gebhart/patrepeval huggingface dataset:
Crystal Structure of Novel Dye-linked l-Proline Dehydrogenase from Hyperthermophilic Archaeon Aeropyrum pernix (2012)

Two types of dye-linked L-proline dehydrogenase (PDH1, α4β4-type hetero-octamer, and PDH2, αβγδ-type heterotetramer) have been identified so far in hyperthermophilic archaea. Here, we report the crystal structure of a third type of L-proline dehydrogenase, found in the aerobic hyperthermophilic archaeon Aeropyrum pernix, whose structure (homodimer) is much simpler than those of previously studied L-proline dehydrogenases. The structure was determined at a resolution of 1.92 Å. The asymmetric unit contained one subunit, and a crystallographic 2-fold axis generated the functional dimer. The overall fold of the subunit showed similarity to that of the PDH1 β-subunit, which is responsible for catalyzing L-proline dehydrogenation. However, the situation at the subunit-subunit interface of the A. pernix enzyme was totally different from that in PDH1. The presence of additional surface elements in the A. pernix enzyme contributes to a unique dimer association. Moreover, the C-terminal Leu(428), which is provided by a tail extending from the FAD-binding domain, shielded the active site, and an L-proline molecule was entrapped within the active site cavity. The K(m) value of a Leu(428) deletion mutant for L-proline was about 800 times larger than the K(m) value of the wild-type enzyme, although the k(cat) values did not differ much between the two enzymes. This suggests the C-terminal Leu(428) is not directly involved in catalysis, but it is essential for maintaining a high affinity for the substrate. This is the first description of an LPDH structure with L-proline bound, and it provides new insight into the substrate binding of LPDH.
010 Insights into hypertensive heart disease phenotypes: Spectrum of myocyte, interstitial and vascular changes by cardiovascular MRI (2016)

<h3>Introduction</h3> Hypertensive heart disease (HHD) can be classified into 4 left ventricular (LV) phenotypes: 1) normal, 2) concentric LV remodelling (LVr), 3) concentric LV hypertrophy (cLVH) and 4) eccentric LV hypertrophy (eLVH). The pathophysiology of the phenotypes is incompletely understood. We investigate extent of myocardial interstitial fibrosis and aortic impairment in HHD with cardiovascular magnetic resonance (CMR) <h3>Methods</h3> 88 hypertensives (49 ± 14yrs, 57% male, SBP: 167 ± 30mmHg, DBP: 96 ± 14mmHg) underwent CMR (1.5T) and were compared with 29 age- and sex-matched normotensive controls (47 ± 14years, 59% male, SBP: 128 ± 12mmHg, DBP: 79 ± 10mmHg). Native T1 and extra-cellular volume fraction were measured. Circumferential myocardial strain was calculated by voxel-tracking. Aortic compliance was recorded. <h3>Results</h3> At a structural level, increased LV mass in eccentric and concentric LVH resulted from: i) significantly increased myocardial cell volume (eLVH: 78 ± 19g/m<sup>2</sup> vs cLVH: 73 ± 15g/m<sup>2</sup> vs LVr: 55 ± 9g/m<sup>2</sup> respectively, P &lt; 0.05) and ii) significantly increased interstitial volume (eLVH: 33 ± 10g/m<sup>2</sup> vs cLVH: 30 ± 10g/m<sup>2</sup> vs LVr: 19 ± 2g/m<sup>2</sup> respectively, P &lt; 0.05). Functionally, eccentric and concentric LVH were associated with significantly impaired circumferential strain (eLVH: -12.8 ± 4.6% vs cLVH: -15.5 ± 3.1% vs LVr: -17.1 ± 3.2% vs controls: -17.4 ± 2.6% respectively, P &lt; 0.05). Despite similar BP severity as LVH phenotypes, LV remodelling was associated with reduced aortic compliance but not associated with interstitial fibrosis or myocardial dysfunction relative to controls. <h3>Conclusion</h3> Myocardial interstitial fibrosis is varies across HHD phenotypes with functional consequences. Eccentric LVH demonstrated the most interstitial fibrosis and systolic strain impairment. LV remodelling had normal myocardial, but abnormal aortic, function. Greater understanding of the pathophysiology of HHD phenotypes may help tailor future treatments.
Congestion avoidance and control (1995)

article Free Access Share on Congestion avoidance and control Author: V. Jacobson University of California, Lawrence Berkeley Laboratory, Berkeley, CA University of California, Lawrence Berkeley Laboratory, Berkeley, CAView Profile Authors Info & Claims ACM SIGCOMM Computer Communication ReviewVolume 25Issue 1Jan. 1995 pp 157–187https://doi.org/10.1145/205447.205462Published:11 January 1995Publication History 78citation357DownloadsMetricsTotal Citations78Total Downloads357Last 12 Months164Last 6 weeks14 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Evaluation of the contribution of the renal capsule and cortex to kidney autofluorescence intensity under ultraviolet excitation (2009)

The use of reduced nicotinamide adenine dinucleotide (NADH) fluorescence to gain metabolic information on kidneys in response to an alteration in oxygen availability has previously been experimentally demonstrated, but signal quantification has not, to date, been addressed. In this work the relative contribution to rat kidney autofluorescence of the capsule versus cortex under ultraviolet excitation is determined from experimental results obtained using autofluorescence microscopy and a suitable mathematical model. The results allow for a quantitative assessment of the relative contribution of the signal originating in the metabolically active cortex as a function of capsule thickness for different wavelengths.
An integrated printed circuit board (pcb) microphone. (2000)

An electret microphone has been implemented into a printed circuit board. Due to novel construction the printed circuit board serves as the microphone backplate. Furthermore, other features of printed circuit board manufacturing technology are applied to minimize the number of components of the microphone. This results in a microphone that can be manufactured with the assembly of other electronic components during the manufacturing process. As a result a complete manufacturing process has been developed. To analyze the manufacturing process and the acoustical performance of the so-called PCB-microphone, the acoustics have been modeled, and backplate surface roughness, air gap thickness, electret charge, and overall sensitivity have been measured from prototypes.
Draft Genome Sequence of Pseudomonas sp. Strain MWU12-2534b, Isolated from a Wild Cranberry Bog in Truro, Massachusetts (2018)

An unknown Pseudomonas sp. most closely related to Pseudomonas ficuserectae and Pseudomonas protegens was isolated from the rhizospheres of wild cranberry plants in the Cape Cod National Seashore, in the United States. The draft genome of MWU12-2534b is 6.7 Mbp, has 63.32% GC content, and contains multiple potential virulence and antibiotic resistance genes.
Influences of dispersed generation on the performance of the electricity grid (2004)

Dispersed generation (DG) is playing an increasing role in the electric power system. In order to investigate the influences of DG-units on the performance of the electricity grid, performance-indicators and their classification are useful to be defined. These classifications enable an objective evaluation of the current situation in the grid and the influences of dispersed generation. This paper gives a survey of the most important performance-indicators, presents classifications for reliability and voltage sags and gives an overview of the influence of dispersed generation on these two aspects.
LogPicker: Strengthening Certificate Transparency Against Covert Adversaries (2021)

Abstract HTTPS is a cornerstone of privacy in the modern Web. The public key infrastructure underlying HTTPS, however, is a frequent target of attacks. In several cases, forged certificates have been issued by compromised Certificate Authorities (CA) and used to spy on users at large scale. While the concept of Certificate Transparency (CT) provides a means for detecting such forgeries, it builds on a distributed system of CT logs whose correctness is still insufficiently protected. By compromising a certificate authority and the corresponding log, a covert adversary can still issue rogue certificates unnoticed. We introduce LogPicker, a novel protocol for strengthening the public key infrastructure of HTTPS. LogPicker enables a pool of CT logs to collaborate, where a randomly selected log includes the certificate while the rest witness and testify the certificate issuance process. As a result, CT logs become capable of auditing the log in charge independently without the need for a trusted third party. This auditing forces an attacker to control each participating witness, which significantly raises the bar for issuing rogue certificates. LogPicker is efficient and designed to be deployed incrementally, allowing a smooth transition towards a more secure Web.
Efficacy of maintenance olaparib plus bevacizumab in patients with newly diagnosed advanced ovarian cancer according to BRCA mutation genotype in the phase III PAOLA-1/ENGOT-ov25 trial. (2022)

5571 Background: In the Phase III PAOLA-1/ENGOT-ov25 trial, the addition of maintenance olaparib (ola) to bevacizumab (bev) in patients (pts) with newly diagnosed advanced high-grade ovarian cancer (HGOC) resulted in prolonged progression-free survival (PFS), particularly for pts with HRD-positive tumors including a BRCA1/ BRCA2 mutation (BRCAm; Ray-Coquard et al. NEJM 2019). Preclinical data suggest that pts with mutations (mut) in the RING domain of BRCA1 are less sensitive to ola. The magnitude of benefit from ola + bev, according to the location of mut in the functional domains (FD) of BRCA , remains to be explored. Methods: Pts with newly diagnosed advanced HGOC in response after platinum-based chemotherapy + bev received maintenance bev (15 mg/kg q3w for 15 months [mo]) + either ola (300 mg bid for 24 mo) or placebo (pbo). In this post hoc exploratory analysis, PFS was analyzed in pts with BRCAm according to mut location in the FDs of BRCA1 (RING, DNA-binding domain [DNA-BD], or BRCA1 C terminus [BRCT]) and BRCA2 (RAD51-BD; DNA-BD). Results: Among the 806 randomized pts, 235 (29.2%) harbored a BRCAm: 160 (19.9%) with a BRCA1 mut and 76 (9.4%) with a BRCA2 mut. BRCA1 mut in FDs of RING, DNA-BD and BRCT were detected in 19 (11.8%), 41 (25.6%) and 34 (21.2%) pts, respectively. BRCA2 mut were detected in FDs of RAD51-BD and DNA-BD in 37 (48.7%) and 14 (18.4%) pts, respectively. With a median follow-up of 25.5 mo, 24-mo PFS rates and hazard ratios (HRs) according to mut locations are reported in the Table. In pts with a BRCA1 DNA-BD mut, 24-mo PFS was 89% and 14% (ola + bev vs pbo + bev; HR 0.08, 95% confidence interval [CI] 0.02–0.26) compared with 64% and 24% for pts with mut in RING + BRCT + other domains (HR 0.33, 95% CI 0.19–0.57). In pts with BRCA2 mut, 24-mo PFS for pts with mut in the DNA-BD was 91% vs 100% (ola + bev vs pbo + bev) compared with 82% and 44% for pts with mut in RAD51-BD + other domains (HR 0.21, 95% CI 0.08–0.54). Conclusions: In this exploratory analysis, pts with newly diagnosed advanced HGOC and a BRCAm had a PFS benefit from maintenance ola + bev regardless of mut locations in BRCA1/BRCA2. Sensitivity to ola + bev maintenance was particularly high for pts with mut in the DNA-BD of BRCA1. Pts with a mut in the DNA-BD of BRCA2 commonly had excellent outcomes. Clinical trial information: NCT02477644. [Table: see text]
Sol-gel-based enzymatic assays and immunoassays for residue analysis. (2000)

A novel technology based on the entrapment of biomolecules in a ceramic SiO 2 sol-gel matrix has been developed. The technology was used to entrap enzymes and antibodies for use as pesticide and pollutant sensors and immunochromatographic materials. Three systems were studied: (i) sol-gel-entrapped esterases for monitoring organophosphate (OP) and carbamate (CB) pesticides; (ii) sol-gel- entrapped anti-atrazine monoclonal antibodies for immune-affinity purification of s-triazine herbicides present as contaminants in soil and water; and (iii) sol-gel-entrapped anti-dinitrophenyl (DNP) polyclonal antiserum for clean up and concentration of nitroaromatic pollutants from agricultural and environmental samples. The characteristics of the sol-gel-entrapped enzymes and antibodies are presented.
Ligand‐Accelerated Indium(III)‐Catalyzed Asymmetric Alkynylation of Aldehydes with 2‐Methyl‐3‐butyn‐2‐ol as an Ethyne Equivalent Donor. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Thermodynamics and transport in Ce sub 3 Bi sub 4 Pt sub 3 and related compounds (1992)

The transport and thermodynamic properties of the small-gap semiconductor Ce{sub 3}Bi{sub 4}Pt{sub 3} are reviewed and discussed in relation to other Kondo insulators and metals. The data are consistent with the small-gap semiconductors being Kondo-like metals at temperatures T {ge} E{sub g}/k{sub B}. Kondo insulators appear to be an unusually simple realization of the Anderson Lattice Hamiltonian in which the lower hybridization band is exactly filled, or in Kondo language, the Abrikosov-Suhl resonance exactly fills a Brillouin zone. 8 figs, 40 refs. (DLC)
Interplay between vesicoureteric reflux and kidney infection in the development of reflux nephropathy in mice (2013)

Vesicoureteric reflux (VUR) is a common congenital defect of the urinary tract that is usually discovered after a child develops a urinary tract infection. It is associated with reflux nephropathy, a renal lesion characterized by the presence of chronic tubulointersitial inflammation and fibrosis. Most patients are diagnosed with reflux nephropathy after one or more febrile urinary tract infections, suggesting a potential role for infection in its development. We have recently shown that the C3H mouse has a 100% incidence of VUR. Here, we evaluate the roles of VUR and uropathogenic Escherichia coli infection in the development of reflux nephropathy in the C3H mouse. We find that VUR in combination with sustained kidney infection is crucial to the development of reflux nephropathy, whereas sterile reflux alone fails to induce reflux nephropathy. A single bout of kidney infection without reflux fails to induce reflux nephropathy. The host immune response to infection was examined in two refluxing C3H substrains, HeN and HeJ. HeJ mice, which have a defect in innate immunity and bacterial clearance, demonstrate more significant renal inflammation and reflux nephropathy compared with HeN mice. These studies demonstrate the crucial synergy between VUR, sustained kidney infection and the host immune response in the development of reflux nephropathy in a mouse model of VUR.
FlashBlades (2012)

Presented is a speculative server blade architecture called a FlashBlade that combines 100x I/O performance in both latency and bandwidth with balanced computing. The blade consists of a standard multi-core CPU with attached DRAM. It uses a fast interconnect, such as Intel's QuickPath, to communicate with a FPGA router called the X1. This router handles traffic to the C1 complexes and off-blade. Each C1 complex is a System on a Chip with Package on Package DRAM, connected to local flash memory. There are numerous complexes, giving tremendous I/O performance and computational balance. A large design space of parameters such as flash size, number of complexes, and link bandwidth between each C1 and the X1 is available for power and performance optimization. A single blade server constructed from these blades, just 12.25 inches high and drawing about 10 KW, could support a few hundred thousand basic web searches a second on 1 billion pages. It could also provide triple store performance 100x greater than achievable now for datasets of 6 TB and scales to petabyte datasets although at somewhat reduced performance; with numerous applications to defense, commerce, and science.
Danely P.Slaughters Field Cancerization Concept of Carcinogenesis: The Path Forward to Early Cancer Detection and Chemoprevention (2015)

It is over seven decades since the seminal work of the otolaryngologist, Dr. Danely Slaughter was published. In patients with oral cancer, he critically demonstrated that carcinogen exposure led to the development of “condemned mucosa”, within which multiple cancers emanated. Thus, the histologically normal cells adjacent to the primary tumor harbor invisible features of the cancer. Other workers such as Strong have confirmed Slaughter’s initial observations, and in recent times by many investigators using molecular genetic approaches. This concept of carcinogenesis is partly responsible for our failure to successfully treat some of our cancer patients. With current technological advancements, biomarkers of field cancerization can be assayed using even noninvasive samples such as body fluids such as saliva and bronchial washes. In clinical practice, such validated biomarkers should enable risk stratification, and hence close surveillance of individuals at risk for early cancer detection or the early deployment of chemopreventive strategies. Arguably, this will immensely contribute to the reduction in the socioeconomic, physical and psychological burden of cancer.
Evaluation of a novel stair-climbing transportation aid for emergency medical services (2020)

Acute and planned transportations of patients are major tasks for emergency medical services (EMS) and often result in substantial physical strains with a major impact on the workers' health, because current transportation aids cannot provide sufficient support, especially on stairs. A new stair-climbing and self-balancing approach (SEBARES) has been developed and its usability is evaluated in the context of this paper. Twelve participants operated a prototype in a transportation scenario and user forces, user joint angles and the perceived usability were evaluated. Results show that user forces were within long-term acceptable ergonomic limits for over 90% of the transportation time and a mainly healthy upright posture of the back could be maintained. This resulted in a healthy working posture for 85% of the time, according to the OWAS method, and a good perceived usability. A comparison to the most ergonomic aid according to literature, a caterpillar stair chair, reveals that similar upright postures are assumed, while the operation of SEBARES required only 47% of the forces to operate the caterpillar stair chair. A comparison to a previous field study indicates a reduction of strenuous working postures by a factor of three, which further confirms the ergonomic advantages of this concept.
Homogenous Carboxymethylation of Cellulose in the New Alkaline Solvent LiOH/Urea Aqueous Solution (2010)

Abstract In this work, the carboxymethylation of cellulose in a new alkaline cellulose solvent, LiOH/urea aqueous solution, was investigated. Carboxymethyl cellulose (CMC) samples were characterized with FT‐IR, NMR, HPLC, and viscosity measurements. Water‐soluble CMC with DS = 0.36∼0.65 was prepared, from both Avicel cellulose and cotton linters in the LiOH/urea system. The total DS of CMC could be controlled by varying the molar ratio of reagents and the reaction temperature. The results from structure analysis by HPLC after complete depolymerization showed that the mole fractions of the different carboxymethylated repeating units as well as those of unmodified glucose follow a simple statistic pattern. A distribution of the carboxymethyl groups of the AGU was determined to be in the order O‐6 &gt; O‐2 &gt; O‐3 position at the level.
Synthesis of ethylbenzene on zeolite catalysts (2009)

Scaling of the process for zeolite-catalyzed ethylbenzene synthesis used as an example is shown, and the catalyst characteristics and product yields are given. The properties of the catalysts and their stability were studied in laboratory, micro-pilot, pilot, and demonstration units with reactor volumes of 0.01, 1, 100, and 1000 dm3, respectively, a sequence that, in combination with the selection of an optimal catalyst, made it possible to determine more exactly the role of each scaling level. The design of the last reactor was practically identical to that of the industrial reactor. The results of the experiments showed that the product quality and the catalyst service life were the same in the pilot and demonstration reactors operating at identical temperatures, feedstock compositions, and olefin space velocities. To confirm the results under conditions identical to those of an industrial reactor and to devise a mathematical model of the process, the pilot and demonstration units used were designed in such a manner that the basic engineering principles of the industrial reaction could be verified. As a result, the domestic technology of industrial-scale ethylbenzene production on heterogeneous catalysts was implemented.
SIR proteins create compact heterochromatin fibers (2018)

Heterochromatin is a silenced chromatin region essential for maintaining genomic stability and driving developmental processes. The complicated structure and dynamics of heterochromatin have rendered it difficult to characterize. In budding yeast, heterochromatin assembly requires the SIR proteins-Sir3, believed to be the primary structural component of SIR heterochromatin, and the Sir2-4 complex, responsible for the targeted recruitment of SIR proteins and the deacetylation of lysine 16 of histone H4. Previously, we found that Sir3 binds but does not compact nucleosomal arrays. Here we reconstitute chromatin fibers with the complete complement of SIR proteins and use sedimentation velocity, molecular modeling, and atomic force microscopy to characterize the stoichiometry and conformation of SIR chromatin fibers. In contrast to fibers with Sir3 alone, our results demonstrate that SIR arrays are highly compact. Strikingly, the condensed structure of SIR heterochromatin fibers requires both the integrity of H4K16 and an interaction between Sir3 and Sir4. We propose a model in which a dimer of Sir3 bridges and stabilizes two adjacent nucleosomes, while a Sir2-4 heterotetramer interacts with Sir3 associated with a nucleosomal trimer, driving fiber compaction.
Synthetic modification of salinomycin: selective O-acylation and biological evaluation (2013)

Salinomycin has found renewed interest as an agent for prevention of cancer recurrence through selectively targeting cancer stem cells. Strategies for generation of improved salinomycin analogs by individual modification of its hydroxyl groups are presented. An evaluation of the dose-response effects of the resulting library on breast cancer cell lines shows that acylation of the C20 hydroxyl can be used to improve IC50 values down to one fifth that of salinomycin.
Σ0 production in proton nucleus collisions near threshold (2018)

The production of 0 baryons in the nuclear reaction p (3.5 GeV) + Nb (corresponding to s N N = 3.18 GeV) is studied with the detector set-up HADES at GSI, Darmstadt. 0 s were identified via the decay 0 with subsequent decays p -in coincidence with a e + e -pair from either external ( e + e -) or internal (Dalitz decay * e + e -) gamma conversions. The differential 0 cross section integrated over the detector acceptance, i.e. the rapidity interval 0.5 < y < 1.1, has been extracted as 0 = 2.3 (0.2) stat +0.6 -0.6 sys (0.2) norm mb, yielding the inclusive production cross section in full phase space total 0 = 5.8 (0.5) stat +1.4 -1.4 sys (0.6) norm (1.7) extrapol mb by averaging over different extrapolation methods. The all / 0 ratio within the HADES acceptance is equal to 2.3 (0.2) stat ( +0.6 -0.6 ) sys . The obtained rapidity and momentum distributions are compared to transport model calculations. The 0 yield agrees with the statistical model of particle production in nuclear reactions.