gebhart/patrepeval huggingface dataset:
Structural Basis of Chaperone Function and Pilus Biogenesis (1999)

Many Gram-negative pathogens assemble architecturally and functionally diverse adhesive pili on their surfaces by the chaperone-usher pathway. Immunoglobulin-like periplasmic chaperones escort pilus subunits to the usher, a large protein complex that facilitates the translocation and assembly of subunits across the outer membrane. The crystal structure of the PapD-PapK chaperone-subunit complex, determined at 2.4 angstrom resolution, reveals that the chaperone functions by donating its G(1) beta strand to complete the immunoglobulin-like fold of the subunit via a mechanism termed donor strand complementation. The structure of the PapD-PapK complex also suggests that during pilus biogenesis, every subunit completes the immunoglobulin-like fold of its neighboring subunit via a mechanism termed donor strand exchange.
Structural Elucidation of Antibiotic TKR2999, an Antifungal Lipodepsipeptide Isolated from the Fungus Foliophoma fallens (2020)

An antifungal lipodepsipeptide was obtained from cultures of the fungus <i>Foliophoma fallens</i> CF-236885. Its structure, elucidated by HRMS and NMR spectroscopy, contained Gly, Thr, Asn, β-Ala, Orn, Ala, two Ser residues, and 3-hydroxy-4-methylhexadecanoic acid. The absolute configuration of its amino acid residues was determined using Marfey's analysis and <i>J</i>-based configuration analysis helped to establish the relative configuration of the 3-hydroxy-4-methylhexadecanoic acid moiety. A literature search retrieved a patent describing antibiotic TKR2999 (<b>1</b>), whose non-disclosed structure was confirmed to be identical to that found for our compound, according to its physicochemical properties and NMR spectra. Compound <b>1</b> displayed potent antifungal activity against <i>Aspergillus fumigatus</i> and a panel of <i>Candida</i> strains.
Optimal placement of multiple finite-size rectangular facilities in an existing layout (2023)

In this paper, we investigate a new problem of optimal placement of multiple finite-size rectangular facilities with known dimensions in the presence of existing rectangular facilities. This problem has applications in facility layout (re)design in manufacturing, distribution systems, services, and electronic circuit design. Three types of facility interactions are considered: between new facilities and existing facilities; between pairs of existing facilities; and between pairs of new facilities. All interactions are serviced through a finite number of input/output points located on the facility boundaries. Travel is assumed to occur according to the rectilinear (or Manhattan) metric and travel through facilities is prohibited. The objective is to find the simultaneous and non-overlapping placement of new facilities, which minimises the total weighted distance (Minisum objective) between the interacting facilities. To arrive at a solution, we divide the feasible region into sub-regions and prove that the candidates for optimal placement of the new facilities can be drawn from the sub-region boundaries. Being a continuous generalisation of the quadratic assignment problem, the solution complexity of this procedure is exponential in the number of new facilities. Our main contribution is the rigorous treatment of an important problem that unifies facility location and layout theories with minisum objective and rectilinear metrics.
[New derivatives of clofibrate and probucol. Preliminary study of their hypolipemic activity]. (1985)

The preparation is reported of compounds with a free or esterified hydroxyisobutyric acid grouping characteristic of clofibrate, on various supporting molecules related to clofibrate itself or to probucol. Some compounds showed clear hypolipemic activity and for one compound (MG 6893) the effect was not accompanied by hepatomegalia.
Simultaneous real-time imaging of the ocular anterior segment including the ciliary muscle during accommodation (2013)

We demonstrated a novel approach of imaging the anterior segment including the ciliary muscle using combined and synchronized two spectral domain optical coherence tomography devices (SD-OCT). In one SD-OCT, a Complementary Metal-Oxide-Semiconductor Transistor (CMOS) camera and an alternating reference arm was used to image the anterior segment from the cornea to the lens. Another SD-OCT for imaging the ciliary muscle was equipped with a light source with a center wavelength of 1,310 nm and a bandwidth of 75 nm. Repeated measurements were performed under relaxed and 4.00 D accommodative stimulus states in six eyes from 6 subjects. We also imaged dynamic changes in the anterior segment in one eye during accommodation. The biometry of the anterior segment and the ciliary muscle was obtained. The combined system appeared to be capable to simultaneously real-time image the biometry of the anterior segment, including the ciliary muscle, in vivo during accommodation.
Dose reduction using prior image constrained compressed sensing (DR-PICCS) (2011)

A technique for dose reduction using prior image constrained compressed sensing (DR-PICCS) in computed tomography (CT) is proposed in this work. In DR-PICCS, a standard FBP reconstructed image is forward projected to get a fully sampled projection data set. Meanwhile, it is low-pass filtered and used as the prior image in the PICCS reconstruction framework. Next, the prior image and the forward projection data are used together by the PICCS algorithm to obtain a low noise DR-PICCS reconstruction, which maintains the spatial resolution of the original FBP images. The spatial resolution of DR-PICCS was studied using a Catphan phantom by MTF measurement. The noise reduction factor, CT number change and noise texture were studied using human subject data consisting of 20 CT colonography exams performed under an IRB-approved protocol. In each human subject study, six ROIs (two soft tissue, two colonic air columns, and two subcutaneous fat) were selected for the CT number and noise measurements study. Skewness and kurtosis were used as figures of merit to indicate the noise texture. A Bland-Altman analysis was performed to study the accuracy of the CT number. The results showed that, compared with FBP reconstructions, the MTF curve shows very little change in DR-PICCS reconstructions, spatial resolution loss is less than 0.1 lp/cm, and the noise standard deviation can be reduced by a factor of 3 with DR-PICCS. The CT numbers in FBP and DR-PICCS reconstructions agree well, which indicates that DR-PICCS does not change CT numbers. The noise textures indicators measured from DR-PICCS images are in a similar range as FBP images.
An Efficiency Analysis of a Ferrite Magnet assisted Synchronous Reluctance Machine for Low Power Drives including Flux Weakening (2020)

In this paper a ferrite magnet assisted synchronous reluctance machine for a low power industrial spooling drive with a constant power characteristic at high rotational speeds is discussed. To combine an efficient machine topology at rather low product cost the permanent magnet assisted synchronous reluctance machine is proposed. Different rotor topologies are investigated and compared by simulation. Finally a three layer magnet topology was chosen, constructed and experimentally tested. The experimental results confirm a high torque and power capability even in the flux weakening operation above the nominal speed. Further, this machine type shows a significant high efficiency in a wide operation range.
Technological aspects of U and Pu recycle as most important element of closed nuclear fuel cycle (1993)

The concept of nuclear power development in Russia proceeds from the need of closing its fuel cycle. Along with the solution of economical aspects (self-support with fuel) the closed cycle will significantly improve the safety due to burning Pu and other radiologically dangerous nuclides and the reliable immobilization of waste arising there from. The paper discusses conversion of Pu and secondary U into fast and light water reactor based power and results of R and D of U-Pu oxide fuel manufacture. The choice of particular methods is also related to safety: minimum dust of high toxicity materials; and remotely handled processes to be performed commercially. The scale of successful tests of MOX fuel assemblies in BN-800, BN-600, BOR-60 (more than 2,500 fuel rods) confirms the correctness of selected technological solutions.
Multichannel restoration of single channel images using a wavelet decomposition (1993)

Multichannel linear filtering is applied to the restoration of single-channel images through the use of a wavelet decomposition. A novel matrix structure for the separable 2-D wavelet transform is presented which allows the transformation of block circulant operators, found in 2-D linear filtering problems, into semiblock circulant operators, which are defined here. These operators are easily treated as block diagonal matrices in the wavelet-frequency domain. An adaptive Wiener filter is implemented in this domain, which uses the cross-correlations between subbands in the decomposition to improve substantially the restoration of noisy-blurred images over that found with single-channel filtering. This improvement is especially evident when the power spectrum of the original image is available.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
PERCEPTUAL, MOTOR AND ATTENTIONAL DEFICITS IN SEVEN‐YEAR‐OLD CHILDREN: NEUROLOGICAL AND NEURODEVELOPMENTAL ASPECTS (1983)

This study presents the results of neurological assessments of a representative sample of seven-year-old Swedish children with perceptual, motor and attentional deficits and their controls (N = 141). Among those children diagnosed as suffering from minimal brain dysfunction (MBD), the majority showed neurodevelopmental deviations indicative of the "clumsy child syndrome'. However, 20 per cent had slight signs of choreoathetosis, diparesis, hemiparesis or ataxia. Other associated neurodevelopmental deviations are considered. The correlation between neurological findings and background factors is discussed: the MBD group had higher scores for various "organic' background factors than the comparison children, and the children with neurological syndromes had somewhat higher scores than the remaining children with MBD. The difficulties in distinguishing MBD from mental retardation, cerebral palsy and childhood psychoses is clearly illustrated. Long-term follow-up will indicate the prognostic significance of these findings.
Large-scale application of free energy perturbation calculations for antibody design (2022)

Alchemical free energy perturbation (FEP) is a rigorous and powerful technique to calculate the free energy difference between distinct chemical systems. Here we report our implementation of automated large-scale FEP calculations, using the Amber software package, to facilitate antibody design and evaluation. In combination with Hamiltonian replica exchange, our FEP simulations aim to predict the effect of mutations on both the binding affinity and the structural stability. Importantly, we incorporate multiple strategies to faithfully estimate the statistical uncertainties in the FEP results. As a case study, we apply our protocols to systematically evaluate variants of the m396 antibody for their conformational stability and their binding affinity to the spike proteins of SARS-CoV-1 and SARS-CoV-2. By properly adjusting relevant parameters, the particle collapse problems in the FEP simulations are avoided. Furthermore, large statistical errors in a small fraction of the FEP calculations are effectively reduced by extending the sampling, such that acceptable statistical uncertainties are achieved for the vast majority of the cases with a modest total computational cost. Finally, our predicted conformational stability for the m396 variants is qualitatively consistent with the experimentally measured melting temperatures. Our work thus demonstrates the applicability of FEP in computational antibody design.
P2‐076: GENERATION OF AD ANIMAL MODELS USING A NOVEL RNA‐GUIDED GENE EDITING TECHNOLOGY (2019)

Alzheimer's disease (AD) is the most common cause of dementia worldwide. A small number of patients with autosomal-dominant inheritance are known to carry mutations in Amyloid precursor protein (App) or PRESENILIN-1 (PSEN1) genes. Knock-in mice with those familial AD-related mutations have several advantages over overexpressing transgenic mice. Because conventional gene targeting technology is time-consuming and inapplicable to some cases, we have utilized a novel RNA-guided gene editing technology based on the CRISPR/Cas9 system to generate new AD mouse models. The Cas9 nucleases fused with a cytidine deaminase, named Base editor (BE) and Target-AID, are known to efficiently substitute the target C to T (or G to A) under presence of targeting RNAs (single guide RNA, sgRNA). We designed several sgRNAs targeting mouse App or Psen1, and injected them with BE mRNA or Target-AID mRNA into mouse zygotes. Two out of 43 mice that were injected with BE had a P436S mutation (4.7%), and 14 had a P436L mutation (32.6%). On the other hand, one out of 34 mice that were edited by Target-AID had a P436S mutation (2.9%). When we targeted PS1-P117 using a mutant version of BE, we were able to generate multiple mouse lines harboring various point mutations which were familial AD-related (such as PS1-P117L, and -P117S) and unrelated (such as PS1-P117V). These mice showed elevation of Aβ42: Aβ40 ratio in brain, which is one of the key pathologic changes in AD. Interestingly, not only PS1-P436S and -P117L mice, but also PS1-P436L mice exhibited pathological features characteristic of amyloid β (Aβ) production in the brain, suggesting that the PS1-P436L mutation is likely pathogenic although it has not been clinically identified as a familial AD-causing mutation. BE and Target-AID enable us to generate animal models with high efficiency in a short time. Using a similar strategy, we will try to generate a non-human primate model of AD.
Experimental Investigation of Scaling Laws for Electrospraying: Dielectric Constant Effect (1997)

ABSTRACT Experiments were performed to investigate the effect of liquid dielectric constant on existing scaling laws for the electrospraying process. The variations of the droplet size and the emitted current were measured as a function of the dielectric constant for the electrospray operating in the cone-jet mode. Eight different solvents with dielectric constants, κ, ranging from 12.5 to 182 were tested. The residue particle size distributions were measured using a TSI scanning mobility particle sizer, (SMPS). The produced liquid droplet sizes were then calculated from the known solution concentrations. The results show that: (1) For the produced droplet size, Dd , experimental data are in agreement with the scaling law (G(κ) = 1.66κ −1/6) proposed by Gañán-Calvo et al. (1994) for solvents with high dielectric constants. The derivation in low dielectric constant cases may be that the assumption of Gañán-Calvo (1994) on the characteristic length may not hold for the present system; (2) for the emitted current, I, experimental data deviate from those given by Fernández de la Mora and Loscertales (1994) except for the case of benzyl alcohol. The difference may be partially explained by the use of different electrolytes. A larger deviation is found in comparing with the equation, f(κ) = 6.46κ1/4, provided by Gañán-Calvo et al. (1994). The reasons may be due to the inapplicable characteristic length assumption and the role of ion drifting current in the total emitted current. Based on the experimental data collected, some problems are pointed out regarding the criteria proposed in the previous studies for predicting the minimum liquid feed rate. A formula is given based on these data to estimate the maximum feed rate and to explain the observations reported in Chen et al. (1995).
Effect of a 2D Hill on the Propagation of Wind Turbine Noise (2022)

A good understanding of wind turbine noise propagation is relevant to better measure the impact of turbines on the environment. In this study, we developed numerical simulations to study the impact of a 2D hill on the sound propagation for a turbine in non flat terrain. The simulations employed a propagation model derived from the linearized Euler equations, solved in a moving frame following the wavefront. The wind turbine noise was modeled using a point source approach. The flow structure in the atmospheric boundary layer and the wind turbine wake were obtained from large-eddy simulations. We find that the wind turbine wake acts as a waveguide that focuses sound propagation towards the ground. This effect is most pronounced for the flat terrain case and when the turbine is placed on the hill. The sound attenuation is more localized and closer to the turbine when the wind turbine is placed on the hilltop than in the flat case. As the wind speed increases, the sound focusing is observed closer to the turbine. For a turbine placed in front of the hill, the sound propagation is mainly determined by the flow over the hill. This demonstrates that terrain topography can have surprising effects on wind turbine noise propagation.
Tin(II) Fluoride (2001)

[7783-47-3] F2Sn (MW 156.71) InChI = 1S/2FH.Sn/h2*1H;/q;;+2/p-2 InChIKey = ANOBYBYXJXCGBS-UHFFFAOYSA-L (Knoevenagel2 and aldol-type3 catalyst; oxidative addition to carbon–halogen bonds;4, 5 stereocontrolled [3 + n] (n = 3, 4, or 5) annulations;6, 8, 9 conversion of allylic phosphonates to allyltin intermediates7) Alternate Name: stannous fluoride. Physical Data: mp 213 °C, 219.5 °C; bp 850 °C; d 4.570 g cm−3. Solubility: v sol water (>30% w/w); sol aq potassium hydroxide, fluoride solutions, mineral acids. Readily dissolves in donor solvents such as acetone, ethyl acetate, or pyridine, forming presumed pyramidal (Ψ-tetrahedral) complexes. Form Supplied in: white, monoclinic crystals; widely available. Handling, Storage, and Precautions: slowly hydrolyzes in water to SnO. Converts to SnOF2 upon exposure to air. Stable in aq mineral acids. Aq solutions are readily oxidized (catalyzed by light). Fluoride solutions react with SnF2, providing SnF3− (pK = 10) which absorbs oxygen but does not oxidize. Containers of SnF2 should be stored under a dry, inert atmosphere. LD50 128.4 mg/kg (mouse), 188.2 mg/kg (rat).
Effect of shape and size of wood on primary fragmentation in labotatory scale fluidized bed combustor (2006)

An experimental investigation was conducted to study the primary fragmentation of hard wood (Casuarina Equisetifolia) of cylindrical, cuboidal and spherical shapes with sizes varying from 10 mm to 30 mm in a laboratory-scale atmospheric bubbling fluidized bed combustor. The extent of primary fragmentation was found to increase with the size of the wood particle. Particles above 10 mm size were found to fragment, though to different degrees. The process of primary fragmentation is due to a complex combination of volatiles pressure and thermal and shrinkage stresses. Thermal shock was not found to cause primary fragmentation.
Automatic fracture hit detection in low-frequency distributed acoustic sensing using a computer vision workflow (2021)

Distributed acoustic sensing (DAS) is increasingly used in hydraulic fracturing operations. The low-frequency band of DAS (LFDAS) contains high-resolution information of the far-field strain perturbations that can be used to constrain fracture geometry. Nevertheless, the interpretation of fracture hits (frachits) in LFDAS is mostly made using simple cumulative strain maps, which can be subjective and inefficient. We introduce a computer vision workflow to automate the detection and extraction of frac-hits. The workflow is applied to a real LFDAS dataset from Western Canada, and results demonstrate the effectiveness of the proposed methodology for automating the detection of fracture hits.
[Severe bleeding in a case of factor VIII inhibitor associated with intravascular lymphomatosis]. (1993)

A 70-year-old man was admitted to Jichi Medical School Hospital on October 1, 1990, complaining of spontaneous severe hemorrhage in his extremities. He had prolonged APTT value and normal PT value. Factor VIII level was markedly diminished, and a high titer of factor VIII inhibitor was observed. He was diagnosed as having idiopathic factor VIII inhibitor because of no sign of underlying disorders. He received prednisolone and immunosuppressants, subsequently with plasma exchange and bolous factor VIII, resulting in disappearance of the inhibitor. He was admitted again in February 1991, because of the reappearance of factor VIII inhibitor. In June, furthermore, bone marrow smears showed infiltration of atypical B cells, although no evidence of organomegaly and adenopathy was observed. Therefore, he was suspected to have primary bone marrow lymphoma. He received CHOP therapy, but he died of multiorgan failure. Postmortem autopsy demonstrated multifocal intravascular lymphomatosis with marked intravascular involvement of the lung, liver, kidney, adrenal glands, spleen and bone marrow. Lymph nodes were not swollen, showing little evidence of intravascular lymphomatosis.
Genetic ancestry and skeletal toxicities among childhood acute lymphoblastic leukemia patients in the DFCI 05-001 cohort (2021)

Hispanic children have a higher incidence of acute lymphoblastic leukemia (ALL) and inferior treatment outcomes relative to non-Hispanic White children. We previously reported that Hispanic children with ALL had lower risk of fracture and osteonecrosis. To unravel the genetic root of such ethnic differences, we genotyped 449 patients from the DFCI 05-001 cohort and analyzed their ancestry. Patients with discordant clinical and genetic ancestral groups were reclassified, and those with unknown ancestry were reassigned on the basis of genetic estimates. Both clinical and genetic ancestries were analyzed in relation to risk of bone toxicities and survival outcomes. Consistent with clinically reported race/ethnicity, genetically defined Hispanic and Black patients had significantly lower risk of fracture (Hispanic: subdistribution hazard ratio [SHR], 0.42; 95% confidence interval [CI], 0.22-0.81; P = .01; Black: SHR, 0.28; 95% CI, 0.10-0.75; P = .01), and osteonecrosis (Hispanic: SHR, 0.12; 95% CI, 0.02-0.93; P = .04; Black: SHR, 0.24; 95% CI, 0.08-0.78; P = .02). The lower risk was driven by African but not Native American or Asian ancestry. In addition, patients with a higher percentage of Native American ancestry had significantly poorer overall survival and event-free survival. Our study revealed that the lower risk of bone toxicities among Black and Hispanic children treated for ALL was attributed, in part, to the percentage of African ancestry in their genetic admixture. The findings provide suggestive evidence for the protective effects of genetic factors associated with African decent against bone damage caused by ALL treatment and clues for future studies to identify underlying biological mechanisms.
A Cost and Metric Comparison of Disposable Negative-Pressure Wound Therapy Systems (2023)

We present a cost and metric comparison of currently available dNPWT systems. Despite significant differences in the cost of treatment with each dNPWT device, there has been limited research on their relative efficacies.
Multi-directional energy harvesting by piezoelectric cantilever-pendulum with internal resonance (2015)

This letter reports a piezoelectric cantilever-pendulum design for multi-directional energy harvesting. A pendulum is attached to the tip of a piezoelectric cantilever-type energy harvester. This design aims at taking advantage of the nonlinear coupling between the pendulum motion in 3-dimensional space and the beam bending vibration at resonances. Experimental studies indicate that, under properly chosen parameters, 1:2 internal resonance can be induced, which enables the multi-directional energy harvesting with a single cantilever. The advantages of the design with respect to traditional piezoelectric cantilever are examined.