gebhart/patrepeval huggingface dataset:
Cochlear synaptopathy in acquired sensorineural hearing loss: Manifestations and mechanisms (2017)

Common causes of hearing loss in humans - exposure to loud noise or ototoxic drugs and aging - often damage sensory hair cells, reflected as elevated thresholds on the clinical audiogram. Recent studies in animal models suggest, however, that well before this overt hearing loss can be seen, a more insidious, but likely more common, process is taking place that permanently interrupts synaptic communication between sensory inner hair cells and subsets of cochlear nerve fibers. The silencing of affected neurons alters auditory information processing, whether accompanied by threshold elevations or not, and is a likely contributor to a variety of perceptual abnormalities, including speech-in-noise difficulties, tinnitus and hyperacusis. Work described here will review structural and functional manifestations of this cochlear synaptopathy and will consider possible mechanisms underlying its appearance and progression in ears with and without traditional 'hearing loss' arising from several common causes in humans.
Zebrafish model of tuberous sclerosis complex reveals cell-autonomous and non-cell-autonomous functions of mutant tuberin (2010)

Tuberous sclerosis complex (TSC) is an autosomal dominant disease caused by mutations in either the TSC1 (encodes hamartin) or TSC2 (encodes tuberin) genes. Patients with TSC have hamartomas in various organs throughout the whole body, most notably in the brain, skin, eye, heart, kidney and lung. To study the development of hamartomas, we generated a zebrafish model of TSC featuring a nonsense mutation (vu242) in the tsc2 gene. This tsc2(vu242) allele encodes a truncated Tuberin protein lacking the GAP domain, which is required for inhibition of Rheb and of the TOR kinase within TORC1. We show that tsc2(vu242) is a recessive larval-lethal mutation that causes increased cell size in the brain and liver. Greatly elevated TORC1 signaling is observed in tsc2(vu242/vu242) homozygous zebrafish, and is moderately increased in tsc2(vu242/+) heterozygotes. Forebrain neurons are poorly organized in tsc2(vu242/vu242) homozygous mutants, which have extensive gray and white matter disorganization and ectopically positioned cells. Genetic mosaic analyses demonstrate that tsc2 limits TORC1 signaling in a cell-autonomous manner. However, in chimeric animals, tsc2(vu242/vu242) mutant cells also mislocalize wild-type host cells in the forebrain in a non-cell-autonomous manner. These results demonstrate a highly conserved role of tsc2 in zebrafish and establish a new animal model for studies of TSC. The finding of a non-cell-autonomous function of mutant cells might help explain the formation of brain hamartomas and cortical malformations in human TSC.
Synthesis of messenger RNAs for transforming growth factors alpha and beta and the epidermal growth factor receptor by human tumors. (1987)

Human tumors and tumor cell lines were analyzed for the presence of mRNA coding for transforming growth factors alpha and beta (TGF-alpha and -beta) and the epidermal growth factor receptor. TGF-alpha mRNA was not detectable in hematopoietic tumor cell lines but was found in a variety of solid tumor cells, particularly carcinomas. Many of the tumors that contained TGF-alpha mRNA also expressed high levels of epidermal growth factor receptor mRNA. The concentration of TGF-alpha in the media of several tumor cell lines did not necessarily correlate with TGF-alpha mRNA levels, as a substantial fraction of TGF-alpha can remain cell associated. The levels of TGF-beta mRNA in tumor cell lines and tumor specimens were variable, but higher in tumors than in the adjacent normal tissues.
The clinical and immunological significance of GAD-specific autoantibody and T-cell responses in type 1 diabetes (2013)

Antigen-specific interventions are desirable approaches in Type 1 Diabetes (T1D) as they can alter islet-specific autoimmunity without systemic side effects. Glutamic acid decarboxylase of 65 kDa (GAD65) is a major autoantigen in type 1 diabetes (T1D) and GAD-specific autoimmunity is a common feature of T1D in humans but also in mouse models of the disease. In humans, administration of the GAD65 protein in an alum formulation has been shown to reduce C-peptide decline in recently diagnosed patients, however, these observations were not confirmed in subsequent phase II/III clinical trials. As GAD-based immune interventions in different formulations have successfully been employed to prevent the establishment of T1D in mouse models of T1D, we sought to analyze the efficacy of GAD-alum treatment and the effects on the GAD-specific immune response in two different mouse models of T1D. Consistent with the latest clinical trials, mice treated with GAD-alum were not protected from diabetes, although GAD-alum induced a GAD-specific Th2-deviated immune response in transgenic rat insulin promoter-glycoprotein (RIP-GP) mice. These observations underline the importance of a thorough, preclinical evaluation of potential drugs before the initiation of clinical trials.
Targeting cellular pathways in glioblastoma multiforme (2017)

Glioblastoma multiforme (GBM) is a debilitating disease that is associated with poor prognosis, short median patient survival and a very limited response to therapies. GBM has a very complex pathogenesis that involves mutations and alterations of several key cellular pathways that are involved in cell proliferation, survival, migration and angiogenesis. Therefore, efforts that are directed toward better understanding of GBM pathogenesis are essential to the development of efficient therapies that provide hope and extent patient survival. In this review, we outline the alterations commonly associated with GBM pathogenesis and summarize therapeutic strategies that are aimed at targeting aberrant cellular pathways in GBM.
Enabling email confidentiality through the use of opportunistic encryption (2003)

Software for encrypting email messages has been widely available for more than 15 years, but the email-using public has failed to adopt secure messaging. This failure can be explained through a combination of technical, community, and usability factors. This paper proposes a new approach to email security that employs opportunistic encryption and a security proxy to facilitate the opportunistic exchange of keys and encryption of electronic mail. While it appears that this approach offers less security than established systems that employ certificates, the security is in fact equivalent to today's systems based on PGP, PGP/MIME and S/MIME.
Ultrathin PtSi layers patterned by scanned probe lithography (2001)

A process for patterning ultrathin layers of PtSi with high spatial resolution is presented. In this process, scanned probe anodic oxidation is used to pattern a surface oxide layer on a H-passivated Si surface. This oxide pattern prevents the reaction of a deposited Pt film with the underlying Si in the formation of PtSi. The unreacted Pt on the oxide is removed by a selective etch before any annealing. This process greatly reduces lateral diffusion and produces a 2-nm-thick PtSi layer with good electrical properties that maintains the fidelity of the patterned oxide mask. Such nanostructured PtSi films are a good candidate for use in constructing lateral Si-based quantum devices.
Isolation of cDNA clones encoding small nuclear ribonucleoparticle-associated proteins with different tissue specificities. (1989)

Alternative RNA processing, such as brain- and heart-specific generation of calcitonin gene-related peptide (CGRP) transcripts from the calcitonin/CGRP gene, is thought to be mediated by tissue-specific factors. We have cloned three related but distinct cDNAs encoding small nuclear ribonucleoparticle (snRNP)-associated proteins from rat PC12 cells. One clone (Sm51) has the capacity to encode a 240-amino acid protein and its RNA transcript is expressed selectively in rat brain and pituitary but not in heart. A related cDNA, designated Sm11, predicts a protein highly homologous to but distinct from Sm51. The Sm11 transcript is very abundant in heart but barely detectable in brain. Sm51 and Sm11 appear to encode the brain and heart forms of a 28-kDa snRNP-associated protein detected by anti-Sm serum, respectively. A third clone (Sm21) encodes a protein with an altered N terminus relative to Sm51. The Sm51 transcript is expressed in the pituitary, and analysis of the pituitaries of transgenic mice harboring a mouse metallothionein I promoter-calcitonin/CGRP fusion gene reveals the splice choice to be predominantly CGRP. In situ hybridization indicates Sm51 RNA is expressed throughout neuronal structures within rat brain, including the inferior colliculus, which does not possess the machinery to generate CGRP. Although Sm51 alone cannot be sufficient to account for CGRP splicing choice in all tissues, the demonstration of discrete tissue-specific expression patterns of closely related snRNP-associated proteins is consistent with their potential role in differential RNA processing events.
Modulation of adjuvant arthritis by endogenous nitric oxide (1993)

1. The role of endogenous nitric oxide (NO) in adjuvant arthritis in Lewis rats has been studied by use of L-arginine, the amino acid from which NO is synthesized, and NG-nitro-L-arginine methyl ester (L-NAME), an inhibitor of NO synthase. Prolonged modulation (35 days) of the L-arginine: NO pathway in rats was achieved by dissolving test compounds in the drinking water (L-arginine: 3, 10 and 30 mg ml-1; L-NAME: 0.1, 1 and 10 mg ml-1). 2. Arthritis was exacerbated by L-arginine and suppressed by L-NAME in a dose-related fashion. Combined treatment with L-NAME (1 mg ml-1) and L-arginine (30 mg ml-1) did not modify the arthritis. 3. Reduced weight gain, which is a feature of adjuvant arthritis, was modified by these compounds so that L-arginine reduced weight gain whereas L-NAME increased weight gain compared with that in control animals. 4. D-Arginine (30 mg ml-1), NG-nitro-D-arginine methyl ester (D-NAME: 1 mg ml-1) and L-lysine (30 mg ml-1), an amino acid not involved in the generation of NO, were without effect on either arthritis or body weight gain. 5. Antigen-stimulated proliferation of T-lymphocytes as well as generation of nitrite (NO2-) and release of acid phosphatase from macrophages were all enhanced in L-arginine-treated arthritic rats and reduced in L-NAME-treated animals. 6. These results suggest that endogenous NO modulates adjuvant arthritis, possibly by interfering with the activation of T-lymphocytes and/or macrophages.
The proteasome of malaria parasites: A multi-stage drug target for chemotherapeutic intervention? (2012)

The ubiquitin/proteasome system serves as a regulated protein degradation pathway in eukaryotes, and is involved in many cellular processes featuring high protein turnover rates, such as cell cycle control, stress response and signal transduction. In malaria parasites, protein quality control is potentially important because of the high replication rate and the rapid transformations of the parasite during life cycle progression. The proteasome is the core of the degradation pathway, and is a major proteolytic complex responsible for the degradation and recycling of non-functional ubiquitinated proteins. Annotation of the genome for Plasmodium falciparum, the causative agent of malaria tropica, revealed proteins with similarity to human 26S proteasome subunits. In addition, a bacterial ClpQ/hslV threonine peptidase-like protein was identified. In recent years several independent studies indicated an essential function of the parasite proteasome for the liver, blood and transmission stages. In this review, we compile evidence for protein recycling in Plasmodium parasites and discuss the role of the 26S proteasome as a prospective multi-stage target for antimalarial drug discovery programs.
Enhancement of Antimicrobial Activity of Neuropeptide Y by N-Terminal Truncation (1998)

The activity of neuropeptide Y (NPY) against Candida albicans, which was revealed to be fungicidal, was enhanced significantly by the truncation of amino acid residues at the N terminus. The most active peptides (MICs, approximately 1 microM) were about 10-fold more potent than the intact NPY (MIC, approximately 10 microM). The enhancement was weakened by the replacement of the N terminus by negatively charged residues and/or acylation of the alpha-amino group. These results suggest that only the alpha-helical region of NPY is necessary for the antimicrobial activity and that the net charge of the peptide is important for the activity.
Membrane properties and response to opioids of identified dopamine neurons in the guinea pig hypothalamus (1990)

The electrophysiological properties and opioid responsiveness of the dopamine-containing neurons in the arcuate nucleus of the guinea pig hypothalamus were examined. Dopamine-containing neurons, identified immunocytochemically by the presence of tyrosine hydroxylase, had a mean length-to-width profile of 14.9 +/- 4.4 x 11.5 +/- 3.1 microns (N = 14). The Na+ action potential of these neurons was of short duration, and induction of repetitive firing (20-50 Hz) caused an afterhyperpolarization of 6-9 mV in amplitude, with a decay half-time of approximately 1.5 sec. Dopamine-containing cells exhibited a low threshold spike, which induced 1-4 Na+ action potentials. This potential had a threshold close to -65 mV, could not be induced without prior hyperpolarization and was not sensitive to TTX. Dopamine-containing neurons also exhibited a time- and voltage-dependent inward current at potentials negative to -70 mV, and Cs+ blocked this conductance. The mu-opioid agonist Tyr-D-Ala-Gly-mePhe-Gly-ol hyperpolarized (14 +/- 3 mV) dopamine neurons via induction of an outward current (93 +/- 44 pA near the resting membrane potential) which had a reversal potential similar to that expected for a selective potassium conductance. TTX (1 microM) did not block the opioid effects. These results show that dopamine neurons of the arcuate nucleus differ in their intrinsic conductances and their responsiveness to opioids from other CNS dopaminergic neurons. Furthermore, opioid activation of a potassium conductance resulted in a direct hyperpolarization of dopamine neurons of the arcuate nucleus, and we suggest that this mechanism may underlie the effects of opioids on dopamine-mediated prolactin release.
Achaete-scute homologue-1 (ASH1) stimulates migration of lung cancer cells through Cdk5/p35 pathway (2012)

Our previous data suggested that the human basic helix-loop-helix transcription factor achaete-scute homologue-1 (hASH1) may stimulate both proliferation and migration in the lung. In the CNS, cyclin-dependent kinase 5 (Cdk5) and its activator p35 are important for neuronal migration that is regulated by basic helix-loop-helix transcription factors. Cdk5/p35 may also play a role in carcinogenesis. In this study, we found that the neuronal activator p35 was commonly expressed in primary human lung cancers. Cdk5 and p35 were also expressed by several human lung cancer cell lines and coupled with migration and invasion. When the kinase activity was inhibited by the Cdk5 inhibitor roscovitine or dominant-negative (dn) Cdk5, the migration of lung cancer cells was reduced. In neuroendocrine cells expressing hASH1, such as a pulmonary carcinoid cell line, knocking down the gene expression by short hairpin RNA reduced the levels of Cdk5/p35, nuclear p35 protein, and migration. Furthermore, expression of hASH1 in lung adenocarcinoma cells normally lacking hASH1 increased p35/Cdk5 activity and enhanced cellular migration. We were also able to show that p35 was a direct target for hASH1. In conclusion, induction of Cdk5 activity is a novel mechanism through which hASH1 may regulate migration in lung carcinogenesis.
Use of a heat-stable microtubule-associated protein class-specific antibody to investigate the mechanism of microtubule binding. (1991)

Members of the heat-stable family of microtubule-associated proteins (MAPs), MAP 2, tau, and MAP 4, contain three or four tandem imperfect repeated sequences close to their carboxyl termini. These sequences lie within the microtubule-binding domains of the MAPs; they have been proposed to be responsible for microtubule binding and the ability of these MAPs to lower the critical concentration for microtubule assembly. Their spacing may reflect that of the regularly arrayed tubulin subunits on the microtubule surface. We here characterize the 32- and 34-kDa chymotryptic microtubule-binding fragments of MAP 2 identified in earlier work. We identify the primary chymotryptic cleavage site in high molecular weight MAP 2 as between Phe1525 and Lys1526, within 13 amino acids of the known MAP 2 splice junction. We have raised a monoclonal antibody to the 32- and 34-kDa fragments and find that it reacts with all members of the heat-stable MAPs class. To determine where it reacts, we sequenced immunoreactive subfragments of the 32- and 34-kDa fragments, selected several cDNA clones with the antibody, and tested for antibody reactivity against a series of synthetic MAP 2 and tau peptides. We identify the epitope sequence as HHVPGGG (His-His-Val-Pro-Gly-Gly-Gly). The antibody also recognized several other MAP 2 and tau repeats. Despite reacting with this highly conserved element, we find that the antibody does not block microtubule binding, but binds to the MAPs and co-sediments with microtubules. These results suggest that there are other regions besides the repeated elements which are essential for microtubule binding.
Method for multiplex cellular detection of mRNAs using quantum dot fluorescent in situ hybridization (2005)

The photostability and narrow emission spectra of non-organic quantum dot fluorophores (QDs) make them desirable candidates for fluorescent in situ hybridization (FISH) to study the expression of specific mRNA transcripts. We developed a novel method for direct QD labeling of modified oligonucleotide probes through streptavidin and biotin interactions, as well as protocols for their use in multiple-label FISH. We validated this technique in mouse brainstem sections. The subcellular localization of the vesicular monoamine transporter (Vmat2) mRNA corresponds when using probes labeled with two different QDs in the same hybridization. We developed protocols for combined direct QD FISH and QD immunohistochemical labeling within the same neurons as well as for simultaneous study of the subcellular distribution of multiple mRNA targets. We demonstrated increased sensitivity of FISH using QDs in comparison with organic fluorophores. These techniques gave excellent histological results both for multiplex FISH and combined FISH and immunohistochemistry. This approach can facilitate the ultrasensitive simultaneous study of multiple mRNA and protein markers in tissue culture and histological section.
Research Ethics Education for Community-Engaged Research: A Review and Research Agenda (2012)

Community engagement is increasingly becoming an integral part of research. "Community-engaged research" (CEnR) introduces new stakeholders as well as unique challenges to the protection of participants and the integrity of the research process. We--a group of representatives of CTSA-funded institutions and others who share expertise in research ethics and CEnR--have identified gaps in the literature regarding (1) ethical issues unique to CEnR; (2) the particular instructional needs of academic investigators, community research partners, and IRB members; and (3) best practices for teaching research ethics. This paper presents what we know, as well as what we still need to learn, in order to develop quality research ethics educational materials tailored to the full range of stakeholder groups in CEnR.
La revisión estratégica de la defensa impulsa una nueva logística para las Fuerzas Armadas (2002)

El siglo XXI comienza con un nuevo impulso a la politica de defensa que, desde las metas alcanzadas en la pasada legislatura, vertebra su plan de accion en torno a cinco grandes objetivos establecidos por el presidente del Gobierno en la Directiva de Defensa Nacional (DDN) 1/2000: intensificar la proyeccion exterior de las Fuerzas Armadas; culminar el proceso de profesionalizacion; modernizar su armamento, mate­ rial y equipamiento; racionalizar la organizacion de la Defensa y fomentar la cultura de defensa.
Gleevec inhibits β-amyloid production but not Notch cleavage (2003)

Amyloid-beta (Abeta) peptides, consisting mainly of 40 and 42 aa (Abeta40 and Abeta42, respectively), are metabolites of the amyloid precursor protein and are believed to be major pathological determinants of Alzheimer's disease. The proteolytic cleavages that form the Abeta N and C termini are catalyzed by beta-secretase and gamma-secretase, respectively. Here we demonstrate that gamma-secretase generation of Abeta in an N2a cell-free system is ATP dependent. In addition, the Abl kinase inhibitor imatinib mesylate (Gleevec, or STI571), which targets the ATP-binding site of Abl and several other tyrosine kinases, potently reduces Abeta production in the N2a cell-free system and in intact N2a cells. Both STI571 and a related compound, inhibitor 2, also reduce Abeta production in rat primary neuronal cultures and in vivo in guinea pig brain. STI571 does not inhibit the gamma-secretase-catalyzed S3 cleavage of Notch-1. Furthermore, production of Abeta and its inhibition by STI571 were demonstrated to occur to similar extents in both Abl-/- and WT mouse fibroblasts, indicating that the effect of STI571 on Abeta production does not involve Abl kinase. The efficacy of STI571 in reducing Abeta without affecting Notch-1 cleavage may prove useful as a basis for developing novel therapies for Alzheimer's disease.
Digital Communication Over Fading Channels (2002)

noncoherent communication systems, as well as a large variety of fading channel models typical of communication links often found in the real world, including single- and multichannel reception with a large variety of types. The book gives many numerical illustrations expressed in large collections of system performance curves, allowing the researchers or system designers to perform trade-off studies of the average bit error rate and symbol error rate. This book is a very good reference book for researchers and communication engineers and may also be a source for supplementary material of a graduate course on communication or signal processing. Nowadays, many new books attach a CD-ROM for more supplementary material. With the many numerical examples in this book, it appears that an attached CD-ROM would be ideal for this book. It would be even better to present the computer program in order to be interactive so that the readers can plug in their arbitrary parameters for the performance evaluation. —H. Hsu