gebhart/patrepeval huggingface dataset:
Persistent Sin Nombre Virus Infection in the Deer Mouse ( <i>Peromyscus maniculatus</i> ) Model: Sites of Replication and Strand-Specific Expression (2002)

To address Sin Nombre (SN) virus persistence in deer mice, we sacrificed experimentally infected deer mice at eight time points from day 21 to day 217 postinoculation (p.i.) and examined their tissues for viral nucleocapsid (N) antigen expression and both negative-strand (genomic) and positive-strand (replicative/mRNA) viral S segment RNA titers. All the animals that we inoculated developed persistent infections, and SN virus could be isolated from tissues throughout the course of infection. The transition from an acute to a persistent pattern of infection appeared to occur between days 60 and 90 p.i. Beginning on day 60 p.i., the heart, brown adipose tissue (BAT), and lung retained antigen expression and genomic viral RNA the most frequently. We found a statistically significant association among the presence of replicative RNA in the heart, lung, and BAT, widespread antigen expression (in > or =5 tissues), and RNA viremia. Of these three tissues, the heart retained negative-strand RNA and viral N antigen the most consistently (in 25 of 26 animals). During persistence, there were two distinct patterns of infection: restricted versus disseminated tissue involvement. Mice with the restricted pattern exhibited N antigen expression in < or =3 tissues, an absence of viral RNA in the blood, neutralizing antibody titers of < or =1:1,280 (P = 0.01), and no replicative RNA in the heart, lung, or BAT. Those with the "disseminated" pattern showed N antigen expression in > or =5 tissues, neutralizing antibody titers of 1:160 to 1:20,480, replicative RNA in the heart, lung, and BAT at a high frequency, and RNA viremia. Virus could be isolated consistently only from mice that demonstrated the disseminated pattern. The heart, lung, and BAT are important sites for the replication and maintenance of SN virus during persistent infection.
Conformational Ensembles of Calmodulin Revealed by Nonperturbing Site-Specific Vibrational Probe Groups (2018)

Seven native residues on the regulatory protein calmodulin, including three key methionine residues, were replaced (one by one) by the vibrational probe amino acid cyanylated cysteine, which has a unique CN stretching vibration that reports on its local environment. Almost no perturbation was caused by this probe at any of the seven sites, as reported by CD spectra of calcium-bound and apo calmodulin and binding thermodynamics for the formation of a complex between calmodulin and a canonical target peptide from skeletal muscle myosin light chain kinase measured by isothermal titration. The surprising lack of perturbation suggests that this probe group could be applied directly in many protein-protein binding interfaces. The infrared absorption bands for the probe groups reported many dramatic changes in the probes' local environments as CaM went from apo- to calcium-saturated to target peptide-bound conditions, including large frequency shifts and a variety of line shapes from narrow (interpreted as a rigid and invariant local environment) to symmetric to broad and asymmetric (likely from multiple coexisting and dynamically exchanging structures). The fast intrinsic time scale of infrared spectroscopy means that the line shapes report directly on site-specific details of calmodulin's variable structural distribution. Though quantitative interpretation of the probe line shapes depends on a direct connection between simulated ensembles and experimental data that does not yet exist, formation of such a connection to data such as that reported here would provide a new way to evaluate conformational ensembles from data that directly contains the structural distribution. The calmodulin probe sites developed here will also be useful in evaluating the binding mode of calmodulin with many uncharacterized regulatory targets.
PHOTO INJECTOR CATHODE LASER BEAM INTENSITY AND POINTING STABILITY DIAGNOSTICS. (2007)

A photo cathode laser with unique parameters is used at the Photo Injector Test facility at DESY in Zeuthen, PITZ [1, 2]. It is capable of producing laser pulse trains consisting of up to 800 pulses with a separation of 1 µs where each laser pulse has a flat-top temporal profile. The knowledge of the laser stability is very important for the emittance measurements procedure. Therefore, a system for monitoring the laser beam intensity and pointing po-sition stability was created at PITZ. It is capable of mea-suring the laser spot position and pulse intensity for each of the laser pulses in the train using a quadrant diode and a photomultiplier tube, respectively. Taking into account the laser beam spot transverse intensity distribution mea-sured by a CCD camera allows to study the position of the laser spot on the photo cathode with a resolution of 8.3 µm. Laser intensity measurements can be done for a wide dy-namical range of intensities due to the tuneable photo mul-tiplier tube gain. The first experiments with the new system show very small laser spot position jitter on the cathode surface of about 20 µm and laser intensity fluctuations of about 14 %.
Cost-Efficient Online Hyperparameter Optimization (2021)

Recent work on hyperparameters optimization (HPO) has shown the possibility of training certain hyperparameters together with regular parameters. However, these online HPO algorithms still require running evaluation on a set of validation examples at each training step, steeply increasing the training cost. To decide when to query the validation loss, we model online HPO as a time-varying Bayesian optimization problem, on top of which we propose a novel \textit{costly feedback} setting to capture the concept of the query cost. Under this setting, standard algorithms are cost-inefficient as they evaluate on the validation set at every round. In contrast, the cost-efficient GP-UCB algorithm proposed in this paper queries the unknown function only when the model is less confident about current decisions. We evaluate our proposed algorithm by tuning hyperparameters online for VGG and ResNet on CIFAR-10 and ImageNet100. Our proposed online HPO algorithm reaches human expert-level performance within a single run of the experiment, while incurring only modest computational overhead compared to regular training.
Rosuvastatin reduces experimental left ventricular infarct size after ischemia-reperfusion injury but not total coronary occlusion (2004)

This study compared the effects of rosuvastatin on left ventricular infarct size in mice after permanent coronary occlusion vs. 60 min of ischemia followed by 24 h of reperfusion. Statins can inhibit neutrophil adhesion, increase nitric oxide synthase (NOS) expression, and mobilize progenitor stem cells after ischemic injury. Mice received blinded and randomized administration of rosuvastatin (20 mg.kg(-1).day(-1)) or saline from 2 days before surgery until death. After 60 min of ischemia with reperfusion, infarct size was reduced by 18% (P = 0.03) in mice randomized to receive rosuvastatin (n = 18) vs. saline (n = 22) but was similar after permanent occlusion in rosuvastatin (n = 17) and saline (n = 20) groups (P = not significant). Myocardial infarct size after permanent left anterior descending coronary artery occlusion (n = 6) tended to be greater in NOS3-deficient mice than in the wild-type saline group (33 +/- 4 vs. 23 +/- 2%, P = 0.08). Infarct size in NOS3-deficient mice was not modified by treatment with rosuvastatin (34 +/- 5%, n = 6, P = not significant vs. NOS3-deficient saline group). After 60 min of ischemia-reperfusion, neutrophil infiltration was similar in rosuvastatin and saline groups as was the percentage of CD34(+), Sca-1(+), and c-Kit(+) cells. Left ventricular NOS3 mRNA and protein levels were unchanged by rosuvastatin. Rosuvastatin reduces infarct size after 60 min of ischemia-reperfusion but not after permanent coronary occlusion, suggesting a potential anti-inflammatory effect. Although we were unable to demonstrate that the myocardial protection was due to an effect on neutrophil infiltration, stem cell mobilization, or induction of NOS3, these data suggest that rosuvastatin may be particularly beneficial in myocardial protection after ischemia-reperfusion injury.
Adjuvant combined paclitaxel and carboplatin chemotherapy for glassy cell carcinoma of the uterine cervix: Report of three cases with clinicopathological analysis (2011)

Glassy cell carcinoma of the uterine cervix (GCC) is a rare form of cervical carcinoma that is characterized by aggressiveness and poor prognosis. We reviewed a variety of clinicopathological features, treatment strategies, and outcomes in three women with GCC. The three patients were successfully treated by radical hysterectomy with pelvic/para-aortic lymphadenectomy. The patients had stage Ib1, stage IIa, and stage Ib2 tumors without lymph node metastases. A 44-year-old woman with stage Ib1 tumor did not undergo adjuvant chemotherapy or radiation therapy. She had recurrent pelvic tumors 12 months after surgery, and died 6 months after the recurrent disease. The histological findings of her cervix, which were different from the other two patients, did not show the marked infiltration of eosinophils. The other two patients with stage Ib2 and IIa tumors underwent adjuvant chemotherapy with paclitaxel and carboplatin, and had disease-free survival for 4.5 and 9 years. We think that all patients with GCC of stage Ib1 or more should undergo adjuvant chemotherapy of paclitaxel and carboplatin or other adjuvant therapies.
A novel murine system for validating the specific targeting of peptides to light chain associated (AL) amyloid (2017)

"A novel murine system for validating the specific targeting of peptides to light chain associated (AL) amyloid." Amyloid, 24(sup1), pp. 74–75
<i>In Vivo</i>Pathogenic Role of Mutant SOD1 Localized in the Mitochondrial Intermembrane Space (2011)

Mutations in Cu,Zn superoxide dismutase (SOD1) are associated with familial amyotrophic lateral sclerosis (ALS). Mutant SOD1 causes a complex array of pathological events, through toxic gain of function mechanisms, leading to selective motor neuron degeneration. Mitochondrial dysfunction is among the well established toxic effects of mutant SOD1, but its mechanisms are just starting to be elucidated. A portion of mutant SOD1 is localized in mitochondria, where it accumulates mostly on the outer membrane and inside the intermembrane space (IMS). Evidence in cultured cells suggests that mutant SOD1 in the IMS causes mitochondrial dysfunction and compromises cell viability. Therefore, to test its pathogenic role in vivo we generated transgenic mice expressing G93A mutant or wild-type (WT) human SOD1 targeted selectively to the mitochondrial IMS (mito-SOD1). We show that mito-SOD1 is correctly localized in the IMS, where it oligomerizes and acquires enzymatic activity. Mito-G93ASOD1 mice, but not mito-WTSOD1 mice, develop a progressive disease characterized by body weight loss, muscle weakness, brain atrophy, and motor impairment, which is more severe in females. These symptoms are associated with reduced spinal motor neuron counts and impaired mitochondrial bioenergetics, characterized by decreased cytochrome oxidase activity and defective calcium handling. However, there is no evidence of muscle denervation, a cardinal pathological feature of ALS. Together, our findings indicate that mutant SOD1 in the mitochondrial IMS causes mitochondrial dysfunction and neurodegeneration, but per se it is not sufficient to cause a full-fledged ALS phenotype, which requires the participation of mutant SOD1 localized in other cellular compartments.
Coordinated Wide-Area Control of Multiple Controllers in a Power System Embedded With HVDC Lines (2020)

This paper develops a coordinated wide-area control of power system stabilizers (PSSs), static VAr compensators (SVCs), and supplementary damping controllers (SDCs) for damping low frequency oscillations (LFOs) in a power system embedded with multiple high voltage DC (HVDC) lines. The improved damping is achieved by designing a coordinated wide-area damping controller (CWADC) that employs partial state feedback. The design methodology uses a linear matrix inequality (LMI)-based mixed H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> /H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</sub> robust control for multiple operating scenarios. To reduce the high computational burden, an enhanced version of selective modal analysis (SMA) is employed that not only reduces the number of required wide-area feedback signals, but also identifies alternate feedback signals, in case of failure of the primary signals. Additionally, the impact of delays on the performance of the control design is investigated. The studies are performed on a 29 machine, 127 bus equivalent model of the Western Electricity Coordinating Council (WECC) system-embedded with three HVDC lines and two wind farms.
ASSESSMENT OF THE OPERATIONAL AND COMMERCIAL VIABILITY OF THE SEAGRAVES, WHITEFACE AND LUBBOCK RAILROAD COMPANY. FINAL REPORT (1995)

The Lubbock District of the Texas Department of Transportation (TxDOT) is planning the acquisition of railroad right-of-way from the Seagraves, Whiteface, and Lubbock Railroad Company (SWLR) as part of the U.S. 82 East-West Freeway project. During the planning process, several questions have arisen regarding the long term commercial viability of the railroad. The SWLR is faced with several situations and conditions that could adversely impact the longer-term viability of the line. The schedule and form of debt service established with the purchase of the line requires renegotiation, refinancing, or as an alternative, sale of the line. Resolution of debt issues should be accomplished within a six-month period. Given the fact that Amerail has been looking for a buyer for several months, the railroad entering receivership appears to be a relatively high probability outcome. The impacts of past deferred maintenance will continue to be an operating challenge for any owner of the railroad. The effects of past maintenance decisions and practices are beginning to be acutely felt in several aspects of the railroad's operations. Resolution of rehabilitation and maintenance issues is contingent upon sale or refinancing of the railroad. Regardless of the status of railroad ownership, rehabilitation must be carried out and a sound maintenance program must be in place within a five-year period. The analysis suggests that as far as TxDOT is concerned, stable ownership and operation of the SWLR is the key issue. Financial sources and the current owners of the company indicate that Amerail is actively seeking a buyer, and has been for some time. The current owners, however, prefer refinancing and continued operation of the SWLR. It is reasonable to expect ownership issues to be resolved within a one-year time frame. TxDOT's options with respect to the SWLR are discussed in terms of four likely scenarios: (1) a buyer is found and the SWLR is sold, (2) Amerail refinances the SWLR and continues operations, (3) a buyer is not found and the SWLR enters receivership, and (4) TxDOT determines that buying the SWLR best protects its investment and the regional transportation system.
zuo leng gu jia ni cui hua ji zai yi er chun ye xiang cui hua zhong zheng zhi qing fan ying zhong de xing neng yan jiu (2005)

将猝冷法制备的Ni50Al50合金经碱处理活化得到猝冷骨架Ni(RQ Ni)催化剂,以ICP-AES、N2物理吸附、XRD、H2-TPD、SEM等手段对合金及催化剂的物化性质进行了表征.与Raney Ni相比,猝冷骨架Ni催化剂残留了较多的Ni2Al3相,有更小的比表面,更高的平均孔径和孔体积,更大的平均粒径和晶胞参数.将催化剂用于乙二醇液相催化重整制氢反应,发现RQ Ni比Raney Ni更易生成烷烃,而生成CO含量较低.结合表征结果,讨论了RQ Ni与Raney Ni在反应中催化行为的区别.
Prevalence of Dentatorubral-Pallidoluysian Atrophy in a Large Series of White Patients With Cerebellar Ataxia (2003)

This study enables us to estimate the frequency of the disease as 0.25% in both families with autosomal dominant cerebellar ataxia and sporadic cases of ataxia in our series, confirming the very low frequency of DRPLA in Europe. In both familial and sporadic cases, molecular testing for DRPLA could be restricted to patients with ataxia with one of the following features: chorea, dementia, or myoclonic epilepsy.
Virtual Chimera States for Delayed-Feedback Systems (2013)

Time-delayed systems are found to display remarkable temporal patterns the dynamics of which split into regular and chaotic components repeating at the interval of a delay. This novel long-term behavior for delay dynamics results from strongly asymmetric nonlinear delayed feedback driving a highly damped harmonic oscillator dynamics. In the corresponding virtual space-time representation, the behavior is found to develop as a chimeralike state, a new paradigmatic object from the network theory characterized by the coexistence of synchronous and incoherent oscillations. Numerous virtual chimera states are obtained and analyzed, through experiment, theory, and simulations.
Susceptibility of monomicrobial or polymicrobial biofilms derived from infected diabetic foot ulcers to topical or systemic antibiotics in vitro (2020)

Diabetic foot ulcers can become chronic and non-healing despite systemic antibiotic treatment. The penetration of systematically-administered antibiotics to the site of infection is uncertain, as is the effectiveness of such levels against polymicrobial biofilms. We have developed an in vitro model to study the effectiveness of different treatments for infected diabetic foot ulcers in a wound-like environment and compared the activity of systemic levels of antibiotics with that for topically applied antibiotics released from calcium sulfate beads. This is the first study that has harvested bacteria from diabetic foot infections and recreated similar polymicrobial biofilms to those present in vivo for individual subjects. After treatment with levels of gentamicin attained in serum after systemic administration (higher than corresponding tissues concentrations) we measured a 0-2 log reduction in bacterial viability of P. aeruginosa, S. aureus or a polymicrobial biofilm. Conversely, addition of gentamicin loaded calcium sulfate beads resulted in 5-9 log reductions in P. aeruginosa, S aureus and polymicrobial biofilms derived from three subjects. We conclude that systemically administered antibiotics are likely to be inadequate for successfully treating these infections, especially given the vastly increased concentrations required to inhibit cells in a biofilm, and that topical antibiotics provide a more effective alternative.
Comparative Measurement of of an Antineoplastic Glucan the Molecular Weight from BCG Vaccine (1998)

Bacillus Calmette-Guérin (BCG) vaccine, developed originally for the prophylaxis of tuberculosis, is a potent immunostimulant used to treat superficial bladder carcinoma in man. The aim of this study was to compare the molecular weight and self-association properties of an antineoplastic glucan (PS1A1) extracted from BCG vaccine as determined by different techniques including diffusion, light-scattering and chromatographic methods. In the diffusion experiments, a semi-empirical relationship was derived between the effective diffusion coefficients, Dp, and the weight-average molecular weights, Mw, of several dextrans used as standards, according to the equation Dp = 2.233 x 10(-6) x Mw(-0.66). On the basis of this relationship, the molecular weight of PS1A1 was found to be 57.4 kDa, although, unexpectedly, membrane association was high, most probably because of molecular branching. In the light-scattering experiment it was observed that, unlike dextran, PS1A1 undergoes concentration-dependent multimerization in water. However, the molecular weight of PS1A1 in 0.1 M sodium chloride ranged from 60 to 68 kDa, with a mean of 65 kDa, over the same concentration range. This value was in agreement with the molecular weight determined for PS1A1 by gel-filtration chromatography in previous studies, suggesting that 65 kDa represents the approximate monomeric size of the unassociated molecule. Thus, it was evident that the aggregation was suppressed by electrolyte. Elemental analysis by X-ray fluorescence showed that PS1A1 contained carbon, oxygen, hydrogen and phosphorus, indicating that hitherto unobserved ionized phosphate groups might promote electrostatic interactions.
Left Atrial and Pulmonary Venous Flow Visualization by Phase Encoding Magnetic Resonance Imaging (1996)

In order to study the blood flow patterns in the left atrium, as well as the pulmonary venous inflow, Magnetic Resonance Imaging (MRI) was used to visualize the three-dimensional velocity fields in the transversal plane Left Ventricular Outflow Tract (LVOT) view and sagittal plane LVOT view in humans. A dedicated visualization and analysis software named &amp;lsquo;cardiac MARIAN&amp;rsquo;&amp;trade; was developed on a Silicon Graphics Onyx computer. Temporal velocity profiles were measured and vector animations of the flow fields produced throughout the cardiac cycle. This provided a dynamic visualization of the complex flow fields in the left atrium.
Basi della selettività delle diaminopirimidine antibatteriche (1994)

SommarioÈ stata analizzata la base dell'alta aifinità e selettività del trimetoprim [2,4-diamino-5-(3′,4′,5′-trimetoxibenzil)pirimidina, TMP] e di altri analoghi strutturali molto simili. La sostituzione di un gruppo metoxilico sull'anello benzilico della 2,4-diaminobenzilpirimidina influenza spiccatamente sia i valori di Ki della diidrofolico reduttasi (DHFR) di Escherichia coli sia l'attività antibatterica in vitro. Il TMP è molte centinaia di volte più potente della benzilpirimidina non-sostituita, e gli analoghi monometoxi e dimetoxi esplicano un'attività intermedia.Tuttavia, le costanti dell'equilibrio di dissociazione determinate in assenza del cofattore (NADPH) indicano che la capacità di legame di queste diaminobenzilpirimidine nel complesso enzima-inibitore è considerevolmente più debole e non varia fra i composti. Pertanto, la affinità di legame del TMP con la DHFR di E. coli è incrementata dal NADPH nel complesso ternario e questa aumentata affinità (cooperatività) varia in funzione della sostituzione con gruppi metoxilici. In contrasto la DHFR del topo ha una affinità di legame più debole per le diaminobenzilpirimidine e nessuno degli analoghi mostra forti effetti cooperativi con NADPH. La differenza nella entità della cooperatività di NADPH/TMP tra DHFR batterica e di mammifero rappresenta un importante fattore nella selettività. L'enzima di E. coli si lega al TMP più fortemente nel complesso binario ed un ulteriore fattore di selettività di circa 30 volte emerge dalle differenze nella cooperatività. Benchè la struttura cristallina ai raggi X della DHFR batterica e dei vertebrati sia stata studiata estensivamente nessuna ipotesi convincente può darci ragione delle basi molecolari per la selettività del TMP. Tuttavia, la informazione sulla struttura tridimensionale dell'enzima è stata sfruttata per programmare razionalmente nuovi inibitori dotati di elevata affinità.