gebhart/patrepeval huggingface dataset:
Polymorphisms ofMethionine SynthaseandMethionine Synthase Reductaseand Risk of Squamous Cell Carcinoma of the Head and Neck: a Case-Control Analysis (2005)

Although tobacco and alcohol use are the major risk factors, folate deficiency has been implicated in the risk of squamous cell carcinoma of the head and neck (SCCHN). We hypothesized that polymorphisms of methionine synthase (MTR) and methionine synthase reductase (MTRR) in the folate metabolic pathway are associated with SCCHN risk. In a hospital-based case-control study of 721 SCCHN cases and 1,234 controls of non-Hispanic Whites, frequency matched by age, sex, and smoking status, we genotyped the MTR A2756G and MTRR G66A polymorphisms. We found that the MTR variant AG and AG/GG genotypes were associated with a significantly increased SCCHN risk [adjusted odd ratio (OR), 1.31; 95% confidence interval (95% CI), 1.07-1.60 for AG and OR, 1.28; 95% CI, 1.05-1.56 for AG/GG] compared with the AA genotype. In contrast, the MTRR variant AA genotype was associated with a significantly decreased SCCHN risk (OR, 0.68; 95% CI, 0.52-0.90) compared with the 66GG genotype. When the two polymorphisms were evaluated together by the number of risk alleles, the SCCHN risk was significantly increased in a dose-dependent manner (P(trend) = 0.002). The risk of SCCHN was 1.47 (95% CI, 1.08-1.99) for one risk allele, 1.67 (95% CI, 1.23-2.27) for two risk alleles, and 1.74 (95% CI, 1.18-2.54) for three or four risk alleles compared with the wild-type (0 risk allele) genotype. In conclusion, our data provide evidence that support the association between the MTR A2756G and MTRR G66A polymorphisms and SCCHN risk and that these two polymorphisms may have a joint effect on risk of SCCHN.
Macrophage migration inhibitory factor (MIF) sustains macrophage proinflammatory function by inhibiting p53: Regulatory role in the innate immune response (2001)

The importance of the macrophage in innate immunity is underscored by its secretion of an array of powerful immunoregulatory and effector molecules. We report herein that macrophage migration inhibitory factor (MIF), a product of activated macrophages, sustains macrophage survival and function by suppressing activation-induced, p53-dependent apoptosis. Endotoxin administration to MIF(-/-) mice results in decreased macrophage viability, decreased proinflammatory function, and increased apoptosis when compared with wild-type controls. Moreover, inhibition of p53 in endotoxin-treated, MIF-deficient macrophages suppresses enhanced apoptosis and restores proinflammatory function. MIF inhibits p53 activity in macrophages via an autocrine regulatory pathway, resulting in a decrease in cellular p53 accumulation and subsequent function. Inhibition of p53 by MIF coincides with the induction of arachidonic acid metabolism and cyclooxygenase-2 (Cox-2) expression, which is required for MIF regulation of p53. MIF's effect on macrophage viability and survival provides a previously unrecognized mechanism to explain its critical proinflammatory action in conditions such as sepsis, and suggests new approaches for the modulation of innate immune responses.
Langmuir-Blodgett Films Based on Prussian Blue Derivatives: towards New Hybrid Magnetic Materials (1999)

Abstract The adsorption of dissolved Prussian Blue derivatives along a positively charged monolayer leads to new Langmuir-Blodgett (LB) films presenting a ferromagnetic state at low temperature. Such organic/inorganic systems containing inorganic sheets between organic amphiphilic layers constitute a new series of magnetic lamellar materials.
Microcomputer programs for back translation of protein to DNA sequences and analysis of ambiguous DNA sequences (1984)

Three computer programs are described which may be used to translate a DNA sequence into a protein sequence, back translate the protein sequence into an ambiguous DNA sequence, and then do pattern searching in the ambiguous sequence. The programs are written in the C programming language, have been compiled to run on a microcomputer under the CP/M 80 operating system, and may be copied in binary format through a modem. They are also to become available for the IBM/PC.
Understanding TERT Promoter Mutations: A Common Path to Immortality (2016)

Telomerase (TERT) activation is a fundamental step in tumorigenesis. By maintaining telomere length, telomerase relieves a main barrier on cellular lifespan, enabling limitless proliferation driven by oncogenes. The recently discovered, highly recurrent mutations in the promoter of TERT are found in over 50 cancer types, and are the most common mutation in many cancers. Transcriptional activation of TERT, via promoter mutation or other mechanisms, is the rate-limiting step in production of active telomerase. Although TERT is expressed in stem cells, it is naturally silenced upon differentiation. Thus, the presence of TERT promoter mutations may shed light on whether a particular tumor arose from a stem cell or more differentiated cell type. It is becoming clear that TERT mutations occur early during cellular transformation, and activate the TERT promoter by recruiting transcription factors that do not normally regulate TERT gene expression. This review highlights the fundamental and widespread role of TERT promoter mutations in tumorigenesis, including recent progress on their mechanism of transcriptional activation. These somatic promoter mutations, along with germline variation in the TERT locus also appear to have significant value as biomarkers of patient outcome. Understanding the precise molecular mechanism of TERT activation by promoter mutation and germline variation may inspire novel cancer cell-specific targeted therapies for a large number of cancer patients.
(R,S)-Tetrahydropapaveroline production by stepwise fermentation using engineered Escherichia coli (2014)

Tetrahydropapaveroline (THP), a benzylisoquinoline alkaloid (BIA) found in diverse pharmaceutical compounds, is used as a starting material for the production of BIA. THP also has various neurobiological properties but is difficult to synthesize. Therefore, a simple method for THP production is desired. Recent studies have shown that microbes, especially bacteria, can serve as platforms for synthesizing these complex compounds; however, because bacteria lack organelles, the designed synthetic pathway cannot be compartmentalized. Thus, the metabolic flow is frequently inhibited or disrupted by undesirable reactions. Indeed, in the first attempt to synthesize THP using a single strain of engineered Escherichia coli, the yield was quite low (<5 μM), mainly because of the oxidation of THP by tyrosinase, an essential enzyme in our production system. To circumvent these problems, we constructed a stepwise (R,S)-THP production system, in which the dopamine-producing step and the subsequent THP-producing step were separated. The yield of (R,S)-THP reached 1.0 mM (287 mg/L), the highest yielding BIA production method using a microbe reported to date. Furthermore, we demonstrated that (R,S)-THP produced by stepwise fermentation is useful for the production of reticuline, an important BIAs intermediate. Based on these observations, applying the stepwise fermentation method is discussed.
Those Blinking Single Molecules (1997)

Recent advances in optical techniques have permitted researchers to probe the behavior of single molecules in a solid or liquid sample. In his Perspective, Moerner discusses work published in the same issue by
 Vanden Bout
 et al.
 in which single-molecule methods were used to study the phenomenon of molecular blinking. In many cases, single molecules have been observed to emit flickering fluorescent light. The work examines this phenomenon in light-emitting polymer materials.
Heat Index Flow Monitoring in Capillaries with Interferometric Backscatter Detection (2000)

Independent control of fluid is important for small volume fluid applications including separation science techniques and analytical microchip devices. To effectively control fluid, a monitoring system is necessary to ensure proper response to the control input. Proof of principle for a new online technique for flow monitoring is demonstrated here. It offers near real-time measurements of small-volume flows in a noninvasive, simple, and robust design. The measurement is accomplished by the introduction of a plug of heat into the fluid and detection of the time of its appearance a short distance downstream. Using heat indexing and laser induced interferometric backscatter as the detector, flow monitoring is demonstrated in 184-microm diameter capillary tubing over a range of 2-25 cm/s (500 nL/s to 7 mL/s.).
Li4C60:  A Polymeric Fulleride with a Two-Dimensional Architecture and Mixed Interfullerene Bonding Motifs (2004)

All known fullerene polymers have interfullerene connections via either [2 + 2] cycloaddition or single C-C bonds. The high-resolution synchrotron X-ray powder diffraction technique was employed here to determine the crystal structure of the Li4C60 fulleride. We find that the ground state of Li4C60 is a two-dimensional polymer with monoclinic crystal symmetry and an unprecedented architecture, combining both the [2 + 2] cycloaddition and the single C-C bridging motifs. The small size of the Li+ cations is crucial in stabilizing the resulting tightly packed polymeric structure.
On Adaptation, Maximization, and Reinforcement Learning Among Cognitive Strategies. (2005)

Analysis of binary choice behavior in iterated tasks with immediate feedback reveals robust deviations from maximization that can be described as indications of 3 effects: (a) a payoff variability effect, in which high payoff variability seems to move choice behavior toward random choice; (b) underweighting of rare events, in which alternatives that yield the best payoffs most of the time are attractive even when they are associated with a lower expected return; and (c) loss aversion, in which alternatives that minimize the probability of losses can be more attractive than those that maximize expected payoffs. The results are closer to probability matching than to maximization. Best approximation is provided with a model of reinforcement learning among cognitive strategies (RELACS). This model captures the 3 deviations, the learning curves, and the effect of information on uncertainty avoidance. It outperforms other models in fitting the data and in predicting behavior in other experiments.
Eliciting knowledge and transferring it effectively to a knowledge-based system (1993)

The knowledge acquisition bottleneck impeding the development of expert systems is being alleviated by the development of computer-based knowledge acquisition tools. These work directly with experts to elicit knowledge, and structure it appropriately to operate as a decision support tool within an expert system. However, the elicitation of expert knowledge and its effective transfer to a useful knowledge-based system is complex and involves diverse activities. The complete development of a decision support system using knowledge acquisition tools is illustrated. The example is simple enough to be completely analyzed but exhibits enough real-world characteristics to give significant insights into the processes and problems of knowledge engineering.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Combined Immunodeficiency of Arabian Horses: Confirmation of Autosomal Recessive Mode of Inheritance (1980)

A 3-year prospective breeding trial was designed to verify the mode of inheritance of combined immunodeficiency (CID) in Arabian horses. Twenty-six mares that had previously produced foals with CID were mated to a stallion that had sired foals with CID. Of 53 foals obtained, 15 (28.3%) had CID. The ratio of female to male foals was 28:25, and the ratio of female CID to male CID foals was 8:7. The results of this trial confirmed a suggestion that CID in Arabian horses is inherited as an autosomal recessive trait.
Facial thermography is a sensitive and specific method for assessing food challenge outcome (2007)

Facial thermography consistently detects a significant early rise in nasal temperature during positive compared with negative food challenges, which is evident before objective symptoms occur. Thermography may therefore provide a sensitive method to determine outcome of food challenges and investigate the pathophysiology of food allergic reactions.
Inhibition of Simian Virus 40 DNA replication in CV-1 cells by an oligodeoxynucleotide covalently linked to an intercalating agent (1990)

An octathymidylate covalently linked via its 3'-end to an acridine derivative inhibited the cytopathic effect of Simian Virus SV40 on CV-1 cells in culture. Control experiments revealed that this effect was virus-specific and did not arise as a result of oligonucleotide degradation by nucleases. A photoactive probe was covalently attached to the 5'-end of the oligonucleotide-acridine conjugate. Upon UV-irradiation, photocrosslinking was shown to occur at the A. T-rich region within the viral origin of replication. A local triple helix can form at moderate salt concentrations with two octathymidylate-acridine conjugates bound to the octaadenylate sequence. Alternatively the octathymidylate-acridine conjugate can bind to the major groove of duplex DNA forming a local triple helix. Different mechanisms are discussed to explain the inhibition of viral DNA replication.
Biomarker discovery by CE‐MS enables sequence analysis via MS/MS with platform‐independent separation (2006)

CE-MS is a successful proteomic platform for the definition of biomarkers in different body fluids. Besides the biomarker defining experimental parameters, CE migration time and molecular weight, especially biomarker's sequence identity is an indispensable cornerstone for deeper insights into the pathophysiological pathways of diseases or for made-to-measure therapeutic drug design. Therefore, this report presents a detailed discussion of different peptide sequencing platforms consisting of high performance separation method either coupled on-line or off-line to different MS/MS devices, such as MALDI-TOF-TOF, ESI-IT, ESI-QTOF and Fourier transform ion cyclotron resonance, for sequencing indicative peptides. This comparison demonstrates the unique feature of CE-MS technology to serve as a reliable basis for the assignment of peptide sequence data obtained using different separation MS/MS methods to the biomarker defining parameters, CE migration time and molecular weight. Discovery of potential biomarkers by CE-MS enables sequence analysis via MS/MS with platform-independent sample separation. This is due to the fact that the number of basic and neutral polar amino acids of biomarkers sequences distinctly correlates with their CE-MS migration time/molecular weight coordinates. This uniqueness facilitates the independent entry of different sequencing platforms for peptide sequencing of CE-MS-defined biomarkers from highly complex mixtures.
[7-Chloro(phenylthio)-4-phenylaminoquinolines. Study of its anti-inflammatory and analgesic activity]. (1986)

Some 7-chloro(phenylthio)-4-phenylaminoquinolines substituted in the benzene rings were prepared and subject to the Winter test for potential antiinflammatory activity and the acetic acid test for analgesic activity. Derivative (I) was devoid of antiinflammatory properties but showed interesting analgesic activity although this was 30 times weaker than that of indomethacin used as reference substance. The DL50/DE50 ratio is greater than 16 for derivative (I) and 3 for indomethacin. The other compounds had no or only slight activity.
Killing effect of coexpressing cytosine deaminase and thymidine kinase on rat vascular smooth muscle cells. (2004)

The killing effect on rat VSMCs mediated by adenoviral CD/TK double suicide genes is superior to that of single suicide gene. The killing mechanism of recombinant adenovirus coexpressing CD/TK double suicide genes is mainly through cytotoxic effect and apoptosis.
Novel Complementary Resistive Switch Crossbar Memory Write and Read Schemes (2015)

Recent trends in emerging nonvolatile memory systems necessitate efficient read/write (R/W) schemes. Efficient solutions with zero sneak path current, nondestructive R/W operations, minimum area and low power are some of the key requirements. Toward this end, we propose a novel crossbar memory scheme using a configuration row of cells for assisting R/W operations. The proposed write scheme minimizes the overall power consumption compared to the previously proposed write schemes and reduces the state drift problem. We also propose two read schemes, namely, assisted-restoring and self-resetting read. In assisted-restoring scheme, we use the configuration cells which are used in the write scheme, whereas we implement additional circuitry for self-reset which addresses the problem of destructive read. Moreover, by formulating an analytical model of R/W operation, we compare the various schemes. The overhead for the proposed assisted-restoring write/read scheme is an extra redundant row for the given crossbar array. For a typical array size of 200 × 200 the area overhead is about 0.5%, however, there is a 4X improvement in power consumption compared to the recently proposed write schemes. Quantitative analysis of the proposed scheme is analyzed by using simulation and analytical models.
Wrapping windows NT software for robustness (2003)

As Windows NT workstations become more entrenched in enterprise-critical and even mission-critical applications, the dependability of the Windows 32-bit (Win32) platform is becoming critical. To date, studies on the robustness of system software have focused on Unix-based systems. This paper describes an approach to assessing the robustness for Win32 software and providing robustness wrappers for third party commercial off-the-shelf (COTS) software. The robustness of Win32 applications to failing operating system (OS) functions is assessed by using fault injection techniques at the interface between the application and the operating system. Finally, software wrappers are developed to handle OS failures gracefully in order to mitigate catastrophic application failures.
Reverse Evolution: Driving Forces Behind the Loss of Acquired Photosynthetic Traits (2009)

Our results suggest that, provided the mixotroph's photosynthetic advantage is not too large, the (small) heterotroph will also dominate in nutrient-poor environments and will readily invade a community of mixotrophs and bacteria, due to its higher efficiency exploiting the ultramicrobacteria. As carbon-limited conditions were presumably widespread throughout Earth history, such a scenario may explain the numerous transitions from phototrophy to mixotrophy and further to heterotrophy within virtually all major algal lineages. We challenge prevailing concepts that affiliated the evolution of phagotrophy with eutrophic or strongly light-limited environments only.
Learning Speaker-Specific Characteristics With a Deep Neural Architecture (2011)

Speech signals convey various yet mixed information ranging from linguistic to speaker-specific information. However, most of acoustic representations characterize all different kinds of information as whole, which could hinder either a speech or a speaker recognition (SR) system from producing a better performance. In this paper, we propose a novel deep neural architecture (DNA) especially for learning speaker-specific characteristics from mel-frequency cepstral coefficients, an acoustic representation commonly used in both speech recognition and SR, which results in a speaker-specific overcomplete representation. In order to learn intrinsic speaker-specific characteristics, we come up with an objective function consisting of contrastive losses in terms of speaker similarity/dissimilarity and data reconstruction losses used as regularization to normalize the interference of non-speaker-related information. Moreover, we employ a hybrid learning strategy for learning parameters of the deep neural networks: i.e., local yet greedy layerwise unsupervised pretraining for initialization and global supervised learning for the ultimate discriminative goal. With four Linguistic Data Consortium (LDC) benchmarks and two non-English corpora, we demonstrate that our overcomplete representation is robust in characterizing various speakers, no matter whether their utterances have been used in training our DNA, and highly insensitive to text and languages spoken. Extensive comparative studies suggest that our approach yields favorite results in speaker verification and segmentation. Finally, we discuss several issues concerning our proposed approach.
Chronic antioxidant supplementation attenuates nuclear factor-κB activation and preserves endothelial function in hypercholesterolemic pigs (2002)

This study demonstrates for the first time that in vivo chronic interruption of the endogenous oxidative stress cascade reduces HC-induced NF-kappa B activation and normalizes NO bioactivity in association with preservation of coronary endothelial function. This study suggests a role for increased oxidative stress and NF-kappa B activation in early atherosclerosis.
A Novel JAK3 Inhibitor, R348, Attenuates Chronic Airway Allograft Rejection (2009)

R348 is an effective drug, and it is expected to be introduced into clinical transplant pharmacology soon.
Gene Therapy for Duchenne Muscular Dystrophy (2021)

Duchenne muscular dystrophy (DMD) is an X-linked, muscle wasting disease that affects 1 in 5000 males. Affected individuals become wheelchair bound by the age of twelve and eventually die in their third decade due to respiratory and cardiac complications. The disease is caused by mutations in the DMD gene that codes for dystrophin. Dystrophin is a structural protein that maintains the integrity of muscle fibres and protects them from contraction-induced damage. The absence of dystrophin compromises the stability and function of the muscle fibres, eventually leading to muscle degeneration. So far, there is no effective treatment for deteriorating muscle function in DMD patients. A promising approach for treating this life-threatening disease is gene transfer to restore dystrophin expression using a safe, non-pathogenic viral vector called adeno-associated viral (AAV) vector. Whilst microdystrophin gene transfer using AAV vectors shows extremely impressive therapeutic success so far in large animal models of DMD, translating this advanced therapy medicinal product from bench to bedside still offers scope for many optimization steps. In this paper, the authors review the current progress of AAV-microdystrophin gene therapy for DMD and other treatment strategies that may apply to a subset of DMD patients depending on the mutations they carry.