gebhart/patrepeval huggingface dataset:
Activation of PI3K signaling prevents aminoglycoside-induced hair cell death in the murine cochlea (2016)

Loss of sensory hair cells of the inner ear due to aminoglycoside exposure is a major cause of hearing loss. Using an immortalized multipotent otic progenitor (iMOP) cell line, specific signaling pathways that promote otic cell survival were identified. Of the signaling pathways identified, the PI3K pathway emerged as a strong candidate for promoting hair cell survival. In aging animals, components for active PI3K signaling are present but decrease in hair cells. In this study, we determined whether activated PI3K signaling in hair cells promotes survival. To activate PI3K signaling in hair cells, we used a small molecule inhibitor of PTEN or genetically ablated PTEN using a conditional knockout animal. Hair cell survival was challenged by addition of gentamicin to cochlear cultures. Hair cells with activated PI3K signaling were more resistant to aminoglycoside-induced hair cell death. These results indicate that increased PI3K signaling in hair cells promote survival and the PI3K signaling pathway is a target for preventing aminoglycoside-induced hearing loss.
Physiological Significance of Resistin and Resistin-Like Molecules in the Inflammatory Process and Insulin Resistance (2006)

Resistin was initially identified as a protein, secreted by adipocytes, which inhibits insulin action and adipose differentiation. The three proteins homologous to resistin were termed resistin-like molecules (RELM) alpha, beta and gamma. Resistin and RELMalpha are abundantly expressed in adipose, but RELMbeta and RELMgamma are secreted mainly from the gut. Recently, resistin and RELMs were reported to be associated with inflammation. For example, RELMalpha, viewed as an inflammation-related protein, was originally identified in broncho-alveolar lavage fluid obtained from animals with experimentally induced pulmonary inflammation. RELMbeta is also related to bacterial colonization, but RELMbeta injection or hepatic overexpression of RELMbeta induced insulin resistance. RELMgamma isolated from rat nasal respiratory epithelium was found to be altered by cigarette smoke. Thus, resistin and RELMs could be useful for assessing the inflammatory condition in vivo. On the other hand, whether the serum resistin or RELM concentration is strongly related to insulin resistance remains unclear. However, taking recent studies showing a close relationship between inflammation and insulin resistance in diabetes into consideration, these proteins may have interactive roles linking inflammation and insulin resistance, both of which major involvement in the progression of atherosclerosis. If so, the serum resistin or RELM concentration may be a good marker of atherosclerotic risk. In addition, these proteins or unidentified receptors are potential therapeutic targets for the treatment of diabetes and prevention of atherosclerosis. These possibilities merit further study.
Feedback-Based Path Failure Detection and Buffer Blocking Protection for MPTCP (2016)

A multipath TCP (MPTCP) is a promising protocol that has been standardized by the Internet Engineering Task Force to support multipath operations in the transport layer. However, although the MPTCP can provide multiple transmission paths and aggregate the bandwidth of multiple paths, it does not consistently achieve more throughput (goodput) nor a greater connection resilience. Currently, the MPTCP is vulnerable to path failure or underperforming subflows, which cause transmission interruption or throughput (goodput) degradation. Unfortunately, there is no exact rule for declaring a path failure or preventing the usage of underperforming subflows in the MPTCP. In this paper, we propose a novel path failure detection method referred to as feedback-based path failure (FPF) detection. In addition, we propose a new decision method called buffer blocking protection (BBP) to address the underperforming subflows for the MPTCP. Measurement results indicate that the FPF detection reduces transmission interruption time by the fast path failure decision, which can prevent duplicate transmission interruption events and unnecessary retransmissions. Furthermore, the FPF detection is sufficiently robust in terms of packet loss and the delay difference between paths. The results additionally show that the BBP method prevents goodput degradation due to underperforming subflows. Consequently, the MPTCP with the BBP method can at least achieve the throughput performance of a single Transmission Control Protocol (TCP), which uses the best path regardless of the delay difference between paths.
Cold survival in freeze‐intolerant insects (2004)

Antifreeze proteins (AFPs) designate a class of proteins that are able to bind to and inhibit the growth of macromolecular ice. These proteins have been characterized from a variety of organisms. Recently, the structures of AFPs from the spruce budworm (Choristoneura fumiferana) and the yellow mealworm (Tenebrio molitor) have been determined by NMR and X-ray crystallography. Despite nonhomologous sequences, both proteins were shown to consist of beta-helices. We review the structures and dynamics data of these two insect AFPs to bring insight into the structure-function relationship and explore their beta-helical architecture. For the spruce budworm protein, the fold is a left-handed beta-helix with 15 residues per coil. The Tenebrio molitor protein consists of a right-handed beta-helix with 12 residues per coil. Mutagenesis and structural studies show that the insect AFPs present a highly rigid array of threonine residues and bound water molecules that can effectively mimic the ice lattice. Comparisons of the newly determined ryegrass and carrot AFP sequences have led to models suggesting that they might also consist of beta-helices, and indicate that the beta-helix might be used as an AFP structural motif in nonfish organisms.
Digital audio coding for visual communications (1995)

Current and future visual communications for applications such as broadcasting videotelephony, video- and audiographic-conferencing, and interactive multimedia services assume a substantial audio component. Even text, graphics, fax, still images, email documents, etc. will gain from voice annotation and audio clips. A wide range of speech, wideband speech, and wideband audio coders is available for such applications. In the context of audiovisual communications, the quality of telephone-bandwidth speech is acceptable for some videotelephony and videoconferencing services. Higher bandwidths (wideband speech) may be necessary to improve the intelligibility and naturalness of speech. High quality audio coding including multichannel audio will be necessary in advanced digital TV and multimedia services. This paper explains basic approaches to speech, wideband speech, and audio bit rate compressions in audiovisual communications. These signal classes differ in bandwidth, dynamic range, and in listener expectation of offered quality. It will become obvious that the use of our knowledge of auditory perception helps minimizing perception of coding artifacts and leads to efficient low bit rate coding algorithms which can achieve substantially more compression than was thought possible only a few years ago. The paper concentrates on worldwide source coding standards beneficial for consumers, service providers, and manufacturers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Rapid screening of synthetic cathinones as trace residues and in authentic seizures using a portable mass spectrometer equipped with desorption electrospray ionization (2012)

Coupling DESI-MS with portable instrumentation allowed sensitive and selective examination of synthetic cathinones from various substrates, in complex mixtures, and directly from mock and authentic forensic evidence. This instrumental method has the potential to assess the evidentiary value of forensic samples at crime scenes, reducing backlogs and expediting criminal investigations.
Expression of stress protein gp96, a tumor rejection antigen, in human colorectal cancer (2000)

Preparations of stress protein gp96 from tumor cells are active as tumor vaccines by eliciting immune responses against mixtures of individual tumor peptide antigens which are complexed to gp96. Due to the individual antigenicity of tumors, a vaccine consisting of tumor-derived gp96 has to be prepared individually for each patient from autologous tumor tissue. So far, gp96 expression by human tumors has not been analyzed. Here, we report stable and mostly homogenous expression of gp96 by colorectal cancer, which was enhanced compared to surrounding tumor stroma in 70% to 80% of colorectal cancer specimens. Fewer non-metastatic than metastatic primary cancer specimens showed enhanced gp96 expression. Glucose deprivation increased gp96 protein and RNA expression in the human colon cancer cell line HT-29 in accordance with the role of gp96 as a glucose-regulated stress protein. Additionally, TNF-alpha, interferons and other cytokines induced an increase of gp96 RNA expression in HT-29 cells, suggesting that gp96 expression by colorectal cancer cells can be influenced by different methods of immunomodulation. The stable and homogenous expression of gp96 in 19 primary and metastatic colorectal cancer specimens and the up-regulation of gp96 in colon cancer cells by glucose deprivation point to an essential role of this stress protein in colorectal cancer, presumably by protecting against hostile conditions of the tumor micro-environment like glucose deprivation. In view of these results, loss of gp96 expression by colorectal cancer cells as an immune escape mechanism is unlikely.
Studies on a lysogenic Bacillus strain. I. A Bacteriophage specific for Bacillus anthracis (1951)

A bacteriophage is described which attacks almost exclusively strains of Bacillus anthracis , and attacks all the strains of this species which have been tested. As well as attacking typical strains of this species it attacks atypical variants. Strains of B. anthracis are not attacked by this phage when they are in a muciod state. A few strains of B. anthracis are only feebly attacked by this phage. Some experiments, conducted in an attempt to discover the reason for this, are described. The results are discussed and arguments in favour of regarding B. anthracis as a valid species are put forward.
Atrial Natriuretic Peptide Gene Delivery Reduces Stroke-Induced Mortality Rate in Dahl Salt-Sensitive Rats (1999)

Atrial natriuretic peptide (ANP) is a powerful hormone with hypotensive, natriuretic, diuretic, and many other beneficial effects. Direct infusion of ANP in therapeutics has limited success because of its short half-life in the circulation. Our previous studies have shown that ANP gene delivery attenuates hypertension, cardiac hypertrophy, and renal injury in Dahl salt-sensitive (Dahl-SS) rats. To investigate the potential therapeutic value of ANP gene delivery on salt-induced stroke and cerebrovascular disorders, an adenovirus harboring the human ANP gene (Ad.RSV-cANP) was injected into Dahl-SS rats on a high salt diet. A single intravenous injection of the ANP gene caused a significant reduction of blood pressure that lasted for more than 3 weeks. A maximal blood pressure reduction of 28 mm Hg was observed 2 weeks after gene delivery as compared with that of control rats injected with adenovirus harboring the LacZ gene under the control of the Rous sarcoma virus promoter (Ad.RSV-LacZ). Immunoreactive human ANP can be detected in the heart, lung, kidney, and brain of rats after gene delivery. The stroke mortality rate of Dahl-SS rats was significantly decreased (from 54% to 17% at 3 weeks and from 70% to 50% at 4 weeks after ANP gene delivery as compared with rats injected with control virus). ANP gene delivery also significantly attenuates salt-induced aortic hypertrophy as evidenced by reduced thickness of the aortic wall. This is the first study to demonstrate the potential of ANP gene delivery in reducing the mortality rate caused by cerebrovascular disorders and stroke. Successful application of this technology may have potential value in treating individuals with a high risk of stroke.
Direct and quantitative detection of HIV-1 RNA in human plasma with a branched DNA signal amplification assay (1993)

In contrast to reverse-transcriptase polymerase chain reaction the branched DNA signal amplification assay does not require a separate extraction step or enzymatic amplification of the target. Therefore this measurement is less affected by the sample matrix and the signal generated is directly proportional to the viral load.
Lipid Bilayer Deposition and Patterning via Air Bubble Collapse (2007)

We report a new method for forming patterned lipid bilayers on solid substrates. In bubble collapse deposition (BCD), an air bubble is first "inked" with a monolayer of phospholipid molecules and then touched to the surface of a thermally oxidized silicon wafer and the air is slowly withdrawn. As the bubble shrinks, the lipid monolayer pressure increases. Once the monolayer exceeds the collapse pressure, it folds back on itself, depositing a stable lipid bilayer on the surface. These bilayer disks have lateral diffusion coefficients consistent with high quality supported bilayers. By sequentially depositing bilayers in overlapping areas, fluid connections between bilayers of different compositions are formed. Performing vesicle rupture on the open substrate surrounding this bilayer patch results in a fluid but spatially isolated bilayer. Very little intermixing was observed between the vesicle rupture and bubble-deposited bilayers.
OCT Study of Mechanical Properties Associated with Trabecular Meshwork and Collector Channel Motion in Human Eyes (2016)

We report the use of a high-resolution optical coherence tomography (OCT) imaging platform to identify and quantify pressure-dependent aqueous outflow system (AOS) tissue relationships and to infer mechanical stiffness through examination of tissue properties in ex vivo human eyes. Five enucleated human eyes are included in this study, with each eye prepared with four equal-sized quadrants, each encompassing 90 degrees of the limbal circumference. In radial limbal segments perfusion pressure within Schlemm's canal (SC) is controlled by means of a perfusion cannula inserted into the canal lumen, while the other end of the cannula leads to a reservoir at a height that can control the pressure in the cannula. The OCT system images the sample with a spatial resolution of about 5 μm from the trabecular meshwork (TM) surface. Geometric parameters are quantified from the 2D OCT images acquired from the sample subjected to controlled changes in perfusion pressures; parameters include area and height of the lumen of SC, collector channel entrances (CCE) and intrascleral collector channels (ISCC). We show that 3D OCT imaging permits the identification of 3-D relationships of the SC, CCE and ISCC lumen dimensions. Collagen flaps or leaflets are found at CCE that are attached or hinged at only one end, whilst the flaps are connected to the TM by cylindrical structures spanning SC. Increasing static SC pressures resulted in SC lumen enlargement with corresponding enlargement of the CCE and ISCC lumen. Pressure-dependent SC lumen area and height changes are significant at the 0.01 levels for ANOVA, and at the 0.05 for both polynomial curves and Tukey paired comparisons. Dynamic measurements demonstrate a synchronous increase in SC, CCE and ISCC lumen height in response to pressure changes from 0 to 10, 30 or 50 mm Hg, respectively, and the response time is within the 50-millisecond range. From the measured SC volume and corresponding IOP values, we demonstrate that an elastance curve can be developed to infer the mechanical stiffness of the TM by means of quantifying pressure-dependent SC volume changes over a 2 mm radial region of SC. Our study finds pressure-dependent motion of the TM that corresponds to collagen leaflet configuration motion at CCE; the synchronous tissue motion also corresponds with synchrony of SC and CCE lumen dimension changes.
Changes in linkage pattern of glucan products induced by substitution of Lys residues in the dextransucrase (2005)

Dextransucrase S (DSRS) is the only active glucansucrase that has been found in Leuconostoc mesenteroides NRRL B-512F strain. Native DSRS produces mainly 6-linked glucopyranosyl residue (Glcp), while Escherichia coli recombinant DSRS was observed to produce a glucan consisting of 70% 6-linked Glcp and 15% 3,6-Glcp. Lys residues were introduced at the N-terminal end of the core domain by site-directed mutagenesis. In glucans produced by the one-point mutants T350K and S455K, the amount of 6-linked Glcp was increased to about 85% of the total glucan produced, more similar in structure to native B-512F dextran. The double mutant T350K/S455K produced adhesive, water-insoluble glucan with 77% 6-linked Glcp, 8% 3,6-linked Glcp and 4% 2,6-linked Glcp. The T350K/S455K mutant exhibited a 10-fold increase in glucosyltransferase activity over those of the parental DSRS-His(6) and its T350K and S455K mutants. This is the first report demonstrating a change in the properties of a dextransucrase or a related glucosyltransferase through simple site-directed mutagenesis to create 2,6-linked Glcp.
Real‐time, on‐line monitoring of organic chemical reactions using extractive electrospray ionization tandem mass spectrometry (2008)

Extractive electrospray ionization mass spectrometry (EESI-MS) for real-time monitoring of organic chemical reactions was demonstrated for a well-established pharmaceutical process reaction and a widely used acetylation reaction in the presence of a nucleophilic catalyst, 4-dimethylaminopyridine (4-DMAP). EESI-MS provides real-time information that allows us to determine the optimum time for terminating the reaction based on the relative intensities of the precursors and products. In addition, tandem mass spectrometric (MS/MS) analysis via EESI-MS permits on-line validation of proposed reaction intermediates. The simplicity and rapid response of EESI-MS make it a valuable technique for on-line characterization and full control of chemical and pharmaceutical reactions, resulting in maximized product yield and minimized environmental costs.
Detection of IDH1 mutation in the plasma of patients with glioma (2012)

With a specificity of 100% and a sensitivity related to the tumor volume and contrast enhancement, IDH1(R132H) identification has a valuable diagnostic accuracy in patients not amenable to biopsy.
Functions of the N-terminal Region of Cyclic Nucleotide Phosphodiesterase 3 (PDE 3) Isoforms (2000)

The N-terminal portion of phosphodiesterase (PDE) 3 was arbitrarily divided into region 1 (amino acids 1-300), which contains a large hydrophobic domain with six predicted transmembrane helices, and region 2 (amino acids 301-500), with a smaller hydrophobic domain ( approximately 50 residues). To analyze these regions, full-length human (H)PDE3A and mouse (M)PDE3B and a series of N-terminal truncated mutants were synthesized in Sf9 cells. Activities of HPDE3A, H3A-Delta189, MPDE3B, and M3B-Delta196, which retained all or part of the hydrophobic domain in region 1, were recovered almost entirely in particulate fractions. H3A-Delta321 and M3B-Delta302, containing region 2, were recovered essentially equally in particulate and cytosolic fractions. H3A-Delta397 and H3A-Delta457, lacking both hydrophobic domains, were predominantly cytosolic. H3A-Delta510 and M3B-Delta604, lacking both regions 1 and 2, were virtually completely cytosolic. M3B-Delta196 eluted as a large aggregated complex during gel filtration. With removal of greater amounts of N-terminal sequence, aggregation of PDE3 decreased, and H3A-Delta607, H3A-Delta721, and M3B-Delta604 eluted as dimers. Truncated HPDE3A proteins were more sensitive than full-length HPDE3A to inhibition by lixazinone. These results suggest that the hydrophobic domains in regions 1 and 2 contain structural determinants important for association of PDE3 with intracellular membranes, as well for self-association or aggregation during gel filtration and sensitivity to a specific inhibitor.
A Spread Spectrum Clock Generator for SATA-II (2005)

In this paper, we proposed a spread spectrum clock generator (SSCG) for the Serial AT Attachment Generation 2 (SATA-II). We use a fractional-N PLL to accomplish the spread spectrum function. The SSCG integrates a conventional PLL, a digital 3/sup rd/ order MASH 1-1-1 delta-sigma modulator and an address generator. The SSCG generates clocks at 1.5 GHz, a 5000 ppm down spread with a triangular waveform frequency modulation of 33 kHz. The circuit has been simulated in 0.18 /spl mu/m CMOS technology. The non spread spectrum clocking has a jitter of 80 ps and the peak amplitude reduction is 23.44 dBm in spread spectrum mode. The power dissipation from a 1.8 V supply is 55 mW.
Multicentre evaluation of the Bayer DAX system. (1993)

The analytical performance of the DAX, a high-throughput random access analyser, was studied according to ECCLS guidelines (ECCLS Document Vol. 3, No. 2, Beuth Verlag, Berlin, 1986) in a multicentre evaluation involving four laboratories. The trial took about 4 months. Determinations of 12 analytes produced more than 60,000 data. The imprecision study on 3 control sera for all analytes gave a within-run CV (median of 4 laboratories) which never exceeded 3% and was below 2% in 94% of the results. The median between-day CV was less than 3% in 92% of the results, with a highest value of 5.0%. No significant drift was detected during the 5-hour work period. No relevant sample- and cuvette-related carry-over was found. The manufacturer's claims concerning linearity were fulfilled or exceeded. The recovery of the assigned values for the control sera (median of 4 laboratories) ranged from 94 to 106%. In the method comparison on patients' samples, deviations were statistically significant in some cases, due to differences either in the methods used or in the calibration of the systems used for comparison; the regression lines, as inspected visually, and the coefficients of correlation were, however, generally acceptable. Imprecision and inaccuracy were within the acceptability limits as recommended by the Société Française de Biologie Clinique (SFBC) (Biochim. Clin. 12 (1988) 284-327) and the Deutsche Gesellschaft für Klinische Chemie (DGKC) (Dt. Arztebl. 85 (11) (1988) A697-A712). The limits of acceptance, proposed more recently by Fraser et al. (Eur. J. Clin. Chem. Clin. Biochem. 30 (1992) 311-317), were met in thirty-three of thirty-six cases. The alpha-amylase assay was significantly affected by bilirubin and haemolysis; interferences for the remaining analytes were predictable and well-known from the literature. The rate of sample throughput was found to be in agreement with that claimed by the manufacturer. The software did not present problems and was readily accepted by the operators. The practicability of the instrument was rated very good. Since the DAX is the primary chemistry analyzer in all four participating laboratories, the present experiments were necessarily intermixed with a large routine workload. Therefore, the system performance was assessed under definitely "usual" conditions. Because of its high productivity and reliability, the DAX is highly suitable for routine use in medium to large sized hospitals.
Searching for information in a hypertext medical handbook (1988)

Medicine is an ideal domain for hypertext applications and research. Implementing a popular medical handbook in hypertext underscores the need to study hypertext in the context of full-text document retrieval, machine learning, and user interface issues.