gebhart/patrepeval huggingface dataset:
High-Order Element Effects of the Green's Function in Quantum Transport Simulation of Nanoscale Devices (2009)

High-order element (HOE) effects of the Green's function are studied by virtue of a comparative study between the recursive Green's function (RGF) method and the contact block reduction approach in double-gate metal-oxide-semiconductor field-effect transistor simulations. In general, quantum-mechanical simulations of 2-D and 3-D nanoscale devices are very computationally challenging. An efficient and widely used approach for the multidimensional problems is the RGF method. As the tridiagonal or block tridiagonal property of a self-energy matrix is exploited in the RGF method, the HOEs of the gate contact self-energy matrix are often omitted. This study on the HOE effects offers a good physical insight as well as provides a necessary measure on the applicability of the RGF method. Specifically, effects on gate current, electron density, and current density are investigated.
Structure of the C-terminally truncated human ProMMP9, a gelatin-binding matrix metalloproteinase (2002)

The X-ray crystal structure of the proform of human matrix metalloproteinase MMP9 has been solved to 2.5 A resolution. The construct includes the prodomain, the catalytic domain and three FnII (fibronectin type II) domains. The prodomain is inserted into the active-site cleft, blocking access to the catalytic zinc. Comparison with the crystal structure of the most closely related MMP, MMP2, indicates that the conformations of residues in the active-site cleft and in the cysteine-switch peptide of the prodomain are highly conserved and that design of MMP9-specific inhibitors will be challenging. In common with MMP2, the MMP9 S1' inhibitor-binding pocket is large compared with that of other MMPs. One small point of difference in the S1' binding pockets of MMP9 and MMP2 may provide an opportunity to explore the design of specific inhibitors. The side chain of Arg424 in MMP9 is angled slightly away from the S1' pocket when compared with the corresponding residue in MMP2, Thr424. The secondary structure of the FnII domains is conserved between the two closely related MMPs, although the second FnII domain makes no contact with the catalytic domain in MMP9, while the same domain in MMP2 has a substantial area of interaction with the catalytic domain.
PLASTIC SURGERY BEYOND THE HUMAN GENOME (2003)

Pleat, Jonathon M.A., M.R.C.S.; Dunkin, Christopher M.R.C.S.(Ed.); Zitzmann, Nicole Ph.D. Author Information
CytomegalovirusInfection Impairs Immunosuppressive and Antimicrobial Effector Functions of Human Multipotent Mesenchymal Stromal Cells (2014)

Human mesenchymal stromal cells (MSC) possess immunosuppressive and antimicrobial effects that are partly mediated by the tryptophan-catabolizing enzyme indoleamine-2,3-dioxygenase (IDO). Therefore MSC represent a promising novel cellular immunosuppressant which has the potential to control steroid-refractory acute graft versus host disease (GvHD). In addition, MSC are capable of reducing the risk of infection in patients after haematopoietic stem cell transplantation (HST). Recent data indicate that signals from the microenvironment including those from microbes may modulate MSC effector functions. As Cytomegalovirus (CMV) represents a prominent pathogen in immunocompromised hosts, especially in patients following HST, we investigated the impact of CMV infection on MSC-mediated effects on the immune system. We demonstrate that CMV-infected MSC lose their cytokine-induced immunosuppressive capacity and are no longer able to restrict microbial growth. IDO expression is substantially impaired following CMV infection of MSC and this interaction critically depends on intact virus and the number of MSC as well as the viral load. Since overt CMV infection may undermine the clinical efficacy of MSC in the treatment of GvHD in transplant patients, we recommend that patients scheduled for MSC therapy should undergo thorough evaluation for an active CMV infection and receive CMV-directed antiviral therapy prior to the administration of MSC.
Reversible exchange of wetting state of a hydrophobic surface via phase change material coating (2018)

Reversible exchange of the wetting state of a hydrophobic surface is examined. Solution crystallization of a polycarbonate surface is carried out to form hierarchically distributed micro/nano size spherules and fibrils on the surface. Although the solution crystallized surface has hydrophobic characteristics, the contact angle hysteresis remains high. Functionalized silica particles are deposited on the crystallized polycarbonate surface to improve the droplet contact angle and lower contact angle hysteresis. The liquid film of <i>n</i>-octadecane with 1.5 μm thickness is formed on the functionalized silica particles deposited crystallized surface, which results in hydrophilic surface characteristics. The <i>n</i>-octadecane film solidifies upon reducing the temperature on the surface and solid flakes of <i>n</i>-octadecane are formed. This arrangement changes the surface wetting state to hydrophobic. Liquefaction and solidifying of the <i>n</i>-octadecane film at the functionalized silica deposited surface gives rise to reversible exchange of surface wetting state. This behavior is attributed to exposure of emerging functionalized silica particles to the free surface in the region of the solid <i>n</i>-octadecane flakes. The water droplet is cloaked by the liquid <i>n</i>-octadecane while forming a ridge around the droplet. In this case, the water droplet becomes mobile at the surface because flow develops in the <i>n</i>-octadecane liquid film at the onset of liquefaction.
Assessing the reproducibility of coral‐based climate records (2004)

We perform replication tests using monthly variations in Sr/Ca and δ 18 O in four cores from three Porites lutea coral heads from New Caledonia to assess the reproducibility of coral‐based climate records. Coral Sr/Ca (δ 18 O) records are well correlated to each other and to the instrumental SST record (1967–1992), especially in terms of differences in the mean values of 25‐year SST records (∼0.2°C, Sr/Ca‐SST; 0.6°C, δ 18 O‐SST). The average error associated with the coral Sr/Ca‐SST (δ 18 O‐SST) of any particular month, season or year is ∼0.8°C (1.1°C), 0.6°C (0.8°C) and 0.5°C (0.6°C), respectively. “Stacking” or averaging the individual proxy records reduces the error between observed and predicted SST, although the reduction is small for coral Sr/Ca. Excellent reproducibility among the coral proxies implies that reliable climate records can be generated from a single coral core and that coral Sr/Ca‐SST records are not compromised, beyond the errors stated herein, by non‐temperature‐related biological effects.
Removing Biases in Communication of Severity Assessments of Intimate Partner Violence: Model Development and Evaluation (2023)

The results show that the computational model mitigates accuracy bias and removes calibration biases. These results suggest that computational models can be used for debiasing the severity evaluations of violence. These findings may have application in a legal context, prioritizing resources in society and how violent events are presented in the media.
Building science or building physics (2012)

I like the ancient pattern, where and instead of one’s title one tells the name of one’s mentor. Three mentors shaped my professional life. The first one was in Warsaw, Poland, Prof. Bohdan Lewicki, whose books on concrete panels were translated in many languages. One day, after his class, he told me: ‘‘We need to evaluate hygrothermal performance of an experimental building with no-fine concrete,—if you would like to do it, I will provide you with all the money needed. From this day on, I have been learning Building Physics. My second mentor was Prof. Lars Eric Nevander in Lund, Sweden, one of the three Swedish professors who in 1972 introduced limit states method into the field of durability assessment, exactly 40 years before the first ISO standard did so. Lars Eric taught me that progress in construction depends on how strong is the continuum between industrial and academic domains in Building Physics. My third mentor was Prof. Neil Hutcheon known in Canada as the father of building science. It is only fair that I start writing my column with his definition of Building Science.
Mutations in MARS identified in a specific type of pulmonary alveolar proteinosis alter methionyl‐tRNA synthetase activity (2018)

Biallelic missense mutations in MARS are responsible for rare but severe cases of pulmonary alveolar proteinosis (PAP) prevalent on the island of La Réunion. MARS encodes cytosolic methionyl-tRNA synthetase (MetRS), an essential translation factor. The multisystemic effects observed in patients with this form of PAP are consistent with a loss-of-function defect in an ubiquitously expressed enzyme. The pathophysiological mechanisms involved in MARS-related PAP are currently unknown. In this work, we analyzed the effect of the PAP-related mutations in MARS on the thermal stability and on the catalytic parameters of the MetRS mutants, relative to wild-type. The effect of these mutations on the structural integrity of the enzyme as a member of the cytosolic multisynthetase complex was also investigated. Our results establish that the PAP-related substitutions in MetRS impact the tRNA<sup>Met</sup> -aminoacylation reaction especially at the level of methionine recognition, and suggest a direct link between the loss of activity of the enzyme and the pathological disorders in PAP.
Independent Spatial and Temporal Functions of Human Sperm Centrosomes After Dispermic Microinjection Into Bovine Oocytes (2009)

During mammalian fertilization, a centrosome is introduced by the sperm during the first cell cycle to organize a radial array of microtubules known as the sperm aster. In nature, multiple human sperm centrosomes may exist in the same egg cytoplasm during polyspermy. However, critical information concerning individual sperm centrosomal function with regards to the latter case remains unknown. We subsequently examined the sperm aster formation after injection of multiple human sperm into a bovine egg. When 2 fertile human sperm were simultaneously microinjected into different regions of the same bovine egg cytoplasm, no difference in sperm aster formation rate was observed compared to cases in which a single sperm was injected. Two human sperm were also microinjected into bovine eggs 30-, 60- and 120-minute intervals apart from one another, and no difference in sperm aster formation rates were observed. Among eggs in which 1 sperm aster was organized, there was no observable bias towards the first or second injected sperm. These findings indicated that when multiple human sperm are present in a single egg cytoplasm, each centrosome can function independently from the other. This fact suggests the possibility of transplanting a normal sperm centrosome into an egg with a sperm known to have centrosomal dysfunction.
Space-alternating generalized expectation-maximization algorithm (1994)

The expectation-maximization (EM) method can facilitate maximizing likelihood functions that arise in statistical estimation problems. In the classical EM paradigm, one iteratively maximizes the conditional log-likelihood of a single unobservable complete data space, rather than maximizing the intractable likelihood function for the measured or incomplete data. EM algorithms update all parameters simultaneously, which has two drawbacks: 1) slow convergence, and 2) difficult maximization steps due to coupling when smoothness penalties are used. The paper describes the space-alternating generalized EM (SAGE) method, which updates the parameters sequentially by alternating between several small hidden-data spaces defined by the algorithm designer. The authors prove that the sequence of estimates monotonically increases the penalized-likelihood objective, derive asymptotic convergence rates, and provide sufficient conditions for monotone convergence in norm. Two signal processing applications illustrate the method: estimation of superimposed signals in Gaussian noise, and image reconstruction from Poisson measurements. In both applications, the SAGE algorithms easily accommodate smoothness penalties and converge faster than the EM algorithms.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Supplementary Data from Harnessing Androgen Receptor Pathway Activation for Targeted Alpha Particle Radioimmunotherapy of Breast Cancer (2023)

&lt;p&gt;Supplementary figure 2&lt;/p&gt;
Thienopyridine‐linked thrombotic microangiopathy: association with endothelial cell apoptosis and activation of MAP kinase signalling cascades (2003)

The thienopyridine platelet antagonist ticlopidine is associated with development of thrombotic thrombocytopenic purpura (TTP) but the pathophysiology of this link is unclear. Severe deficiency of disintegrin and metalloproteinase with thrombospondin motif-13 (ADAMTS13), described in familial cases and a significant fraction of idiopathic TTP, has been reported in only a few ticlopidine-linked cases. As ticlopidine can disrupt production of extracellular matrix (ECM) components critical to microvascular endothelial cell (MVEC) integrity in vitro, we explored the hypotheses that ticlopidine and ticlopidine-linked TTP plasmas induce MVEC apoptosis in a manner similar to that of idiopathic TTP plasmas, and that ECM components and related mitogen-activated protein kinase (MAPK) signalling cascades may be involved in this process. Replicating the activity of plasmas from patients with idiopathic TTP, plasma from five ticlopidine-linked TTP patients induced apoptosis of primary human dermal, glomerular and hepatic MVEC, but had no effect on pulmonary MVEC or large vessel endothelial cells (EC). Pharmacological levels of ticlopidine initiated apoptosis with similar EC lineage restriction. In parallel, ticlopidine and plasmas from idiopathic and ticlopidine-TTP patients decreased transcripts for the ECM component thrombospondin-1 in MVEC, but not in large vessel EC. These changes were accompanied by prolonged induction of MAPKs extracellular signal-related kinase (ERK)-1/2 and p38 only in TTP susceptible MVEC. Induction of apoptosis by ticlopidine and TTP plasma was abrogated by inhibitors of ERK-1/2 and p38 phosphorylation. In conclusion, MVEC apoptosis related to altered ECM-MVEC interactions may be a key part of the pathology of ticlopidine-linked and idiopathic TTP.
Hypoxia-Responsive Lipid–Polymer Nanoparticle-Combined Imaging-Guided Surgery and Multitherapy Strategies for Glioma (2020)

Glioma is the most prevalent type of malignant brain tumor and is usually very aggressive. Because of the high invasiveness and aggressive proliferative growth of glioma, it is difficult to resect completely or cure with surgery. Residual glioma cells are a primary cause of postoperative recurrence. Herein, we describe a hypoxia-responsive lipid polymer nanoparticle (LN) for fluorescence-guided surgery, chemotherapy, photodynamic therapy (PDT), and photothermal therapy (PTT) combination multitherapy strategies targeting glioma. The hypoxia-responsive LN [LN (DOX + ICG)] contains a hypoxia-responsive component poly(nitroimidazole)<sub>25</sub> [P-(Nis)<sub>25</sub>], the glioma-targeting peptide angiopep-2 (A2), indocyanine green (ICG), and doxorubicin (DOX). LN (DOX + ICG) comprises four distinct functional components: (1) A2: A2 modified nanoparticles effectively target gliomas, enhancing drug concentration in gliomas; (2) P-(Nis)<sub>25</sub>: (i) the hydrophobic component of LN (DOX + ICG) with hypoxia responsive ability to encapsulate DOX and ICG; (ii) allows rapid release of DOX from LN (DOX + ICG) after 808 nm laser irradiation; (3) ICG: (i) ICG allows imaging-guided surgery, combining PDT and PTT therapies; (ii) upon irradiation with an 808 nm laser, ICG creates a hypoxic environment; (4) DOX inhibits glioma growth. This work demonstrates that LN (DOX + ICG) might provide a novel clinical approach to preventing post-surgical recurrence of glioma.
Rigid internal fixation of fractures of the proximal humerus in older patients (2000)

In 42 elderly patients, 33 women and nine men with a mean age of 72 years, we treated displaced fractures of the proximal humerus (34 three-part, 8 four-part) using a blade plate and a standard deltopectoral approach. Functional treatment was started immediately after surgery. We reviewed 41 patients at one year and 38 at final follow-up at 3.4 years (2.4 to 4.5). At the final review, all the fractures had healed. The clinical results were graded as excellent in 13 patients, good in 17, fair in seven, and poor in one. The median Constant score was 73 +/- 18. Avascular necrosis of the humeral head occurred in two patients (5%). We conclude that rigid fixation of displaced fractures of the proximal humerus with a blade plate in the elderly patient provides sufficient primary stability to allow early functional treatment. The incidence of avascular necrosis and nonunion was low. Restoration of the anatomy and biomechanics may contribute to a good functional outcome when compared with alternative methods of fixation or conservative treatment. Regardless of the age of the patients, we advocate primary open reduction and rigid internal fixation of three- and four-part fractures of the proximal humerus.
Unprecedented size-sieving ability in polybenzimidazole doped with polyprotic acids for membrane H2/CO2 separation (2017)

Acid doped polybenzimidazole shows exceptionally high performance for H<sub>2</sub>/CO<sub>2</sub> separation with unprecedented selectivity of 140 at 150 °C.
An isogenic cell line panel for sequence-based screening of targeted anticancer drugs (2022)

We describe the creation of an isogenic cell line panel representing common cancer pathways, with features optimized for high-throughput screening. More than 1,800 cell lines from three normal human cell lines were generated using CRISPR technologies. Surprisingly, most of these lines did not result in complete gene inactivation despite integration of sgRNA at the desired genomic site. A subset of the lines harbored biallelic disruptions of the targeted tumor suppressor gene, yielding a final panel of 100 well-characterized lines covering 19 frequently lost cancer pathways. This panel included genetic markers optimized for sequence-based ratiometric assays for drug-based screening assays. To illustrate the potential utility of this panel, we developed a high-throughput screen that identified Wee1 inhibitor MK-1775 as a selective growth inhibitor of cells with inactivation of <i>TP53</i>. These cell lines and screening approach should prove useful for researchers studying a variety of cellular and biochemical phenomena.
Many-to-many and Completely Parallel-data-free Voice Conversion Based on Eigenspace DNN (2018)

Media conversion of image, text, speech, etc., generally requires a large amount of parallel data for training a conversion model. Recently, methods for training the model using no or a small amount of parallel data draw researchers' attention. In many-to-many voice conversion, since it is often hard to collect parallel data from every pair of speakers, the conversion models requiring no parallel data are desired. Conventional many-to-many voice conversion models required a large amount of prestored parallel data to acquire prior knowledge of the entire speaker space. Then, a specific model from an arbitrary speaker to another can be realized by adapting a few model parameters. Although these conversion models certainly do not use parallel data in an adaptation step, they still use parallel data for prior training. In this study, we aim at realizing completely parallel-data-free and many-to-many voice conversion. The proposed method uses both Eigenvoice Gaussian mixture models (EVGMM) and Deep neural network (DNN). EVGMM is a many-to-many conversion model that constructs the entire speaker space (called eigenspace) by analyzing mean vectors of Gaussian mixture models and it is used in our method to decompose training speakers' features into their eigenspace components. By using the speaker features and the obtained components as pseudo parallel data, multiple DNNs are trained to realize conversion between them. With these DNNs, features of any target speaker can be represented by a weighted sum of the components. It should be noted that all the processes of our proposal do not require any parallel data. A key technique is to estimate covariance terms of EVGMM with no parallel data. Experiments indicate that individuality scores of the proposed method using no parallel data are comparable enough to those of a baseline system trained with parallel data.
Rheumatoid factor and antibodies to cyclic citrullinated Peptide differentiate rheumatoid arthritis from undifferentiated polyarthritis in patients with early arthritis. (2002)

The criterion IgM-RF > 40 or anti-CCP > 50 is able to predict the diagnosis of RA in early arthritis patients with high specificity and acceptable sensitivity. Anti-CCP testing combined with IgM-RF testing has additional value over IgM-RF testing alone in patients with early undifferentiated oligo and polyarthritis.
A Prospective Study in 38 Patients with Abruptio Placentae of 70 Cases Complicated by DIC (1987)

Abstract Disseminated intravascular coagulation (DIC) diagnostic criteria for obstetrics as a clinical scoring system were established. These criteria, in which more weight was given to the underlying disease and to clinical findings than to laboratory parameters (coagulation tests), agree closely with the DIC diagnostic criteria of the Japanese Ministry of Health and Welfare. Efficacy evaluation criteria for obstetric DIC were also defined to enable follow‐up of the clinical efficacy of DIC therapy. The clinical usefulness of these criteria was confirmed by comparison of infusion efficacy between AT III concentrate (Behring‐werke AG) and injectable FOY? (Ono Pharmaceutical Co., Ltd.) for the 38 DIC cases with abruptio placentae collected here. The total score, FDP score, and platelet score were improved markedly in the AT III group compared with the FOY group.
POSA: a user-driven, interactive multiple protein structure alignment server (2014)

POSA (Partial Order Structure Alignment), available at http://posa.godziklab.org, is a server for multiple protein structure alignment introduced in 2005 (Ye,Y. and Godzik,A. (2005) Multiple flexible structure alignment using partial order graphs. Bioinformatics, 21, 2362-2369). It is free and open to all users, and there is no login requirement, albeit there is an option to register and store results in individual, password-protected directories. In the updated POSA server described here, we introduce two significant improvements. First is an interface allowing the user to provide additional information by defining segments that anchor the alignment in one or more input structures. This interface allows users to take advantage of their intuition and biological insights to improve the alignment and guide it toward a biologically relevant solution. The second improvement is an interactive visualization with options that allow the user to view all superposed structures in one window (a typical solution for visualizing results of multiple structure alignments) or view them individually in a series of synchronized windows with extensive, user-controlled visualization options. The user can rotate structure(s) in any of the windows and study similarities or differences between structures clearly visible in individual windows.