gebhart/patrepeval huggingface dataset:
Regulation of a Catabolic Pathway (1972)

The regulation of the pathway responsible for l ‐lysine degradation in Pseudomonas putida has been studied. It has been shown that l ‐lysine is the actual inducer of the two first enzymes of the pathway, lysine oxygenase and 5‐aminovaleramidase. No important repression of lysine oxygenase by various carbon sources and by intermediates of the lysine degradation pathway has been found. Activation of lysine oxygenase by its substrate, lysine, has been observed. A physiological function for this phenomenom is proposed. Sodium and potassium ions are activators whereas magnesium ion, phosphate and phosphorylated compounds are inhibitors of lysine oxygenase. Citrate also is inhibitory.
A 24-week, randomized, controlled trial of rivastigmine patch 13.3 mg/24 h versus 4.6 mg/24 h in severe Alzheimer's dementia (2013)

Summary

Aims

The 24-week, prospective, randomized, double-blind ACTION study investigated the efficacy, safety, and tolerability of 13.3 versus 4.6 mg/24 h rivastigmine patch in patients with severe Alzheimer's disease (AD).



Methods

Patients had probable AD and Mini–Mental State Examination scores ≥3–≤12. Primary outcome measures were as follows: Severe Impairment Battery (SIB) and AD Cooperative Study–Activities of Daily Living scale–Severe Impairment Version (ADCS-ADL-SIV). Secondary outcomes were as follows: ADCS-Clinical Global Impression of Change (ADCS-CGIC), 12-item Neuropsychiatric Inventory (NPI-12), and safety/tolerability.



Results

Of 1014 patients screened, 716 were randomized to 13.3 mg/24 h (N = 356) or 4.6 mg/24 h (N = 360) patch. Baseline characteristics/demographics were comparable. Completion rates were as follows: 64.3% (N = 229) with 13.3 mg/24 h and 65.0% (N = 234) with 4.6 mg/24 h patch. The 13.3 mg/24 h patch was significantly superior to 4.6 mg/24 h patch on cognition (SIB) and function (ADCS-ADL-SIV) at Week 16 (P < 0.0001 and P = 0.049, respectively) and 24 (primary endpoint; P < 0.0001 and P = 0.025). Significant between-group differences (Week 24) were observed on the ADCS-CGIC (P = 0.0023), not NPI-12 (P = 0.1437). A similar proportion of the 13.3 mg/24 h and 4.6 mg/24 h patch groups reported adverse events (AEs; 74.6% and 73.3%, respectively) and serious AEs (14.9% and 13.6%).



Conclusions

The 13.3 mg/24 h patch demonstrated superior efficacy to 4.6 mg/24 h patch on SIB and ADCS-ADL-SIV, without marked increase in AEs, suggesting higher-dose patch has a favorable benefit-to-risk profile in severe AD.
Inhibition of cardiac HERG currents by the DNA topoisomerase II inhibitor amsacrine: mode of action (2004)

1 The topoisomerase II inhibitor amsacrine is used in the treatment of acute myelogenous leukemia. Although most anticancer drugs are believed not to cause acquired long QT syndrome (LQTS), concerns have been raised by reports of QT interval prolongation, ventricular fibrillation and death associated with amsacrine treatment. Since blockade of cardiac human ether-a-go-go-related gene (HERG) potassium currents is an important cause of acquired LQTS, we investigated the acute effects of amsacrine on cloned HERG channels to determine the electrophysiological basis for its proarrhythmic potential. 2 HERG channels were heterologously expressed in human HEK 293 cells and Xenopus laevis oocytes, and the respective potassium currents were recorded using patch-clamp and two-microelectrode voltage-clamp electrophysiology. 3 Amsacrine blocked HERG currents in HEK 293 cells and Xenopus oocytes in a concentration-dependent manner, with IC50 values of 209.4 nm and 2.0 microm, respectively. 4 HERG channels were primarily blocked in the open and inactivated states, and no additional voltage dependence was observed. Amsacrine caused a negative shift in the voltage dependence of both activation (-7.6 mV) and inactivation (-7.6 mV). HERG current block by amsacrine was not frequency dependent. 5 The S6 domain mutations Y652A and F656A attenuated (Y652A) or abolished (F656A, Y652A/F656A) HERG current blockade, indicating that amsacrine binding requires a common drug receptor within the pore-S6 region. 6 In conclusion, these data demonstrate that the anticancer drug amsacrine is an antagonist of cloned HERG potassium channels, providing a molecular mechanism for the previously reported QTc interval prolongation during clinical administration of amsacrine.
High-Reflectivity Semiconductor/Benzocyclobutene Bragg Reflector Mirrors for GaInAsP/InP Lasers (2001)

Fabrication techniques of high-reflectivity deeply etched semiconductor/benzocyclobutene (BCB) Bragg reflectors by multiple sequential steps of CH 4 /H 2 reactive ion etching (RIE) and O 2 plasma ashing are presented. 1.55-µm-wavelength GaInAsP/InP lasers with such reflectors exhibited low threshold current and high differential quantum efficiency with high uniformity. Threshold current as low as 7.2 mA and differential quantum efficiency as high as 50% from the front cleaved facet were obtained for a laser with a 160-µm-long active region and 15 distributed Bragg reflectors (DBRs) on the rear side. The reflectivity of the 15 DBRs was estimated to be as high as 95% from the threshold current dependence on the active region length. Finally, a preliminary aging test under room temperature CW conditions showed stable operation for more than 5000 h.
Explosion-induced damage to oilwell perforating gun carriers (2006)

We present an overview of damage to oilwell perforating gun carrier tubes. Gun carriers are sealed hollow steel tubes, used to convey multiple small shaped explosive charges down a wellbore to the vicinity of a hydrocarbon reservoir, isolating the charges from the wellbore fluid and pressure. At the prescribed time and location the charges are detonated, producing perforation tunnels into the reservoir and allowing subsequent hydrocarbon flow into the wellbore and uphole to surface facilities.
Experimental Bacterial Mastitis In The Mouse (1970)

SUMMARY A simple technique was developed for the intramammary inoculation of mice. Experimental mastitis was produced in lactating mice with strains of Staphylococcus aureus, Streptococcus agalactiae, Corynebacterium pyogenes, Pseudomonas aeruginosa and Escherichia coli that had originally been isolated from cases of bovine mastitis. There was evidence that the spectrum of pathogenicity of the different bacterial strains in the bovine species was to some extent paralleled by differences in pathogenicity in the mouse. Mastitis could be produced in BSVS mice by the inoculation of comparatively small numbers of staphylococci. The appearance and histology of the affected mammary glands resembled mastitis produced in the bovine species by the bacterial species concerned. The size of the mouse mammary gland was very convenient for histological and other studies requiring examination of the whole gland. Experimental mastitis in the mouse provides a useful model for certain fundamental studies and for experiments, such as those of a screening nature, prior to studies on cattle.
A rapid destruction-free determination of breakdown voltage of thin insulating layers (1978)

A constant current source is used to load an MOS capacitor. This procedure permits a simple, fast and destruction-free determination of the primary breakdown voltage, Ubr. The application range and limitations are shown by comparing C–U curves before and after Ubr measurements. Polarity, temperature, and material type effects are discussed. I–U characteristics obtained with this technique coincide with voltage controlled ones up to the breakdown point of the latter technique. In this technique, the accessible I–U characteristics range can be expanded by more than a factor of 10 with respect to the current compared to the values at the conventional breakdown point. Ubr and degradation time histograms of thermal and pyrolytic oxides with varying content of trichloroethylene are shown. An example taken from these samples demonstrates the usefulness of the technique for process control. Breakdown voltage determination can be accelerated by more than a factor of 10. Eine Konstantstromquelle wird benutzt, um eine MOS-Kapazität zu laden. Dieses Verfahren erlaubt eine einfache, schnelle und zerstörungsfreie Bestimmung der primären Durchbruchspannung Ubr. Der Anwendungsbereich und die Grenzen werden gezeigt, indem C–U-Kurven vor und nach Ubr-Messungen verglichen werden. Effekte von Polarität, Temperatur und des Materials werden erörtert. Bis zum Durchbruchspunkt der spannungsangesteuerten Methode stimmen die I–U-Kennlinien sowohl der stromangesteuerten als auch der spannungsangesteuerten Methoden überein. Bei der hier gezeigten Methode kann die meßbare Kennlinie bezüglich des Stromes um einen Faktor 10 erweitert werden im Vergleich zu den Werten des üblich definierten Durchbruchs. Ubr- und Abbruchszeitenhistogramme von thermischen und pyrolytischen Oxiden mit unterschiedlichem Trichloräthylengehalt werden gezeigt. Ein aus diesen Proben gewähltes Beispiel zeigt die Nützlichkeit der Methode für die Prozeßkontrolle. Die Bestimmung der Durchbruchsspannungen kann um mehr als einen Faktor 10 beschleunigt werden.
Formate Dehydrogenase (FDH1) Localizes to Both Mitochondria and Chloroplast to Play a Role in Host and Nonhost Disease Resistance (2020)

Nonhost disease resistance is the most common type of plant defense mechanism against potential pathogens. In this study, the metabolic enzyme formate dehydrogenase (FDH1) was identified to be involved in nonhost disease resistance in Nicotiana benthamiana and Arabidopsis thaliana. In Arabidopsis, AtFDH1 was highly upregulated in response to both host and nonhost bacterial pathogens. Arabidopsis Atfdh1 mutants were compromised in nonhost resistance, basal resistance, and gene-for-gene resistance. The expression patterns of salicylic acid (SA) and jasmonic acid (JA) marker genes after pathogen infections in Atfdh1 mutant indicated that SA is most likely involved in the FDH1-mediated plant defense response to both host and nonhost bacterial pathogens. Previous studies reported that FDH1 localizes to only mitochondria, or both mitochondria and chloroplasts. Our results showed that the AtFDH1 localized to mitochondria and the amount of FDH1 localized to mitochondria increased upon infection with host or nonhost pathogens. Interestingly, the subcellular localization of FDH1 was observed in both mitochondria and chloroplasts after infection with a nonhost pathogen in Arabidopsis. We speculate that FDH1 plays a role in cellular signaling networks between mitochondria and chloroplasts to produce coordinated defense responses such as SA-induced reactive oxygen species (ROS) generation and hypersensitive response (HR)-induced cell death against nonhost bacterial pathogens.
Expression of the herpes simplex virus 1 alpha transinducing factor (VP16) does not induce reactivation of latent virus or prevent the establishment of latency in mice (1991)

A feature of the cascade regulation of herpes simplex virus 1 gene expression in productive infection is that the first genes to be expressed, the alpha genes, are transactivated by a structural component of the virion designated as the alpha transinducing factor (alpha TIF). In this study, we have tested the hypothesis that latent infection of sensory neurons results from the failure of alpha TIF, a tegument protein, to be transported from the nerve endings to the nucleus of the sensory neuron. Two viruses were constructed. The first recombinant virus (R6003) contained a second copy of the alpha TIF gene placed under the control of a metallothionein promoter. The second recombinant virus (R6004) is identical to R6003 except for the presence of a stop codon inserted at amino acid 70 of the second alpha TIF gene. The metallothionein promoter inserted into the viral genome was shown to be expressed, and alpha TIF mRNA was detected by in situ hybridization of sections of trigeminal ganglia of mice infected with R6003, both untreated and those given cadmium injections. In all experiments, there were no significant differences in the recovery of latent virus from mice infected with R6003 or R6004, whether injected with cadmium or not. Cadmium administration at the time of infection and at intervals thereafter did not preclude establishment of latency. In another series of experiments, transgenic mice expressing the metallothionein-driven alpha TIF did not differ from nontransgenic siblings with respect to the incidence of latent virus in trigeminal ganglia. We conclude that the absence of alpha TIF cannot alone account for the establishment of latency.
Enhanced nonlinear imaging through scattering media using transmission-matrix-based wave-front shaping (2016)

A method is proposed to optimize signals in nonlinear microscopy in order to circumvent difficulties associated with scattering media. In comparison to traditional nonlinear optimization techniques, the obtained results show a faster and more efficient imaging capability.
Whole Slide Imaging Versus Microscopy for Primary Diagnosis in Surgical Pathology (2017)

Most prior studies of primary diagnosis in surgical pathology using whole slide imaging (WSI) versus microscopy have focused on specific organ systems or included relatively few cases. The objective of this study was to demonstrate that WSI is noninferior to microscopy for primary diagnosis in surgical pathology. A blinded randomized noninferiority study was conducted across the entire range of surgical pathology cases (biopsies and resections, including hematoxylin and eosin, immunohistochemistry, and special stains) from 4 institutions using the original sign-out diagnosis (baseline diagnosis) as the reference standard. Cases were scanned, converted to WSI and randomized. Sixteen pathologists interpreted cases by microscopy or WSI, followed by a wash-out period of ≥4 weeks, after which cases were read by the same observers using the other modality. Major discordances were identified by an adjudication panel, and the differences between major discordance rates for both microscopy (against the reference standard) and WSI (against the reference standard) were calculated. A total of 1992 cases were included, resulting in 15,925 reads. The major discordance rate with the reference standard diagnosis was 4.9% for WSI and 4.6% for microscopy. The difference between major discordance rates for microscopy and WSI was 0.4% (95% confidence interval, -0.30% to 1.01%). The difference in major discordance rates for WSI and microscopy was highest in endocrine pathology (1.8%), neoplastic kidney pathology (1.5%), urinary bladder pathology (1.3%), and gynecologic pathology (1.2%). Detailed analysis of these cases revealed no instances where interpretation by WSI was consistently inaccurate compared with microscopy for multiple observers. We conclude that WSI is noninferior to microscopy for primary diagnosis in surgical pathology, including biopsies and resections stained with hematoxylin and eosin, immunohistochemistry and special stains. This conclusion is valid across a wide variety of organ systems and specimen types.
Ultrafast Photoconductive Switches with a Gap of 43 nm Fabricated by an Atomic Force Microscope (1997)

Photoconductive switches with a gap of 43 nm have been fabricated by using an atomic force microscope. Ultrafast response of the switches have been measured by electrooptic sampling method. Intrinsic response of the switch has been estimated as 210 fs by extrapolation of impulse response at zero distance.
Polycystic kidney disease and the renal cilium (Review Article) (2007)

Polycystic kidney disease (PKD) is a common genetic condition characterized by the formation of fluid-filled cysts in the kidney. Mutations affecting several genes are known to cause PKD and the protein products of most of these genes localize to an organelle called the renal cilium. Renal cilia are non-motile, microtubule-based projections located on the apical surface of the epithelial cells that form the tubules and ducts of the kidney. With the exception of intercalated cells, each epithelial cell bears a single non-motile cilium that projects into the luminal space where it is thought to act as a flow sensor. The detection of fluid flow through the kidney by the renal cilium is hypothesized to regulate a number of pathways responsible for the maintenance of normal epithelial phenotype. Defects of the renal cilium lead to cyst formation, caused primarily by the dedifferentiation and over-proliferation of epithelial cells. Here we discuss the role of renal cilia and the mechanisms by which defects of this organelle are thought to lead to PKD.
Nonlinear Optics of Organic and Polymer Materials (1994)

Over the past decade the study of nonlinear optical processes in organic and polymer systems has enjoyed rapid and sustained growth. One indication of that growth is the increase in the number of articles published inrefereed society journals. The four-year period 1980–83 saw the publication of 124 such articles. For the four-year period a decade later the production of articles in the field had grown to 736—nearly a sixfold increase. In part, the rapid growth of the field can be attributed to the technological promise and interesting physical properties of these materials. Because of their large optical nonlinearities and mechanical, chemical, thermal and optical stability, organic nonlinear optical materials are the leading practical materials for fabricating optoelectronic devices. They also have proven to be excellent subjects in which to study many-body electron correlation effects and exotic states like polarons, excitons and even coherently propagating multiexciton strings.
A 9keV electron-impact liquid-gallium-jet x-ray source (2008)

We demonstrate a high-brightness compact 9 keV electron-impact microfocus x-ray source based on a liquid-gallium-jet anode. A approximately 30 W, 50 kV electron gun is focused onto the approximately 20 ms, 30 mum diameter liquid-gallium-jet anode to produce an approximately 10 microm full width at half maximum x-ray spot. The peak spectral brightness is >2 x 10(10) photons(s mm(2) mrad(2)x0.1% BW). Calculation and experiments show potential for increasing this brightness by approximately three orders of magnitude, making the source suitable for laboratory-scale x-ray crystallography and hard x-ray microscopy.
PredictCBC-2.0: a contralateral breast cancer risk prediction model developed and validated in ~200,000 patients (2022)

Abstract Background: Prediction of contralateral breast cancer (CBC) risk is challenging due to moderate performances of the known risk factors. We aimed to improve our previous risk prediction model (PredictCBC) by updated follow-up and including additional risk factors. Methods: We included data from 207,510 invasive breast cancer patients participating in 23 studies. 8,225 CBC events occurred over a median follow-up of 10.2 years. In addition to the previously included risk factors, PredictCBC-2.0 included CHEK2 c.1100delC, a 313 variant polygenic risk score (PRS-313), body mass index (BMI), and parity. Fine and Gray regression was used to fit the model. Calibration and a time-dependent Area Under the Curve (AUC) at 5 and 10 years were assessed to determine the performance of the models. Decision curve analysis was performed to evaluate the net benefit of PredictCBC-2.0 and previous PredictCBC models. Results: The discrimination of PredictCBC-2.0 at 10 years was higher than PredictCBC with an AUC of 0.65 (95% prediction intervals (PI):0.56–0.74) versus 0.63 (95%PI:0.54–0.71). PredictCBC-2.0 was well-calibrated with an observed/expected (O/E) ratio at 10 years of 0.92 (95%PI:0.34–2.54). Decision curve analysis for contralateral preventive mastectomy (CPM) showed potential clinical utility of PredictCBC-2.0 between thresholds of 4–12% 10-year CBC risk for BRCA1/2 mutation carriers and non-carriers. Conclusions: Additional genetic information beyond BRCA1/2 germline mutations improved CBC risk prediction and might help tailor clinical decision making towards CPM or alternative preventive strategies. Identifying patients who benefit from CPM, especially in the general breast cancer population, remains challenging.
Behavior of Titanium Exposed to Fresh and Spent Dilute HF Acid Well Stimulation Fluids (2018)

Abstract Increasing interest in utilizing hydrofluoric acid (HF) for acid stimulation of offshore wells to improve hydrocarbon productivity has raised acid compatibility concerns with titanium alloy riser system components such as Titanium Stress Joints (TSJs). Recent published lab test findings by the authors1,2 confirmed that UNS R564041 Titanium exposure to warm, naturally-aerated, dilute, HF-containing, fresh acid mixtures does result in unacceptable, elevated etch rates, which dramatically increase with temperature and/or acid concentration. These lab studies, however, also revealed that several common inorganic salts such as aluminum, molybdate, and/or borate salts, can effectively inhibit this attack if added in sufficient molar ratios to free fluoride in these fluids. Corrosion of titanium in these well stimulation acids may also induce significant absorption and/or penetration of byproduct hydrogen, raising additional concern for hydrogen damage to a stressed component if not properly inhibited. Continued lab acid testing of UNS R56404(1) and UNS R56407 titanium coupons confirms that substantial hydrogen uptake and microstructure-dependent penetration can occur during severe HF-containing acid etching. Primary influencing factors are identified from assessment of the effects of CO2 gas saturation; acid formulation, pH, and temperature; fluid flow; and fresh versus spent acid condition; and are considered with respect to inorganic salt inhibitor effectiveness.
Fast search algorithms for ECVQ using projection pyramids and variance of codewords (2004)

Vector quantization for image compression requires expensive time to find the closest codeword through the codebook. Codebook design based on empirical data for entropy-constrained vector quantization (ECVQ) involves a time consuming training phase in which a Lagrangian cost measure has to be minimized over the set of codebook vectors. In this paper, we propose two fast codebook generation methods for ECVQ. In the first one, we use an appropriate topological structure of input vectors and codewords to reject many codewords that are impossible to be candidates for the best codeword. In the second method, we use the variance test to increase the ability of the first algorithm to reject more codewords. These algorithms allow significant acceleration in the codebook design process. Experimental results are presented on image block data. These results show that our algorithms perform better than the previously known methods.