gebhart/patrepeval huggingface dataset:
Carbon Catabolite Repression in Lactobacillus pentosus : Analysis of the ccpA Region (2000)

The catabolite control protein CcpA is a central regulator in low-G+C-content gram-positive bacteria. It confers carbon catabolite repression to numerous genes required for carbon utilization. It also operates as a transcriptional activator of genes involved in diverse phenomena, such as glycolysis and ammonium fixation. We have cloned the ccpA region of Lactobacillus pentosus. ccpA encodes a protein of 336 amino acids exhibiting similarity to CcpA proteins of other bacteria and to proteins of the LacI/GalR family of transcriptional regulators. Upstream of ccpA was found an open reading frame with similarity to the pepQ gene, encoding a prolidase. Primer extension experiments revealed two start sites of transcription for ccpA. In wild-type cells grown on glucose, mRNA synthesis occurred only from the promoter proximal to ccpA. In a ccpA mutant strain, both promoters were used, with increased transcription from the distant promoter, which overlaps a presumptive CcpA binding site called cre (for catabolite responsive element). This suggests that expression of ccpA is autoregulated. Determination of the expression levels of CcpA in cells grown on repressing and nonrepressing carbon sources revealed that the amounts of CcpA produced did not change significantly, leading to the conclusion that the arrangement of two promoters may ensure constant expression of ccpA under various environmental conditions. A comparison of the genetic structures of ccpA regions revealed that lactic acid bacteria possess the gene order pepQ-ccpA-variable while the genetic structure in bacilli and Staphylococcus xylosus is aroA-ccpA-variable-acuC.
Second locus involved in human immunodeficiency virus type 1 resistance to protease inhibitors (1996)

Protease inhibitors are potent antiviral agents against human immunodeficiency virus type 1. As with reverse transcriptase inhibitors, however, resistance to protease inhibitors can develop and is attributed to the appearance of mutations in the protease gene. With the substrate analog protease inhibitors BILA 1906 BS and BILA 2185 BS, 350- to 1,500-fold-resistant variants have been selected in vitro and were found not only to contain mutations in the protease gene but also to contain mutations in Gag precursor p1/p6 and/or NC (p7)/p1 cleavage sites. Mutations in cleavage sites give rise to better peptide substrates for the protease in vitro and to improved processing of p15 precursors in drug-resistant clones. Importantly, removal of cleavage site mutations in resistant clones leads to a decrease or even an absence of viral growth, confirming their role in viral fitness. Therefore, these second-locus mutations indicate that cleavage of p15 is a rate-limiting step in polyprotein processing in highly resistant viruses. The functional constraint of p15 processing also suggests that additional selective pressure could further compromise viral fitness and maintain the benefits of antiviral therapies.
Arabidopsis Research 2000 (2000)

The 11th International Conference on Arabidopsis Research, organized by Rick Amasino, Jeffery Dangl, Mary Lou Guerinot, and Detlef Weigel, was held June 24 to 28, 2000, at the University of Wisconsin, Madison. The conference was attended by more than 900 participants and included a large number of
Estimation of melting curves from enzymatic activity–temperature profiles (1993)

Measuring the reversible thermal unfolding of enzymes is valuable for quantifying the effects of environmental factors on the thermodynamic stability of proteins. The thermal unfolding behavior of enzymes is typically studied using calorimetry or optical techniques such as circular dichroism, fluorescence, or light scattering. These techniques often have practical limitations and usually require the protein to be electrophoretically pure. An alternative technique for analyzing the thermodynamic stability of enzymes is to estimate the melting curve from temperature-activity data. This technique does not require electrophoretically pure enzyme, provided the sample does not have competing enzymatic activities or proteins which can affect enzyme stability (e.g., proteases). Moreover, small amounts of contaminant proteins should not affect the results as long as enzymatic assays are performed at low protein concentrations where nonspecific protein-protein interactions are negligible. To illustrate this technique, the melting curve for beta-galactosidase from Escherichia coli in the presence of 1 mM EDTA, and the shift caused by adding 1 mM Mg(+2), were calculated from activity-temperature data. Melting temperatures predicted from activity-temperature data compared closely with those obtained using other techniques. Application of this analysis to multisubstrate enzymes is illustrated by estimating the melting profiles for partially purified hydrogenases from several thermophilic Methanococcii. Limitations and important considerations for estimating melting profiles from activity-temperature data are discussed.
A Dynamic Bronchial Airway Gene Expression Signature of Chronic Obstructive Pulmonary Disease and Lung Function Impairment (2013)

Our findings demonstrate a molecular field of injury throughout the bronchial airway of active and former smokers with COPD that may be driven in part by ATF4 and is modifiable with therapy. Bronchial airway epithelium may ultimately serve as a relatively accessible tissue in which to measure biomarkers of disease activity for guiding clinical management of COPD.
Molecular Characterization of Iodotyrosine Dehalogenase Deficiency in Patients with Hypothyroidism (2008)

This study describes a functional mutation within IYD, demonstrating the molecular basis of the iodine wasting form of congenital hypothyroidism. This familial genetic defect shows a dominant pattern of inheritance with incomplete penetration.
Recent Advances in Underlying Pathologies Provide Insight into Interleukin-8 Expression-Mediated Inflammation and Angiogenesis (2011)

Interleukin-8 has long been recognized to have anti-inflammatory activity, which has been established in various models of infection, inflammation, and cancer. Several cell types express the receptor for the cytokine IL-8 and upon its recognition produce molecules that are active both locally and systemically. Many different types of cells, in particular monocytes, neutrophils, epithelial, fibroblast, endothelial, mesothelial, and tumor cells, secrete IL-8. Increased expression of IL-8 and/or its receptors has been characterized in many chronic inflammatory conditions, including psoriasis, ARDS, COPD, and RA as well as many cancers, and its upregulation often correlates with disease activity. IL-8 constitutes the CXC class of chemokines, a potent chemoattractant and activator of neutrophils and other immune cells. It is a proangiogenic cytokine that is overexpressed in many human cancers. Therefore, inhibiting the effects of IL-8 signaling may be a significant therapeutic intervention.
A bacteriophage T7 RNA polymerase/promoter system for controlled exclusive expression of specific genes. (1985)

The RNA polymerase gene of bacteriophage T7 has been cloned into the plasmid pBR322 under the inducible control of the lambda PL promoter. After induction, T7 RNA polymerase constitutes 20% of the soluble protein of Escherichia coli, a 200-fold increase over levels found in T7-infected cells. The overproduced enzyme has been purified to homogeneity. During extraction the enzyme is sensitive to a specific proteolysis, a reaction that can be prevented by a modification of lysis conditions. The specificity of T7 RNA polymerase for its own promoters, combined with the ability to inhibit selectively the host RNA polymerase with rifampicin, permits the exclusive expression of genes under the control of a T7 RNA polymerase promoter. We describe such a coupled system and its use to express high levels of phage T7 gene 5 protein, a subunit of T7 DNA polymerase.
Speculative dynamic vectorization (2003)

Traditional vector architectures have shown to be very effective for regular codes where the compiler can detect data-level parallelism. However, this SIMD parallelism is also present in irregular or pointer-rich codes, for which the compiler is quite limited to discover it. In this paper we propose a microarchitecture extension in order to exploit SIMD parallelism in a speculative way. The idea is to predict when certain operations are likely to be vectorizable, based on some previous history information. In this case, these scalar instructions are executed in a vector mode. These vector instructions operate on several elements (vector operands) that are anticipated to be their input operands and produce a number of outputs that are stored on a vector register in order to be used by further instructions. Verification of the correctness of the applied vectorization eventually changes the status of a given vector element from speculative to non-speculative, or alternatively, generates a recovery action in case of misspeculation. The proposed microarchitecture extension applied to a 4-way issue superscalar processor with one wide bus is 19% faster than the,same processor with 4 scalar buses to Ll data cache. This speed up is due basically to 1) the reduction in number of memory accesses, 15% for SpecInt and 20% for SpecFP, 2) the transformation of scalar arithmetic instructions into their vector counterpart, 28% for SpecInt and 23% for SpecFP, and 3) the exploitation of control independence for mispredicted branches.
High definition live 3D-OCT in vivo: design and evaluation of a 4D OCT engine with 1 GVoxel/s (2014)

We present a 1300 nm OCT system for volumetric real-time live OCT acquisition and visualization at 1 billion volume elements per second. All technological challenges and problems associated with such high scanning speed are discussed in detail as well as the solutions. In one configuration, the system acquires, processes and visualizes 26 volumes per second where each volume consists of 320 x 320 depth scans and each depth scan has 400 usable pixels. This is the fastest real-time OCT to date in terms of voxel rate. A 51 Hz volume rate is realized with half the frame number. In both configurations the speed can be sustained indefinitely. The OCT system uses a 1310 nm Fourier domain mode locked (FDML) laser operated at 3.2 MHz sweep rate. Data acquisition is performed with two dedicated digitizer cards, each running at 2.5 GS/s, hosted in a single desktop computer. Live real-time data processing and visualization are realized with custom developed software on an NVidia GTX 690 dual graphics processing unit (GPU) card. To evaluate potential future applications of such a system, we present volumetric videos captured at 26 and 51 Hz of planktonic crustaceans and skin.
Noninvasive Human Brain Stimulation (2007)

Noninvasive brain stimulation with transcranial magnetic stimulation (TMS) or transcranial direct current stimulation (tDCS) is valuable in research and has potential therapeutic applications in cognitive neuroscience, neurophysiology, psychiatry, and neurology. TMS allows neurostimulation and neuromodulation, while tDCS is a purely neuromodulatory application. TMS and tDCS allow diagnostic and interventional neurophysiology applications, and focal neuropharmacology delivery. However, the physics and basic mechanisms of action remain incompletely explored. Following an overview of the history and current applications of noninvasive brain stimulation, we review stimulation device design principles, the electromagnetic and physical foundations of the techniques, and the current knowledge about the electrophysiologic basis of the effects. Finally, we discuss potential biomedical and electrical engineering developments that could lead to more effective stimulation devices, better suited for the specific applications.
Quaternary Structure of ATR and Effects of ATRIP and Replication Protein A on Its DNA Binding and Kinase Activities (2004)

ATR is an essential protein that functions as a damage sensor and a proximal kinase in the DNA damage checkpoint response in mammalian cells. It is a member of the phosphoinositide 3-kinase-like kinase (PIKK) family, which includes ATM, ATR, and DNA-dependent protein kinase. Recently, it was found that ATM is an oligomeric protein that is converted to an active monomeric form by phosphorylation in trans upon DNA damage, and this raised the possibility that other members of the PIKK family may be regulated in a similar manner. Here we show that ATR is a monomeric protein associated with a smaller protein called ATRIP with moderate affinity. The ATR protein by itself or in the form of the ATR-ATRIP heterodimer binds to naked or replication protein A (RPA)-covered DNAs with comparable affinities. However, the phosphorylation of RPA by ATR is dependent on single-stranded DNA and is stimulated by ATRIP. These findings suggest that the regulation and mechanism of action of ATR are fundamentally different from those of the other PIKK proteins.
Asymmetric Synthesis of Spiroketals with Aminothiourea Catalysts (2015)

Chiral spiroketal skeletons are found as core structures in a range of bioactive compounds. These natural compounds and their analogues have attracted much attention in the field of drug discovery. However, methods for their enantioselective construction are limited, and easily available optically active spiroketals are rare. We demonstrate a novel catalytic asymmetric synthesis of spiroketal compounds that proceeds through an intramolecular hemiacetalization/oxy-Michael addition cascade mediated by a bifunctional aminothiourea catalyst. This results in spiroketal structures through the relay formation of contiguous oxacycles, in which multipoint recognition by the catalyst through hydrogen bonding imparts high enantioselectivity. This method offers facile access to spiroketal frameworks bearing an alkyl group at the 2-position, which are prevalent in insect pheromones. Optically active (2S,5S)-chalcogran, a pheromone of the six-spined spruce bark beetle, and an azide derivative could be readily synthesized from the bicyclic reaction product.
Integrin-linked kinase and associated proteins (review). (1999)

Integrin-linked kinase (ILK) is a recently identified cytoplasmic protein serine/threonine kinase implicated in integrin-, growth factor- and Wnt-signaling pathways. It contains several structurally conserved motifs including ankyrin repeats, pleckstrin-homology (PH) domain and protein kinase catalytic domain that are critical for signal transduction. Recent studies have documented that ILK plays important roles in bi-directional ( and ) transmembrane signaling pathways via integrins and other proteins, leading to regulation of cell adhesion, growth, survival, extracellular matrix deposition and potentially differentiation. Furthermore, ILK is implicated in tumorigenesis and ILK appears to be a useful diagnostic marker of certain human tumors. The identification of novel ILK-associated proteins will provide a better understanding of how ILK functions in intracellular signal transduction cascades and tumorigenesis.
Diagnostic Sensitivity of Laboratory Findings in Acute Pulmonary Embolism (1971)

Many different laboratory tests have been used to screen patients for pulmonary embolism. The sensitivity of certain laboratory tests was assessed in a prospective study of 50 patients with angiographically documented acute pulmonary embolism. Electrocardiographic evidence of right heart strain occurred in only nine patients; each had massive pulmonary embolism. Nonspecific chest X-ray abnormalities (infiltrate, effusion, or elevated diaphragm) occurred in 71%; 29% had a normal chest X ray. Lactic dehydrogenase (LDH) was increased in 83% of the patients, but serum glutamic-oxalacetic transaminase (SGOT) and bilirubin were of little value. The triad of increased LDH, normal SGOT, and increased bilirubin occurred in only 12%. Lung scans performed in 24 patients were abnormal. Arterial Po2 (breathing room air) was decreased (≤ 80 mm Hg) in all 36 patients tested. Arterial Po2 and lung scan are the most sensitive tests for screening; if either is normal, acute pulmonary embolism is essentially excluded.
Current Picture Referencing in Versatile Video Coding (2019)

Screen content coding (SCC) is a recognized feature in versatile video coding (VVC), the most recent international video coding standard development. Among all the coding tools that have been evaluated for SCC in the past, current picture referencing (CPR), or by another name intra block copy (IBC), has shown its effectiveness in coding of computer-generated contents such as texts and graphics. Therefore, it has been adopted into the HEVC standard version 4, extensions for SCC. In this paper, several variations of CPR implementations are proposed and discussed. Among those methods, the one with the best trade-off between coding efficiency and implementation cost has been adopted into the new VVC standard working draft and the reference software VTM.
The Pharmacology of Lysergic Acid Diethylamide: A Review (2008)

Lysergic acid diethylamide (LSD) was synthesized in 1938 and its psychoactive effects discovered in 1943. It was used during the 1950s and 1960s as an experimental drug in psychiatric research for producing so-called "experimental psychosis" by altering neurotransmitter system and in psychotherapeutic procedures ("psycholytic" and "psychedelic" therapy). From the mid 1960s, it became an illegal drug of abuse with widespread use that continues today. With the entry of new methods of research and better study oversight, scientific interest in LSD has resumed for brain research and experimental treatments. Due to the lack of any comprehensive review since the 1950s and the widely dispersed experimental literature, the present review focuses on all aspects of the pharmacology and psychopharmacology of LSD. A thorough search of the experimental literature regarding the pharmacology of LSD was performed and the extracted results are given in this review. (Psycho-) pharmacological research on LSD was extensive and produced nearly 10,000 scientific papers. The pharmacology of LSD is complex and its mechanisms of action are still not completely understood. LSD is physiologically well tolerated and psychological reactions can be controlled in a medically supervised setting, but complications may easily result from uncontrolled use by layman. Actually there is new interest in LSD as an experimental tool for elucidating neural mechanisms of (states of) consciousness and there are recently discovered treatment options with LSD in cluster headache and with the terminally ill.
Enhancement of Anti-Herpetic Activity of Antisense Phosphorothioate Oligonucleotides 5′ End Modified with Geraniol (1998)

We have previously shown that antisense phosphorothioate oligonucleotide (SON) targeted against immediate early (IE) pre-mRNA5 of the herpes simplex virus type I (HSV-I) possessed potent anti-herpetic activities in vitro system. However, anti-herpetic activities of SON were not still efficient enough. Lipophilic compounds have been often conjugated with antisense oligonucleotide to enhance the biological activity. In this study, we selected geraniol as a lipophilic compound and newly synthesized SON bearing 5' terminal geraniol (geranyl-SON) toward IE pre-mRNA 5 of the HSV-1 to enhance the anti-herpetic activity. Geraniol is a olefinic terpene alcohol which is found in many essential oils. It possesses lipophilic characteristic. It is thought to be absorbed in tissue. Geraniol enhanced the anti-herpetic activity of SON with less cytotoxicity in a sequence specific manner. Terminal modification with geraniol did not affect binding affinity with complimentary DNA. Cytoplasm distribution of geranyl-SON was confirmed by confocal microscope. While some of the geranyl-SON was seen in the nucleus, unmodified SON had a punctate distribution in the cytoplasm with little in the nucleus. These results suggested that geranyl modification enhances anti-herpetic activity by changing the subcellular distribution of the oligonucleotides. Consequently geraniol-modifica-tion could provide new means for the efficient delivery of oligo-nucleotides.
The forward-backward search algorithm (1991)

The authors introduce a technique that greatly speeds up expensive time-synchronous beam searches in speech recognition. The algorithm is called the forward-backward search and is mathematically related to the Baum-Welch forward-backward training algorithm. It uses a simplified forward pass followed by a detailed backward search. The information stored in the forward pass is used to decrease the computation in the backward pass by a large factor. An increase in speed of a factor of 40 with no increase in search errors was observed. The authors also describe how they have incorporated this algorithm into a real-time speaker-independent spoken language understanding system. One version of this is based on the 1000 word Resource Management vocabulary and is directed by a statistical class grammar. Another version has been incorporated into a military transportation planning application called DART (Dynamic Analysis Re-planning Tool).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Expression, regulation and function of MicroRNAs in endometriosis. (2016)

Endometriosis (EMS), characterized by the presence and growth of functional en do met rial-like tissues outside the uterine cavity, is a common and benign gyneco logical disorder with a poorly understood and somewhat enigmatic etiopathogenesis and pathophysiology. MicroRNAs (miRNAs) are single-stranded 19-25 nucleotide-long RNAs and have an important role in post-transcriptional gene silencing by base pairing with target mRNAs. Recent research has shown that miRNAs and their target mRNAs are differentially expressed in endometriosis and other disorders of the female reproductive system. In this paper, we review the recent progress in understanding the roles of miRNAs in endometriosis, and specific miRNAs as biomarkers and therapeutic targets for endometriosis.
Automated, accurate, and inexpensive solution-preparation on a digital microfluidic biochip (2008)

Solution-preparation is a basic and repetitive step for many biological and chemical experiments in the laboratory. It uses stock solutions of sample, reagents, and diluents to derive various mixed solutions with the required concentration levels. Manual solution-preparation methods are time-consuming, imprecise, and they require large volumes of liquid. We propose an electrowetting-based “digital” microfluidic biochip design for automated solution-preparation. An efficient solution-preparation algorithm is also presented to generate a preparation plan that lists the intermediate mixing steps needed to generate the target solutions with the required concentrations. It determines the type, concentration, and the number of dispensed droplets of stock solutions. The proposed automated solution-preparation algorithm and biochip platform are evaluated using a protein-crystallization application.