gebhart/patrepeval huggingface dataset:
Radiation-Induced Formation of 2′,3′-Dideoxyribonucleosides in DNA: A Potential Signature of Low-Energy Electrons (2012)

We have identified a series of modifications of the 2'-deoxyribose moiety of DNA arising from the exposure of isolated and cellular DNA to ionizing radiation. The modifications consist of 2',3'-dideoxyribonucleoside derivatives of T, C, A, and G, as identified by enzymatic digestion and LC-MS/MS. Under dry conditions, the yield of these products was 6- to 44-fold lower than the yield of 8-oxo-7,8-dihydroguanine. We propose that 2',3'-dideoxyribonucleosides are generated from the reaction of low-energy electrons with DNA, leading to cleavage of the C3'-O bond and formation of the corresponding C3'-deoxyribose radical.
1954. In vivo Efficacy of Delayed Therapy with the Novel Inositol Acyltransferase Inhibitor Fosmanogepix (APX001) in a Murine Model of Candida auris Invasive Candidiasis (2019)

Abstract Background Candida auris is an emerging pathogen associated with antifungal resistance and high mortality. The novel antifungal manogepix (APX001A) prevents glycosylphosphatidylinositol-anchored protein maturation through inhibition of the inositol acyltransferase Gwt1 enzyme, and has demonstrated in vitro and in vivo activity against numerous pathogenic fungi, including C. auris. We evaluated the efficacy of the prodrug fosmanogepix (APX001) following delayed initiation of therapy in a murine model of C. auris invasive candidiasis. Methods Neutropenic outbred mice (10 per cohort) were inoculated intravenously with C. auris (minimum inhibitory concentrations [MICs]: manogepix 0.03 mg/mL, fluconazole &gt;64 mg/mL, caspofungin 0.25 mg/mL).Treatment with placebo, fosmanogepix (104 or 130 mg/kg by intraperitoneal injection [IP] three times daily, or 260 mg/kg IP twice daily), fluconazole (20 mg/kg/day orally), or caspofungin (10 mg/kg/day IP) began 1 day later and continued for 7 days. Mice were followed post therapy until day 21 to assess survival. Kidneys and brains were collected on day 8, on the days that mice succumbed to infection, or on day 21. Fungal burden was assessed by colony-forming units (CFU). Results Survival was significantly improved at each dose level of fosmanogepix (median &gt;21 days; 90–100%) and high dose caspofungin (&gt;21 days; 90%) compared with placebo (5 days; 10%; P &lt; 0.0001). On day 8 post-inoculation, kidney and brain fungal burdens were significantly reduced in mice treated with fosmanogepix 260 mg/kg BID compared with placebo and in kidneys of mice treated with caspofungin (Table 1). In the survival arm, fungal burden in kidneys and brains was significantly lower at each dose level of fosmanogepix and with high dose caspofungin compared with placebo. In contrast, no improvements in survival or reductions in fungal burden were observed with fluconazole. Conclusion Fosmanogepix demonstrated potent in vivo activity against invasive candidiasis caused by C. auris even with delayed initiation of treatment. Improvements in both survival and reductions in fungal burden within the kidneys and brains were observed. These data demonstrate the potential utility of fosmanogepix against C. auris infections. Disclosures All Authors: No reported Disclosures.
Investigations on the balloon as an impulse source (2011)

Measurements of impulses produced by bursting balloons are presented. Various sizes of balloons were popped with a mechanical device in an anechoic chamber and recorded with a spherical microphone array. The power responses and directivity of the balloons are analyzed. Results indicate that power responses have two emphasized frequencies which depend on balloon size and inflation level. Larger balloons radiated more energy and higher inflation levels resulted in stronger high frequency content. Balloon directivity patterns are stable over repetitions. However, balloons do not radiate omnidirectionally. The degree of omnidirectionality improves with balloon size and for midrange frequencies.
Exercise haemodynamics and outcome in patients with dyspnoea (2014)

This editorial refers to ‘Pulmonary capillary wedge pressure during exercise and long-term mortality in patients with suspected heart failure and preserved ejection fraction’[†][1], by S. Dorfs et al. , on page 3103. 

Exercise is the most commonly encountered physiological stress in everyday life. In order for the cardiovascular system to provide up to 5-fold increases in cardiac output with exertion, there must be substantial increases in heart rate and stroke volume.1 Stroke volume enhancement is achieved through decreases in left ventricular (LV) end-systolic volume coupled with increases in LV end-diastolic volume, the latter being mediated by increased venous return and enhanced diastolic suction in the setting of a normally compliant ventricle. The fact that the left ventricle can fill to a larger diastolic volume in a shorter period of time during exercise without increasing filling pressures is an awe-inspiring testament to the remarkable diastolic reserve capacity of the normal heart.2

In people with heart failure (HF), this diastolic ventricular reserve is exhausted.3–5 Haemodynamically, HF is defined as an inability of the heart to pump blood to the body at a rate commensurate with its needs, or to do so only at the cost of high pulmonary capillary wedge pressures (PCWPs).6 These haemodynamic derangements are expressed clinically as symptoms of exercise intolerance, dyspnoea, and fatigue. These are the cardinal symptoms of HF, but they can also be caused by non-cardiovascular aetiologies. The presence of elevated PCWP in a patient with typical symptoms and normal ejection fraction (EF) is diagnostic of HF with preserved EF (HFpEF).7 However, the absence of high PCWP at rest does not exclude …

 [1]: #fn-2
High-resolution X-ray crystal structure of bovine H-protein using the high-pressure cryocooling method (2013)

Recently, many technical improvements in macromolecular X-ray crystallography have increased the number of structures deposited in the Protein Data Bank and improved the resolution limit of protein structures. Almost all high-resolution structures have been determined using a synchrotron radiation source in conjunction with cryocooling techniques, which are required in order to minimize radiation damage. However, optimization of cryoprotectant conditions is a time-consuming and difficult step. To overcome this problem, the high-pressure cryocooling method was developed (Kim et al., 2005) and successfully applied to many protein-structure analyses. In this report, using the high-pressure cryocooling method, the X-ray crystal structure of bovine H-protein was determined at 0.86 Å resolution. Structural comparisons between high- and ambient-pressure cryocooled crystals at ultra-high resolution illustrate the versatility of this technique. This is the first ultra-high-resolution X-ray structure obtained using the high-pressure cryocooling method.
The Laboratory Infection of Triatoma neotomae Neiva with Trypanosoma cruzi Chagas and Subsequent Transmission to White Mice (1948)

Additions are constantly being made to the list of REDUVIIDAE from the United States which are either naturally infected, or can be infected under laboratory conditions with Trypanosoma cruzi Chagas.2 Kofoid and McCulloch (1916) were the first to report the discovery of a trypanosome in the digestive tract of a cone-nosed bug from the United States, Triatoma protracta Uhler, collected near San Diego, California. Subsequently Kofoid and Donat (1933) experimentally transmitted the infection from this species to the probable mammal reservoir, the wood rat (Neotoma sp.), while F. D. Wood (1934) experimentally infected many other species of mammals with cruzi from T. protracta Uhler collected from the same area. Kofoid and Whitaker (1936) found T. uhleri Neiva collected near Tucson, Arizona, naturally infected with cruzi, and experimentally transmitted the infection by inoculation to the white-footed mouse (Peromyscus sp.). Wood and Wood (1938) collected specimens of T. protracta Uhler and T. uhleri Neiva in Arizona, New Mexico, Texas, and Utah, but none was found to be naturally infected. Specimens of both species, however, were experimentally infected in the laboratory by feeding on mice infected with cruzi. Uninfected T. sanguisuga ambigua Neiva from Florida were experimentally infected by Packchanian (1940) by feeding on laboratory animals infected with cruzi, the trypanosomes from the insects establishing an infection when injected into uninfected mammals. Following this, Davis, McGregor, and de Shazo (1943) working in Texas found naturally infected T. sanguisuga (Le Conte) and T. ambigua Neiva (T. sanguisuga ambigua Neiva of Usinger (1944)) and succeeded in transmitting the infection to laboratory animals. T. gerstaeckeri (Stal) and T. heidemanni Neiva (T. lecticularius Stal of Usinger (1944)) from various regions of Texas have also been found to harbor natural infections of cruzi which can be successfully transmitted to laboratory animals (Packchanian, 1939, 1940a). In addition, material from a naturally infected T. heidemanni Neiva(T. lecticularius Stal) has been used to establish a typical case of Chagas' disease in an adult male volunteer (Packchanian, 1943). Wood (1941) reported for the first time natural infections with cruzi of T. longipes Barber from Arizona and T. protracta woodi Usinger from Texas, as well as a new locality in Texas for naturally infected T. gerstaeckeri (Stal). One specimen of T. indictiva (Neiva) from Texas was experimentally infected by him. Wood
Data from An Empirical Approach Leveraging Tumorgrafts to Dissect the Tumor Microenvironment in Renal Cell Carcinoma Identifies Missing Link to Prognostic Inflammatory Factors (2023)

&lt;div&gt;Abstract&lt;p&gt;By leveraging tumorgraft (patient-derived xenograft) RNA-sequencing data, we developed an empirical approach, DisHet, to dissect the tumor microenvironment (eTME). We found that 65% of previously defined immune signature genes are not abundantly expressed in renal cell carcinoma (RCC) and identified 610 novel immune/stromal transcripts. Using eTME, genomics, pathology, and medical record data involving &gt;1,000 patients, we established an inflamed pan-RCC subtype (IS) enriched for regulatory T cells, natural killer cells, T&lt;sub&gt;H&lt;/sub&gt;1 cells, neutrophils, macrophages, B cells, and CD8&lt;sup&gt;+&lt;/sup&gt; T cells. IS is enriched for aggressive RCCs, including &lt;i&gt;BAP1&lt;/i&gt;-deficient clear-cell and type 2 papillary tumors. The IS subtype correlated with systemic manifestations of inflammation such as thrombocytosis and anemia, which are enigmatic predictors of poor prognosis. Furthermore, IS was a strong predictor of poor survival. Our analyses suggest that tumor cells drive the stromal immune response. These data provide a missing link between tumor cells, the TME, and systemic factors.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Significance:&lt;/b&gt; We undertook a novel empirical approach to dissect the renal cell carcinoma TME by leveraging tumorgrafts. The dissection and downstream analyses uncovered missing links between tumor cells, the TME, systemic manifestations of inflammation, and poor prognosis. &lt;i&gt;Cancer Discov; 8(9); 1142–55. ©2018 AACR.&lt;/i&gt;&lt;/p&gt;&lt;p&gt;&lt;i&gt;This article is highlighted in the In This Issue feature, p. 1047&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Effects of Hydrogen on the Vacancy Formation in Magnesium (2007)

Quenching and annealing experiments with electric resistivity measurements were applied to magnesium to investigate the formation of thermal vacancies. Two specimens made from materials differing in impurity contents were examined. One of the specimens that was quenched into a methanol bath at -80°C from elevated temperatures ranging from 160 to 500°C revealed a significant decrease in electrical resistance during subsequent annealing for ten minutes in the bath. This decrease is attributed to the presence of hydrogen in solution, on the basis of annealing behaviors at low temperatures (-100~-60°C) after the quenching from 200°C. Another specimen, presumably containing smaller amounts of hydrogen, was quenched into iced water from elevated temperatures (200~560°C), which yielded results characterized by two thermal activation processes. These processes have the activation energies, 54.1 kJ/mol (0.56 eV) and 89.8 kJ/mol (0.93 eV) for lower and higher quenching temperature range, respectively. The former is ascribed to the formation energy of a vacancy interacting with hydrogen and the latter the intrinsic formation energy of a vacancy. The difference of these energies, namely 35.7 kJ/mol (0.37 eV), can be identified as the binding energy between a vacancy and a hydrogen atom.
Compact image coding from edges with wavelets (1991)

A second generation image coding algorithm based on multiscale edges is described. Edges are detected from the local maxima of the image wavelet transform. The original image can be reconstructed from the corresponding multiscale edge map. For coding purposes, the edges that are important for the image visualization are selected, and an efficient encoding of the corresponding data is described. High compression ratio can be obtained for images where the texture information is not important. Examples with compression ratios of around 30 are given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
De‐intercalation process from Stage‐1 to Stage‐2 graphite intercalation compounds revisited (2012)

Abstract The identification and contribution of the different phonons present in the G‐line Raman response in Stage ‐1 and Stage ‐2 graphite intercalation compounds (GIC) is crucial for a correct stage determination. Different factors like laser induced de‐intercalation play an important role in the precise stage assignment of these phases, and their intrinsic Raman response. In this contribution, an in situ micro‐Raman analysis was conducted under high‐vacuum conditions. Local heating of the samples was induced by using a high laser power (8.5 mW) in order to study the de‐intercalation process from Stage ‐1 to Stage ‐2 GICs. A detailed Raman line‐shape analysis was performed from the recorded spectra to determine the changes from the G‐line response of KC 8 , CaC 6 , and LiC 6 . We confirmed the assignment of the broad E 2 g Fano mode at ∼1510 cm −1 to the intrinsic Stage ‐1 Raman response in GICs. Additionally, the most evident change from Stage ‐1 to Stage ‐2 was observed in an asymmetric Fano mode in the range of 1565–1610 cm −1 . This mode is linked to the first‐order stretching Raman mode of Graphite, which tends to increase in frequency and decrease in width as function of de‐intercalation. Finally, the response of the Stage ‐2 phase after de‐intercalation was confirmed to be a useful benchmark for the identification of the intercalation stage in highly doped GICs.
Comparison of Camera Quality Indexes (2000)

In terms of correlation to the spectral data base SOCS (Standard Object Colour Spectra Database for Colour Reproduction Evaluation), computer simulation was employed to compare five camera quality indexes: CQF (Color Quality Factor) from Neugebauer, Goodness from Vora and Trusell, Squared Difference from ISO 17321 WD1.1, RMS (Root Mean Square) from ISO17321 WD4, and Camera Rendering Indexes (Ra: Average CRI, and Ri: Special CRI) from Hung. Based on the assumption that SOCS encompasses the spectral reflectance of real objects, SOCS was used to simulate real-world spectra. To avoid the disputed population problem of spectral reflectance in SOCS, we used color differences (&#x394;E*ab) containing 95.5%, 99.7%, and 100% (i.e. worst &#x394;E*) of the SOCS data, as well as a simple average, as references. Applied to thirteen sets of camera sensitivities, Average CRI gave correlation coefficients of greater than 0.95 against 95.5%, 99.7%, and average &#x394;E*, and Special CRI gave the best correlation coefficient with the worst &#x394;E* among these quality indexes. Thus, Average CRI appears to be a good index for the evaluation of a camera's colorimetric quality.
A fast, complete, point cloud based loop closure for LiDAR odometry and mapping (2019)

This paper presents a loop closure method to correct the long-term drift in LiDAR odometry and mapping (LOAM). Our proposed method computes the 2D histogram of keyframes, a local map patch, and uses the normalized cross-correlation of the 2D histograms as the similarity metric between the current keyframe and those in the map. We show that this method is fast, invariant to rotation, and produces reliable and accurate loop detection. The proposed method is implemented with careful engineering and integrated into the LOAM algorithm, forming a complete and practical system ready to use. To benefit the community by serving a benchmark for loop closure, the entire system is made open source on Github
Wake effects on lifetime distribution in DFIG-based wind farms (2017)

With the increasing size of the wind farms, the impact of the wake effect on the energy yields and lifetime consumption of wind turbine can no longer be neglected. In this paper, the affecting factors like the wind speed and wind direction are investigated in terms of the single wake and multiple wakes. As the power converter is the most fragile component among the turbine system, its lifetime estimation can be calculated seen from the thermal stress of the power semiconductor. On the basis of the relationship of the power converter in a 5 MW Doubly-Fed Induction Generator (DFIG) wind turbine system and the wind speed, the lifetime consumption of the individual turbine in a 10-turbine and an 80-turbine wind farms can be calculated by considering the real distributions of the wind speed and direction. It can be seen that there is significant lifetime difference among individual turbines, and it guides to the optimized control strategies for the balanced reliability.
Rac1 mediates STAT3 activation by autocrine IL-6 (2001)

The activity of the small GTPase, Rac1, plays a role in various cellular processes including cytoskeletal rearrangement, gene transcription, and malignant transformation. In this report constitutively active Rac1 (Rac V12) is shown to stimulate the activation of STAT3, a member of the family of signal transducers and activators of transcription (STATs). The activity of Rac1 leads to STAT3 translocation to the nucleus coincident with STAT3-dependent gene expression. The expression of Vav (Delta1-187), a constitutively active guanine nucleotide exchange factor for the Rho GTPases, or activated forms of Ras or Rho family members, leads to STAT3-specific activation. The activation of STAT3 requires tyrosine phosphorylation at residue 705, but is not dependent on phosphorylation of Ser-727. Our studies indicate that Rac1 induces STAT3 activation through an indirect mechanism that involves the autocrine production and action of IL-6, a known mediator of STAT3 response. Rac V12 expression results in the induction of the IL-6 and IL-6 receptor genes and neutralizing antibodies directed against the IL-6 receptor block Rac1-induced STAT3 activation. Furthermore, inhibition of the nuclear factor-kappaB activation or disruption of IL-6-mediated signaling through the expression of IkappaBalpha S32AS36A and suppressor of cytokine signaling 3, respectively, blocks Rac1-induced STAT3 activation. These findings elucidate a mechanism dependent on the induction of an autocrine IL-6 activation loop through which Rac1 mediates STAT3 activation establishing a link between oncogenic GTPase activity and Janus kinase/STAT signaling.
Migration of Relational Database to Document-Oriented Database: Structure Denormalization and Data Transformation (2015)

Relational databases remain the leading data storage technology. Nevertheless, many companies want to reduce operating expenses, to make scalable applications that use cloud computing technologies. Use of NoSQL database is one of the possible solutions, and it is forecasted that the NoSQL market will be growing at a CAGR of approximately 50 percent over the next five years. The paper offers a solution for quick data migration from a relational database into a document-oriented database. We have created semi-automatically two logical levels over physical data. Users can refine generated logical data model and configure data migration template for each needed document. Data migration features are implemented into relational database browser Dig Browser. Real patients' database was migrated to Clasterpoint database. The offered approach provides means to obtain at least proof-of-concept for new document-oriented database solution in a couple of days.
Invasive Ductal Breast Carcinoma Response to Neoadjuvant Chemotherapy: Noninvasive Monitoring with Functional MR Imaging— Pilot Study (2003)

EFPcount appears to provide functional information regarding changes in tumor angiogenesis due to neoadjuvant chemotherapy. Functional MR imaging of the breast may be useful in monitoring tumor response to neoadjuvant chemotherapy.
An ultra-compact rejection filter based on spoof surface plasmon polaritons (2017)

In this paper, we propose a scheme to construct a new type of ultra-compact rejection filter by loading split-ring resonators (SRRs) on the transmission line of spoof surface plasmon polaritons (SPPs). From the dispersion analysis of the spoof SPP transmission line with and without the SRR loading, we clearly reveal the mechanism of the rejection characteristic for this compact filter. Meanwhile, we fabricate two spoof SPPs waveguides loaded with different amounts of metamaterials particles, and experimentally test them using an Agilent Vector Network Analyzer (VNA) and a homemade near-field scanning system. Both the simulated and measured results agree well with our theoretical analysis and demonstrate the excellent filtering characteristics of our design. The isolation of both filters can be less than -20 dB, and even reach -40 dB at rejection frequencies. The proposed rejection and stop-band filters show important potentials to develop integrated plasmonic functional devices and circuits at microwave and terahertz frequencies.
Bi-layer encapsulation of utah array based nerual interfaces by atomic layer deposited Al<inf>2</inf>O<inf>3</inf> and parylene C (2013)

We present a novel coating method that combines atomic layer deposited Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> and Parylene C for encapsulation of biomedical implantable devices, focusing on its application on Utah electrode array based neural interfaces. The alumina and Parylene C bi-layer encapsulated wired Utah electrode array showed relatively stable impedance during the 320 days of soak testing at 37°C in phosphate buffered solution. Also bi-layer coated fully integrated Utah array based wireless neural interfaces had stable power-up frequency and constant RF signal strength during the 600 days of equivalent soaking time at 37°C. Bi-layer coated Utah arrays had constant current drawing of about 3 mA during 140 days of soak testing.
Soft-decision-based node synchronization for Viterbi decoders (1995)

Optimum decision methods are employed to discriminate between in-sync and out-of-sync operations in Viterbi decoders when the received data sequence is given in analog form (soft decisions). The exact solution to this discrimination problem, however, appears too complex in many practical cases. A suboptimum algorithm is then proposed that can be implemented as a hardware device, external to the decoder. This algorithm is recognized as a modified version of an earlier technique known as the "reencoding method". Analysis and simulations indicate that the modification produces remarkably good results not only in comparison with the reencoding method but also with previous techniques discussed in literature.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>