections. In particular, it is a disorder of connectivity, which appears, from current evidence, to primarily involve intrahemispheric connectivity. The focus of connectivity studies thus far has been on white matter, but alterations in functional magnetic resonance imaging activation suggest that intracortical connectivity is also likely to be disturbed. Furthermore, the disorder has a broad impact on cognitive and neurologic functioning. Deficits in high-functioning individuals occur in processing that places high demands on integration of information and coordination of multiple neural systems. Intact or enhanced abilities share a dependence on low information-processing demands and local neural connections. This multidomain model with shared characteristics predicts an underlying pathophysiologic mechanism that impacts the brain broadly, according to a common neurobiologic principle. The multiorgan system involvement and diversity of central nervous system findings suggest an epigenetic mechanism.
Neuronal Apoptosis: Current Understanding of Molecular Mechanisms and Potential Role in Ischemic Brain Injury (1995)

Apoptosis is a rediscovered mechanism of cell death crucial in normal development. Recent exploration of the genetic mechanisms of apoptosis has broadened our insight into the regulation of cell death in development as well as disease states. We present an overview on current understanding of the genetic molecular events in apoptosis in all, or most cell types, with emphasis on events observed in a well-characterized model of neuronal death in vitro. The second part of this article reviews recent studies in in vivo stroke models on the mechanism of cell death relevant to apoptosis after cerebral ischemia. Further delineation of the mechanisms of cell death, especially those that trigger apoptosis, is likely to redirect our approaches in the development of new therapeutic interventions for ischemic stroke.
Adenovirus-mediated transfer of a gene encoding human apolipoprotein A-I into normal mice increases circulating high-density lipoprotein cholesterol. (1994)

We conclude that adenovirus-mediated transfer of a gene encoding apo A-I produces transient elevations of circulating HDL cholesterol of a magnitude correlated with important physiological effects. These observations suggest the potential for gene-based therapeutic strategies to reduce cardiovascular risk.
Evidence- and Consensus-Based Practice Guidelines for the Diagnosis of Irritable Bowel Syndrome (2001)

The dearth of available evidence highlights the need for more rigorous scientific validation to identify the most accurate methods of diagnosing IBS. Until such time, the diagnostic algorithm presented herein could inform decision making for a range of providers caring for primary care patients with abdominal discomfort or pain and altered bowel function suggestive of IBS.
Optical Constants of the Noble Metals (1972)

The optical constants $n$ and $k$ were obtained for the noble metals (copper, silver, and gold) from reflection and transmission measurements on vacuum-evaporated thin films at room temperature, in the spectral range 0.5-6.5 eV. The film-thickness range was 185-500 \AA{}. Three optical measurements were inverted to obtain the film thickness $d$ as well as $n$ and $k$. The estimated error in $d$ was \ifmmode\pm\else\textpm\fi{} 2 \AA{}, and that in $n$, $k$ was less than 0.02 over most of the spectral range. The results in the film-thickness range 250-500 \AA{} were independent of thickness, and were unchanged after vacuum annealing or aging in air. The free-electron optical effective masses and relaxation times derived from the results in the near infrared agree satisfactorily with previous values. The interband contribution to the imaginary part of the dielectric constant was obtained by subtracting the free-electron contribution. Some recent theoretical calculations are compared with the results for copper and gold. In addition, some other recent experiments are critically compared with our results.
MUC1-Induced Transcriptional Programs Associated with Tumorigenesis Predict Outcome in Breast and Lung Cancer (2009)

The Mucin 1 (MUC1) oncoprotein is aberrantly overexpressed in diverse human malignancies including breast and lung cancer. Although MUC1 modulates the activity of several transcription factors, there is no information regarding the effects of MUC1 on global gene expression patterns and the potential role of MUC1-induced genes in predicting outcome for cancer patients. We have developed an experimental model of MUC1-induced transformation that has identified the activation of gene families involved in oncogenesis, angiogenesis, and extracellular matrix remodeling. A set of experimentally derived MUC1-induced genes associated with tumorigenesis was applied to the analysis of breast and lung adenocarcinoma cancer databases. A 35-gene MUC1-induced tumorigenesis signature predicts significant decreases in both disease-free and overall survival in patients with breast (n=295) and lung (n=442) cancers. The data show that the MUC1 oncoprotein contributes to the regulation of genes that are highly predictive of clinical outcome in breast and lung cancer patients.
Role of Brain Inflammation in Epileptogenesis (2008)

Inflammation is known to participate in the mediation of a growing number of acute and chronic neurological disorders. Even so, the involvement of inflammation in the pathogenesis of epilepsy and seizure-induced brain damage has only recently been appreciated. Inflammatory processes, including activation of microglia and astrocytes and production of proinflammatory cytokines and related molecules, have been described in human epilepsy patients as well as in experimental models of epilepsy. For many decades, a functional role for brain inflammation has been implied by the effective use of anti-inflammatory treatments, such as steroids, in treating intractable pediatric epilepsy of diverse causes. Conversely, common pediatric infectious or autoimmune diseases are often accompanied by seizures during the course of illness. In addition, genetic susceptibility to inflammation correlated with an increased risk of epilepsy. Mounting evidence thus supports the hypothesis that inflammation may contribute to epileptogenesis and cause neuronal injury in epilepsy. We provide an overview of the current knowledge that implicates brain inflammation as a common predisposing factor in epilepsy, particularly childhood epilepsy.
Contact guidance of CNS neurites on grooved quartz: influence of groove dimensions, neuronal age and cell type (1997)

We used an in vitro system that eliminates competing guidance cues found in embryos to determine whether substratum topography alone provides important neurite guidance information. Dissociated embryonic Xenopus spinal cord neurons and rat hippocampal neurons were grown on quartz etched with a series of parallel grooves. Xenopus neurites grew parallel to grooves as shallow as 14 nm and as narrow as 1 microm. Hippocampal neurites grew parallel to deep, wide grooves but perpendicular to shallow, narrow ones. Grooved substrata determined the sites at which neurites emerged from somas: Xenopus neurites sprouted from regions parallel to grooves but presumptive axons on rat hippocampal neurons emerged perpendicular to grooves and presumptive dendrites emerged parallel to them. Neurites grew faster in the favored direction of orientation and turned through large angles to align on grooves. The frequency of perpendicular alignment of hippocampal neurites depended on the age of the embryos from which neurons were isolated, suggesting that contact guidance is regulated in development. Collectively, the data indicate that substratum topography is a potent morphogenetic factor for developing CNS neurons and suggest that in addition to a role in pathfinding the geometry of the embryo assists in establishing neuronal polarity. In the companion paper (A. M. Rajnicek and C. D. McCaig (1997) J. Cell Sci. 110, 2915-2924) we explore the cellular mechanism for contact guidance of growth cones.
Role of Nitric Oxide in Skin Flap Delay (2004)

Surgical delay of skin flaps before transfer is known to improve flap viability. This study attempts to elucidate the mechanism of vasodilation by exploring the effects of nitric oxide on the microcirculation of delayed skin flaps. Using a skin flap model in 22 CD-1 white mice, the diameter of two nonterminal choke arteries was measured using in vivo videomicroscopy. Vessel flow was also measured using an optical Doppler velocimeter. Similar measurements were recorded in several animals on the same vessels in which subcutaneous dissection without elevation was performed. Average vessel diameter ranged from 21.77 to 25.55 microm before skin flap delay. Average flow ranged from 1.72 to 2.44 nl/sec before delay. Next, each animal received an intraperitoneal dose of nitro-aminomethyl-1-arginine (L-NAME), a nitric oxide synthase inhibitor delivered by means of osmotic pump at a level of 0 (n = 13 arteries), 20 (n = 10), 50 (n = 8), or 100 mg/kg/day (n = 7). Flaps were re-elevated 72 hours later and the aforementioned measurements were repeated. Vessel diameter increased to 44.92 microm in the control (0 mg/kg L-NAME) animals. Flow increased to 7.66 nl/sec in the control animals. Vessel dilation and flow did not change significantly in the nonoperative vessels. As the dose of L-NAME increased in the treated animals, there was a significant decrease in vasodilation and flow (p = 0.015 and p = 0.03, respectively). The authors' results demonstrate that nitric oxide is an important element of vasodilation and contributor to the phenomenon of skin flap delay.
Thermodynamic Stability of the Two Isoforms of Bovine Seminal Ribonuclease (2000)

Bovine seminal ribonuclease (BS-RNase) is a dimeric protein with two identical subunits linked by two disulfide bridges, each subunit showing 80% of sequence identity with pancreatic RNase A. BS-RNase exists in two different quaternary conformations in solution: the MxM form, in which each subunit exchanges its alpha-helical N-terminal segment with its partner, and the M=M form with no exchange. By differential scanning microcalorimetry (DSC), the denaturation of the two dimeric forms of BS-RNase was found to be more complex than a simple two-state process. Monomeric derivatives of the dimeric protein follow instead a simple two-state mechanism, but are distinctly less stable than RNase A. The three-state N if I if D denaturation process of the two quaternary isoforms was interpreted by identifying in the dimers a central highly structured core, enclosing the covalently bonded subunit interface, which unfolds only after the periphery (mainly the N-terminal peptide) unfolds. Circular dichroism spectra of the two forms in the far-ultraviolet region show large differences between the secondary structure of the isoforms and that of the native BS-RNase mixture at equilibrium. This has been attributed to the presence in the equilibrium mixture of intermediate forms with displaced and disordered N-terminal alpha-helical segments.
Hepatoprotective efficacy of certain flavonoids against microcystin induced toxicity in mice (2007)

Toxic cyanobacteria (blue-green algae) water blooms have become a serious problem in several industrialized areas of the world. Microcystin-LR (MC-LR) is a cyanobacterial heptapeptide that represents acute and chronic hazards to animal and human health. Identification of suitable chemprotectants against microcystin is essential considering human health hazards. In the present study, we have evaluated the protective efficacy of three flavanoids namely quercetin (200 mg/kg), silybin (400 mg/kg), and morin (400 mg/kg)] pretreatment against microcystin toxicity (0.75 LD(50), 57.5 microg/kg) in mice. Various biochemical variables were measured to study the recovery profile of protected animals at 1- and 3-days post-toxin treatment. The serum alanine amino transferase (ALT) shows 17-fold increase in MC-LR treated animals compared with control group at 1 day. The silybin and quercetin group showed a decrease in level of ALT compared with MC-LR group but still higher than control group. No significant protection was observed with aspartate aminotransaminase (AST) and lactate dehydrogenase (LDH) levels in flavanoid-treated groups at 1-day post-treatment. But at 3 days, the serum levels of AST and ALT were normalized to control values, but the serum LDH levels were still significantly higher than the control group. No significant changes were observed in glutathione peroxidase and reduced glutathione levels at both 1- and 3-day postexposure. The catalase activity shows a significant decrease in quercetin-treated animals at 3-day postexposure. The protein phosphatase was significantly inhibited in MC-LR group compared to control. The silybin pretreated group showed recovery after 1 day. At 3 days, the PPAse activity was reversed to control values in all the flavanoid-treated groups. Immunoblotting analysis showed microcystin-PPAse adduct in liver tissues of toxin-treated as well as flavanoid-treated mice even after 3 days. The results of this study show that flavanoids, quercetin, silybin, and morin could reverse the hepatotoxic effects of MC-LR in vivo.
Design and Optimization of Wideband Hat-Fed Reflector Antenna with Radome for Satellite Earth Station (2012)

This thesis presents the development of a hat-fed refector antenna with radome to be used as satellite earth station. The antenna with self supported feed is relatively compact, circular symmetric and with low cross polarization. To achieve optimum performance over the satellite Ku-band,covering 10.75-14.50 GHz, a genetic algorithm optimization scheme was implemented and the simulations were done with the electromagnetic solver QuickWave-V2D based on the FDTD method. Optimizations were done towards minimized reflection coefficient, maximized feed efficiency, and finally taking into account the stringent sidelobe requirements defined by the ETSI. Radomes for enclosing the satellite earth station have been analyzed and a low loss homogenous radome was manufactured and successfully measured with the hat-fed reflector antenna. The satellite earth station can after certification be operational.