gebhart/patrepeval huggingface dataset:
An mRNA structure in bacteria that controls gene expression by binding lysine (2003)

Riboswitches are metabolite-responsive genetic control elements that reside in the untranslated regions (UTRs) of certain messenger RNAs. Herein, we report that the 5′-UTR of the lysC gene of Bacillus subtilis carries a conserved RNA element that serves as a lysine-responsive riboswitch. The ligand-binding domain of the riboswitch binds to L-lysine with an apparent dissociation constant (K D ) of ∼1 µM, and exhibits a high level of molecular discrimination against closely related analogs, including D-lysine and ornithine. Furthermore, we provide evidence that this widespread class of riboswitches serves as a target for the antimetabolite S -(2-aminoethyl)-L-cysteine (AEC). These findings add support to the hypotheses that direct sensing of metabolites by messenger RNAs is a fundamental form of genetic control and that riboswitches represent a new class of antimicrobial drug targets.
The long-term outcome in Crohn's disease (1987)

The long-term outcome of Crohn's disease was reviewed in 139 patients who were treated at the Cleveland Clinic for a minimum of 15 years. At the time of diagnosis, 38 (27 percent), 39 (28 percent) and 62 (43 percent) patients had small-bowel, large-bowel, and ileocolic patterns of disease, respectively. The disease progressed with time and, eventually, 104 (75 percent) patients had ileocolic disease. One hundred twenty-two patients (88 percent) underwent at least one definitive operation for the disease. Forty-four (32 percent) patients had proctocolectomies and 65 (47 percent) have ileostomies. Associated manifestations of Crohn's disease occurred in a high proportion of patients; perianal disease in 78 (56 percent), intestinal fistulas in 45 (32 percent), extraintestinal disease in 49 (35 percent). Six patients died of causes directly related to the disease. Specific complications tend to occur at definite times in the course of the disease. Crohn's disease is not a benign condition. There is a relentless progression of the disease and a high incidence of complications when patients are followed over a long period.
DF-DICE: a scalable solution for soft error tolerant circuit design (2006)

The delay filtered dual interlocked storage cell (DF-DICE) offers a scalable solution in different radiation environments for soft error mitigation. The area and speed performance for five different single event transient thresholds have been evaluated. The results show that the cost of soft error mitigation is minimal for terrestrial environments (overall area penalty less than 14% and speed penalty within 6% for flip-flop based typical designs) while it is larger for space environments (overall area penalty up to 30% and speed penalty up to 13% for flip-flop based typical designs). The logic of a conventional application specific integrated circuit (ASIC) can easily be converted to a soft-error tolerant design by replacing the existing storage elements with the respective DF-DICE elements
Structural and optical properties of chemically deposited CdCr2S4thin films (2003)

Reproducible and good quality CdCr2S4 thin films with different thicknesses were deposited on microscopic glass substrates using the chemical bath deposition process. The x-ray and electron diffraction analysis revealed that the as-deposited films were polycrystalline cubic phase. The optical constants of the deposited films were obtained from the analysis of the experimental recorded transmission and reflectance spectral data over the wavelength range 300–2500 nm. It has been found that the refractive index and extinction coefficient are almost independent of the film thickness. The complex dielectric constants of CdCr2S4 films have been calculated in the investigated wavelength range. An analysis of the optical absorption data of the as-deposited films revealed an optical direct transition with the estimation of the corresponding bandgap value. It was found that the refractive index dispersion data obeyed the single oscillator of the Wemple–DiDomenico model, from which the dispersion parameters and the high-frequency dielectric constant were determined. The electric free carrier susceptibility and the carrier concentration to the effective mass ratio were estimated according to the model of Spitzer and Fan.
Sialylation is essential for early development in mice (2002)

Sialic acids are widely expressed as terminal carbohydrates on glycoconjugates of eukaryotic cells. Sialylation is crucial for a variety of cellular functions, such as cell adhesion or signal recognition, and regulates the biological stability of glycoproteins. The key enzyme of sialic acid biosynthesis is the bifunctional UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase (UDP-GlcNAc 2-epimerase), which catalyzes the first two steps of sialic acid biosynthesis in the cytosol. We report that inactivation of the UDP-GlcNAc 2-epimerase by gene targeting causes early embryonic lethality in mice, thereby emphasizing the fundamental role of this bifunctional enzyme and sialylation during development. The need of UDP-GlcNAc 2-epimerase for a defined sialylation process is exemplified with the polysialylation of the neural cell adhesion molecule in embryonic stem cells.
Changes in predominant bacterial populations in human faeces with age and with Clostridium difficile infection (2002)

The bacterial composition of human faeces can vary greatly with factors such as age and disease, although relatively few studies have monitored these events, particularly at species level. In this investigation, bacteria were isolated from faecal samples from healthy young adults and elderly subjects, and elderly patients with Clostridium difficile-associated diarrhoea (CDAD). The organisms were identified to species level on the basis of their cellular fatty acid profiles with the MIDI system. In some groups of bacteria, species diversity was found to change with age despite the overall numbers of organisms being similar at genus level. Bacteroides thetaiotaomicron, B. ovatus and Prevotella tannerae were common gram-negative anaerobes isolated from young adults. Bacteroides species diversity increased in the faeces of healthy elderly people. Bifidobacterial species diversity decreased with age, with Bifidobacterium adolescentis and Bif. angulatum being the most common isolates. CDAD patients were characterised by greater diversity of facultative species, lactobacilli and clostridia, but greatly reduced numbers of bacteroides, prevotella and bifidobacteria. Such bacterial population changes in the normal microbiota could result in metabolic conditions favourable for the establishment of pathogenic micro-organisms, such as clostridia, and would have considerable effects on the biochemical capacity of the large intestine as a whole. Alterations in the community structure of bifidobacteria and lactobacilli have relevance for dietary and therapeutic interventions such as the use of pre- or probiotics that aim to modify the composition or metabolic activities of the intestinal microflora in a beneficial way, particularly in elderly people or individuals at risk of CDAD.
Initial Effects of the Left Ventricular Repair by Plication May Not Last Long in a Rat Ischemic Cardiomyopathy Model (2001)

Initial improvement in LV function and neurohormonal status after LVR did not last for 4 weeks in this rat model when untreated medically. The mechanism of deterioration should be elucidated to improve long-term results of LVR.
Influence of Precursor Route on the Photoluminescence of Bulk Nanocrystalline Gallium Nitride (1997)

GaN derived from gallium imide, {Ga(NH)3/2}n, typically exhibits yellow defect photoluminescence, with the pyrolysis temperature influencing the intensity of the emission. Pyrolysis of this same precursor in relatively high boiling N,N,N‘,N‘-tetramethyl-1,6-hexanediamine yields blue photoluminescence with an emission maximum near 420 nm. In contrast, GaN derived from pyrolysis of gallazane precursors such as [H2GaNH2]3 yields blue light emission whose quantum yield can be improved by a brief HF etch.
Optimizations enabled by a decoupled front-end architecture (2001)

In the pursuit of instruction-level parallelism, significant demands are placed on a processor's instruction delivery mechanism. Delivering the performance necessary to meet future processor execution targets requires that the performance of the instruction delivery mechanism scale with the execution core. Attaining these targets is a challenging task due to I-cache misses, branch mispredictions, and taken branches in the instruction stream. To counter these challenges, we present a fetch architecture that decouples the branch predictor from the instruction fetch unit. A Fetch Target Queue (FTQ) is inserted between the branch predictor and instruction cache. This allows the branch predictor to run far in advance of the address currently being fetched by the cache. The decoupling enables a number of architecture optimizations, including multilevel branch predictor design, fetch-directed instruction prefetching, and easier pipelining of the instruction cache. For the multilevel predictor, we show that it performs better than a single-level predictor, even when ignoring the effects of cycle-timing issues. We also examine the performance of fetch-directed instruction prefetching using a multilevel branch predictor and show that an average 19 percent speedup is achieved. In addition, we examine pipelining the instruction cache to achieve a faster cycle time for the processor pipeline and show that pipelining provides an average 27 percent speedup over not pipelining the instruction cache for the programs examined.
Role of poly (A) tail as an identity element for mRNA nuclear export (2007)

Different RNA species are rigorously discriminated and exported by distinct export factors, but this discrimination mechanism remains largely unknown. We previously showed, by RNA microinjection experiments, that intronless mRNAs are discriminated from U snRNAs based on their difference in RNA length. However, it was unclear how they are discriminated in the natural situation in which their nascent transcripts emerge progressively during transcription. We hypothesized that transcription from the corresponding promoters is important for this discrimination. Here we show that contrary to our hypothesis, the discrimination process was not significantly influenced by whether transcription occurred from an mRNA- versus a U snRNA-type promoter. Rather, the features of transcribed RNAs determined the RNA identity, consistent with our previous results of RNA microinjection. Moreover, we found that the poly (A) tail can function as an identity element for mRNA export. The presence of a poly (A) tail of an appropriate length committed otherwise short Pol II transcripts to the mRNA export pathway in a dominant manner, indicating that the poly (A) tail either contributes to increasing the RNA length or functions as a platform to recruit mRNA export factors. Our results reveal a novel function of the poly (A) tail in mRNA export.
New Parts for a Construction Set of Bifunctional Oligo(het)arylene Building Blocks for Modular Chemistry (2000)

The 100 mg to 5 g scale synthesis of a variety of arylene (6, 11, 13) and hetarylene building blocks (15, 17, 18) by and for Suzuki/Stille type cross-coupling reactions is reported. These building blocks carry solubilizing hexyloxymethyl substituents as well as boronic acid ester and Br/I functionalities. This considerably widens the already existing construction set for the modular chemistry approach to shape persistent and functional compounds on the nanometer scale.
Peptide growth factors can provoke "fetal" contractile protein gene expression in rat cardiac myocytes. (1990)

Cardiac-specific gene expression is intricately regulated in response to developmental, hormonal, and hemodynamic stimuli. To test whether cardiac muscle might be a target for regulation by peptide growth factors, the effect of three growth factors on the actin and myosin gene families was investigated by Northern blot analysis in cultured neonatal rat cardiac myocytes. Transforming growth factor-beta 1 (TGF beta 1, 1 ng/ml) and basic fibroblast growth factor (FGF, 25 ng/ml) elicited changes corresponding to those induced by hemodynamic load. The "fetal" beta-myosin heavy chain (MHC) was up-regulated about four-fold, whereas the "adult" alpha MHC was inhibited greater than 50-60%; expression of alpha-skeletal actin increased approximately two-fold, with little or no change in alpha-cardiac actin. Thus, peptide growth factors alter the program of differentiated gene expression in cardiac myocytes, and are sufficient to provoke fetal contractile protein gene expression, characteristic of pressure-overload hypertrophy. Acidic FGF (25 ng/ml) produced seven- to eightfold reciprocal changes in MHC expression but, unlike either TGF-beta 1 or basic FGF, inhibited both striated alpha-actin genes by 70-90%. Expression of vascular smooth muscle alpha-actin, the earliest alpha-actin induced during cardiac myogenesis, was increased by all three growth factors. Thus, three alpha-actin genes demonstrate distinct responses to acidic vs. basic FGF.
COPPER-ZINC SUPEROXIDE DISMUTASE AND AMYOTROPHIC LATERAL SCLEROSIS (2003)

Copper-zinc superoxide dismutase (CuZnSOD, SOD1 protein) is an abundant copper- and zinc-containing protein that is present in the cytosol, nucleus, peroxisomes, and mitochondrial intermembrane space of human cells. Its primary function is to act as an antioxidant enzyme, lowering the steady-state concentration of superoxide, but when mutated, it can also cause disease. Over 100 different mutations have been identified in the sod1 genes of patients diagnosed with the familial form of amyotrophic lateral sclerosis (fALS). These mutations result in a highly diverse group of mutant proteins, some of them very similar to and others enormously different from wild-type SOD1. Despite their differences in properties, each member of this diverse set of mutant proteins causes the same clinical disease, presenting a challenge in formulating hypotheses as to what causes SOD1-associated fALS. In this review, we draw together and summarize information from many laboratories about the characteristics of the individual mutant SOD1 proteins in vivo and in vitro in the hope that it will aid investigators in their search for the cause(s) of SOD1-associated fALS.
The Power to Deliver: Trends in Smart Grid Solutions (2012)

Looking at the communication industry, one observes how drastically the communication horizon has changed. From letters to e-mails and SMS, from phone calls to video chat and live conferencing, from phone booths to smart phones: since the digitization of communication, a new era of consumer choice has been inaugurated. The potential exists for similar transformation and opportunity in the provision of electricity, embodied in a concept known as the “smart grid”. Smart grid is the electric delivery network from electrical generation to the end user that makes use of the latest advances in wireless communication and intelligent information management systems to ameliorate the electric system robustness, reliability, efficiency, and security. Like the telecommunications and the genesis of the Internet, technology holds the key to the smart grid and its realization.
Cell cycle and aging, morphogenesis, and response to stimuli genes are individualized biomarkers of glioblastoma progression and survival (2011)

Known biomarkers of glioblastoma survival were confirmed, and new general and clinical-dependent gene profiles were uncovered. The comparison of biomarkers across glioblastoma phases and functional analyses offered insights into the role of genes. These findings support the development of more accurate and personalized prognostic tools and gene-based therapies that improve the survival and quality of life of individuals afflicted by glioblastoma multiforme.
Extracellular Matrix-Associated Bone Morphogenetic Proteins Are Essential for Differentiation of Murine Osteoblastic Cells in Vitro (1999)

Osteoblastic differentiation is an essential part of bone formation that compensates resorbed bone matrix to maintain its structural integrity. Cells in an osteoblast lineage develop differentiated phenotypes during a long-term culture in vitro. However, intrinsic mechanisms whereby these cells differentiate into mature osteoblasts are yet unclear. Bone morphogenetic proteins (BMPs) stimulate osteoblastic differentiation and bone formation. We demonstrate that mouse osteoblastic MC3T3-E1 cells constitutively expressed messenger RNAs (mRNAs) for BMP-2 and BMP-4 and accumulated BMPs in collagen-rich extracellular matrices. BMPs associated with the extracellular matrices were involved in the induction of osteoblastic differentiation of nonosteogenic mesenchymal cells as well as cells in the osteoblast lineage. MC3T3-E1 cells constitutively expressed type IA and type II BMP receptors. When a kinase-deficient type IA BMP receptor was stably transfected to MC3T3-E1 cells to obliterate BMP-2/4 signaling, these cells not only failed to respond to exogenous BMP-2 but lost their capability of differentiation into osteoblasts that form mineralized nodules. These observations strongly suggest that endogenous BMP-2/4 accumulated in extracellular matrices are essential for the osteoblastic differentiation of cells in the osteoblast lineage. Therefore, the regulatory mechanism of BMP-2/4 actions in osteoblastic cells is a principal issue to be elucidated for better understanding of pathogenesis of bone losing diseases such as osteoporosis.
Frequently Methylated Tumor Suppressor Genes in Head and Neck Squamous Cell Carcinoma (2008)

Head and neck squamous cell carcinoma (HNSCC) is a very aggressive cancer. In advanced stages, the patient has poor chances of receiving effective treatment, and survival rates are low. To facilitate timely diagnosis and improve treatment, elucidation of early detection markers is crucial. DNA methylation markers are particularly advantageous because DNA methylation is an early event in tumorigenesis, and the epigenetic modification, 5-methylcytosine, is a stable mark. A genome-wide screen using Restriction Landmark Genomic Scanning found a set of genes that are most commonly methylated in head and neck cancers. Five candidate genes: septin 9 (SEPT9), sodium-coupled monocarboxylate transporter 1 (SLC5A8), functional smad-suppressing element on chromosome 18 (FUSSEL18), early B-cell factor 3 (EBF3), and iroquois homeobox 1 (IRX1) were methylated in 27% to 67% of the HNSCC patient samples tested. Furthermore, approximately 50% of the methylated tumor samples shared methylation between two of the five genes (most commonly between EBF3 and IRX1), and 15% shared methylation between three of the five genes. Expression analysis revealed candidate gene down-regulation in 25% to 93% of the HNSCC samples, and 5-aza-2'-deoxycytidine treatment was able to restore expression in at least 2 of 5 HNSCC cell lines for all of the genes tested. Overexpression of the three most frequently down-regulated candidates, SLC5A8, IRX1, and EBF3, validated their tumor suppressor potential by growth curve analysis and colony formation assay. Interestingly, all of the candidates identified may be involved in the transforming growth factor beta signaling pathway, which is often disrupted in HNSCC.
The essential Staphylococcus aureus gene fmhB is involved in the first step of peptidoglycan pentaglycine interpeptide formation (1999)

The factor catalyzing the first step in the synthesis of the characteristic pentaglycine interpeptide in Staphylococcus aureus peptidoglycan was found to be encoded by the essential gene fmhB. We have analyzed murein composition and structure synthesized when fmhB expression is reduced. The endogenous fmhB promoter was substituted with the xylose regulon from Staphylococcus xylosus, which allowed glucose-controlled repression of fmhB transcription. Repression of fmhB reduced growth and triggered a drastic accumulation of uncrosslinked, unmodified muropeptide monomer precursors at the expense of the oligomeric fraction, leading to a substantial decrease in overall peptidoglycan crosslinking. The composition of the predominant muropeptide was confirmed by MS to be N-acetylglucosamine-(beta-1,4)-N-acetylmuramic acid(-L-Ala-D-iGln-L-Lys-D-Ala-D-Ala), proving that FmhB is involved in the attachment of the first glycine to the pentaglycine interpeptide. This interpeptide plays an important role in crosslinking and stability of the S. aureus cell wall, acts as an anchor for cell wall-associated proteins, determinants of pathogenicity, and is essential for the expression of methicillin resistance. Any shortening of the pentaglycine side chain reduces or even abolishes methicillin resistance, as occurred with fmhB repression. Because of its key role FmhB is a potential target for novel antibacterial agents that could control the threat of emerging multiresistant S. aureus.
Geographical relation between Alzheimer's disease and aluminum in drinking water. (1989)

In a survey of eighty-eight county districts within England and Wales, rates of Alzheimer's disease in people under the age of 70 years were estimated from the records of the computerised tomographic (CT) scanning units that served these districts. Rates were adjusted to compensate for differences in distance from the nearest CT scanning unit and for differences in the size of the population served by the units. Aluminium concentrations in water over the past 10 years were obtained from water authorities and water companies. The risk of Alzheimer's disease was 1.5 times higher in districts where the mean aluminium concentration exceeded 0.11 mg/l than in districts where concentrations were less than 0.01 mg/l. There was no evidence of a relation between other causes of dementia, or epilepsy, and aluminium concentrations in water.
Reduction of Infarct Size and Prevention of Cardiac Rupture in Transgenic Mice Overexpressing FrzA (2003)

Overexpression of FrzA, through direct or indirect interaction with different phases of infarct healing, reduced infarct size and improved cardiac function.
Bipolar transistor action in ion implanted diamond (1982)

Using a natural type IIb diamond, which is p-type semiconducting, as a substrate material, and implanting this diamond with carbon ions to induce n-type regions, diode and bipolar transistor action could be obtained. Owing to the geometrical positions of the collector, base, and emitter, which in this case were lateral to the surface, very low current gain was obtained. However, the results indicate that an improvement in the geometry will probably lead to a diamond transistor of high gain.
Novel Oncogenic Protein Kinase Inhibitors for Cancer Therapy (2004)

Small-molecule drug discovery for cancer therapy is making extraordinary progress within the realm of advancing novel oncogenic protein kinase inhibitor lead compounds of significant impact to both basic research and clinical testing. In this perspective, structure- and mechanism-based drug design are highlighted relative to such progress. Also, evolving concepts in novel oncogenic protein kinase inhibitor drug discovery is highlighted relative to therapeutic target selectivity, including the recent identification of oncogenic kinase mutants effecting drug-resistance or enhanced drug susceptibility to small-molecule inhibitors.
Electroencephalographic Recovery, Hypnotic Emergence, and the Effects of Metabolite after Continuous Infusions of a Rapidly Metabolized Etomidate Analog in Rats (2012)

In rats, methoxycarbonyl etomidate metabolism is sufficiently fast to produce pharmacologically active MOC-ECA concentrations in the brain with prolonged methoxycarbonyl etomidate infusion.
First experience with endovascular ultrasound renal denervation for the treatment of resistant hypertension (2012)

Ultrasound renal denervation appears to be a safe and effective treatment for resistant hypertension and further studies will be performed to confirm these preliminary results.