gebhart/patrepeval huggingface dataset:
The Johns Hopkins manual of cardiac surgical care (1994)

Filled with practical help for the cardiac care team, this handy manual covers all aspects of care of the surgical heart patient. The chapters include: definition of the team approach to the cardiac surgical patient, preoperative assessment, the operation, and postoperative management - with individual chapters on various surgical conditions such as valve replacement and repair, heart and lung transplantation, and more.
Development of SSQ Based 157 nm Photoresist. (2002)

Siloxane/silsesquioxane (SSQ) and fluorocarbon materials have been identified to be relatively transparent at 157nm. While the main stream of material research effort has been focused on the synthesis of fluorocarbon polymers, we have made significant progress on developing silsesquioxane polymers for 157nm photoresist application. Our current SSQ based photoresists (α, ε, and δ type shown in this paper) have absorbance value ranging from 3.4 to 2.5μm-1. With a 1200Å thickness, α type has demonstrated 60nm L/S using a 0.85 NA F2 Exitech tool with an alt-PSM and ε and δ type have demonstrated 75nm L/S using a 0.60 NA tool. α type resist patterns (L/S) have been successfully transferred down to underlying spin-on carbon hard mask (HM) using N2/O2 RIE. Progress also has been made on reducing the absorbance of SSQ polymers. A new λ type SSQ polymer showed absorbance value of 1.66μm-1. The design concept and physical properties of synthesized SSQ polymers are presented. Lithographic performance of SSQ based resists is also discussed.
Electronic sensing of the taste of beer and other foodstuffs (2002)

A recently developed electronic sensing system with global selectivity is composed of several kinds of lipid/polymer membranes for transforming information of taste substances into an electric signal. The sensor output shows different patterns for chemical substances which have different taste qualities such as saltiness and sourness. Amino acids can be classified into several groups according to their own tastes with sensor outputs. The taste of foodstuffs such as beer, coffee, mineral water and vegetables can be discussed quantitatively using the taste sensor, which provides the objective scale for the human sensory expression.
A rapid room temperature chemical route for the synthesis of graphene: metal-mediated reduction of graphene oxide (2012)

A rapid and facile route for the synthesis of reduced graphene oxide sheets (rGOs) at room temperature by the chemical reduction of graphene oxide using Zn/acid in aqueous solution is demonstrated.
Engineering Approach for the Evaluation of Mechanical Wear Considering the Experimental Holloman High-Speed Test Track (2012)

This research is directed toward an understanding of the high-speed interaction effects that two bodies have on each other. The experimental high-speed test track at Holloman AFB has undergone many design innovations over 50 years. One of the problems that remains in the modern era related to improving the speed characteristics of a rocket test sled is the wear that the interconnecting device, called the slipper, undergoes as it slides down the rail and impacts local asperities. The research is separated into two main areas. The first is the metallurgical investigation in which the material change is brought about by the surface friction through surface collision, and characteristics are determined that lead to a numerical model. The second is the development of a finite-element model using the commercial code ABAQUS, which is used in an attempt to capture the physics involved in the overall phenomenon. It became evident that the wear is not uniform, but is dictated by the evolving aerodynamics of a sled moving at close to 1,500 m/s, the speed considered in this research, creating an uneven wear surface at the interface of the slipper and rail. The finite-element analysis is separated into two models, one related to the global effects of movement using a predefined velocity versus time function, and the other defining a microlocal collision with a surface asperity. The Johnson-Cook flow equation is used to establish a von Mises maximum stress failure criterion within ABAQUS to arrive at the results. A method has been developed that allows the prediction of wear for a time-dependent forcing function obtained through a structural dynamics approach. Results indicate that the method is sufficiently robust that the physics of the wear process at high speeds is reasonably modeled. The metallurgical investigation is accomplished by testing component parts of a slipper recovered after a January 2008 sled test run, and this is used as the evidence of wear.
Protein Allostery at the Solid–Liquid Interface: Endoglucanase Attachment to Cellulose Affects Glucan Clenching in the Binding Cleft (2011)

At phase boundaries, physical activities of enzymes such as substrate complexation play critical roles in driving biocatalysis. A prominent example is the cellulase cocktails secreted by fungi and bacteria for deconstructing crystalline cellulose in biomass into soluble sugars. At interfaces, molecular mechanisms of the physical steps in biocatalysis remain elusive due to the difficulties of characterizing protein action with high temporal and spatial resolution. Here, we focus on endoglucanase I (Cel7B) from the fungus Trichoderma reesei that hydrolyzes glycosidic bonds on cellulose randomly. We employ all-atom molecular dynamics (MD) simulations to elucidate the interactions of the catalytic domain (CD) of Cel7B with a cellulose microfibril before and after complexing a glucan chain in the binding cleft. The calculated mechanical coupling networks in Cel7B-glucan and Cel7B-microfibril complexes reveal a previously unresolved allosteric coupling at the solid-liquid interface: attachment of the Cel7B CD to the cellulose surface affects glucan chain clenching in the binding cleft. Alternative loop segments of the Cel7B CD were found to affix to intact or defective surface structures on the microfibril, depending on the complexation state. From a multiple sequence alignment, residues in surface-affixing segments show strong conservation, highlighting the functional importance of the physical activities that they facilitate. Surface-affixing residues also demonstrate significant sequence correlation with active-site residues, revealing the functional connection between complexation and hydrolysis. Analysis of the Cel7B CD exemplifies that the mechanical coupling networks calculated from atomistic MD simulations can be used to capture the conservation and correlation in sequence alignment.
Enhanced Production of Matrix Metalloproteinase-2 in Human Head and Neck Carcinomas is Correlated with Lymph Node Metastasis (2002)

Matrix metalloproteinase (MMP)-2 and -9 degrade type IV collagen, which is one of the major components of the basement membrane in normal tissue and expressed in the surroundings of the cancer nest in squamous cell carcinoma. The degeneration of type IV collagen is an essential step in the metastasis to lymph nodes and distant organs. In this study, we examined MMP-2 and -9 levels of cancer tissue and serum obtained from patients with head and neck squamous cell carcinoma (HNSCC) in order to evaluate the relationship between the clinicopathologic features and MMPs. We examined the production of MMP-2 and -9 in cancer tissue homogenates of 73 patients who had HNSCC and the serum MMP levels of 16 patients with HNSCC and 8 healthy volunteers. We also studied the localization of MMP-2 in the carcinoma using an immunohistochemical approach. The concentrations of MMP-2 and -9 in the tissue homogenates and serum were measured by means of a sandwich enzyme immunoassay using a monoclonal antibody. Immunohistochemical analyses were performed with monoclonal antibody to MMP-2. The concentration of MMP-2 in the tumor tissue homogenates was unrelated to tumor size, but that in patients with lymph node metastases was significantly higher than in those without lymph node metastases. The concentration of MMP-9 was unrelated to lymph node metastasis and tumor size. The levels of both MMP-2 and -9 in serum were unrelated to lymph node metastasis. Immunohistochemistry indicated that MMP-2 was mainly expressed in cancer cells. Because MMP-2 degrades type IV collagen, the level of MMP-2 in carcinomas may be a useful indicator of the degree of invasion and metastasis.
Dependence of the rates of dissolution of the Fe 4 S 4 clusters of Chromatium vinosum high-potential iron protein and ferredoxin on cluster oxidation state (1977)

The influence of oxidation state on the pH dependence of the dissolution of the Fe 4 S 4 clusters of Chromatium vinosum ferredoxin and high-potential iron protein (HIPIP) has been studied. The first-order rate constants ( k obs ) for dissolution of both the Fe 4 S 4 (S-Cys) 4 2- and Fe 4 S 4 (S-Cys) 4 3- clusters of the ferredoxin follow the same overall kinetic equation but with differing specific rate and equilibrium constants. The dependence of rate and equilibrium constants upon oxidation state may be rationalized on the basis of the accompanying change in electrostatic affinity of a cluster toward H + and HO - . A more drastic change in the pH dependence of the kinetics of dissolution of the Fe 4 S 4 cluster of the HIPIP accompanies its change in oxidation state. Whereas the values of k obs for dissolution of HIPIP containing the Fe 4 S 4 (S-Cys) 4 2- cluster are strictly second order to [H + ] and [HO - ], the pH dependence for dissolution of the HIPIP Fe 4 S 4 (S-Cys) 4 1- cluster indicates a first-order dependence upon [H + ], a second-order dependence upon [HO - ], and a spontaneous or water rate. These reactivity differences may be related to changes in cluster charge density. Mechanisms of dissolution involve preequilibrium protonation at acidic pH and preequilibrium ligand exchange at basic pH.
Human papillomavirus genotype distribution and factors associated among female sex workers in West Africa (2020)

Our study found a very high prevalence of HPV infection as well as high frequency of multiple HPV type infections in FSWs in two countries in West Africa. These findings suggest the necessity to emphasize cervical cancer prevention in this high-risk group.
Salp15 Binding to DC-SIGN Inhibits Cytokine Expression by Impairing both Nucleosome Remodeling and mRNA Stabilization (2008)

Ixodes ticks are major vectors for human pathogens, such as Borrelia burgdorferi, the causative agent of Lyme disease. Tick saliva contains immunosuppressive molecules that facilitate tick feeding and B. burgdorferi infection. We here demonstrate, to our knowledge for the first time, that the Ixodes scapularis salivary protein Salp15 inhibits adaptive immune responses by suppressing human dendritic cell (DC) functions. Salp15 inhibits both Toll-like receptor- and B. burgdorferi-induced production of pro-inflammatory cytokines by DCs and DC-induced T cell activation. Salp15 interacts with DC-SIGN on DCs, which results in activation of the serine/threonine kinase Raf-1. Strikingly, Raf-1 activation by Salp15 leads to mitogen-activated protein kinase kinase (MEK)-dependent decrease of IL-6 and TNF-alpha mRNA stability and impaired nucleosome remodeling at the IL-12p35 promoter. These data demonstrate that Salp15 binding to DC-SIGN triggers a novel Raf-1/MEK-dependent signaling pathway acting at both cytokine transcriptional and post-transcriptional level to modulate Toll-like receptor-induced DC activation, which might be instrumental to tick feeding and B. burgdorferi infection, and an important factor in the pathogenesis of Lyme disease. Insight into the molecular mechanism of immunosuppression by tick salivary proteins might provide innovative strategies to combat Lyme disease and could lead to the development of novel anti-inflammatory or immunosuppressive agents.
Sing Your Ethnicity Aloud! Grundtvigian Danes at the Intersection of Denmark and America (2018)

Most people familiar with Danish American history have encountered a narrative about the allegedly quick and unproblematic assimilation of Danish immigrants in the US, as presented here on the website of the Museum of Danish America: “Danes assimilated quickly, aided by the fact that they were white, northern european, and Protestant. Furthermore, Danes are practical and believed that assimilating into American society promised greater rewards than hanging onto their Danish identity and traditional ways.”1 even though this master narrative does, to some extent, capture the larger trajectory of the Danish immigrant experience, it disregards those Danish immigrants who played a pivotal role in creating and preserving a Danish American cultural heritage in the US. The fortieth anniversary conference of the Danish American heritage Society held in Schaumburg, Illinois in October 2017 proved that this heritage is still alive and vibrant today. The divergence between the master narrative’s emphasis on Danes’ rapid assimilation and the still-existing Danish American heritage raises several questions: how was the Danish culture transmitted to the US? how did a distinct Danish American cultural heritage evolve? Who created and preserved this heritage? how has it influenced the lives of Danish Americans through succeeding generations?
Capridine β (C-1748): A novel 1-nitroacridine derivative targets the cyclin dependent kinase, cdk4, and the tumor suppressor gene, p16 in prostate cancer. (2004)

Proc Amer Assoc Cancer Res, Volume 45, 2004

3034 

Aromatase inhibitors (anastrozole, letrozole, and exemestane) are considered viable alternatives to tamoxifen for breast cancer therapy because they work by blocking the conversion of androgens to estrogen in post-menopausal women. Indeed, anastrozole has been shown to be superior to tamoxifen for the first-line treatment of postmenopausal women with advanced breast cancer, and letrozole is being investigated in several large adjuvant trials. However, there are concerns that like tamoxifen, patients who initially respond to aromatase inhibitors will eventually develop resistance. To address the issue of acquired resistance to aromatase inhibitors, we have developed a hormone-independent breast cancer cell line, MCF7:5C, which was originally cloned from the wild-type MCF7 cells [Jiang et al ., Mol. Cell. Endocrinol. 1992., 90(1):77-86]. Using DNA quantitation and trypan blue exclusion assays, we examined the effects of E2 and the antiestrogens 4-hydroxytamoxifen (4OHT), raloxifene, and fulvestrant on the growth of MCF7:5C cells. Our results showed that while E2 treatment (1 nM) stimulated the growth of parental MCF7 cells (∼10-fold above control), it caused a dramatic reduction in the growth of MCF7:5C cells with maximum inhibition (∼90%) at day 7. 4OHT, raloxifene, and fulvestrant (at 1 μM) also reduced the growth of MCF7:5C cells (55%, 62%, and 80%, respectively), however, their inhibitory effects were less than that of E2. To investigate whether the E2-induced growth inhibition of MCF7:5C cells was due to apoptosis, analyses were performed by Annexin V-FITC/Propidium iodide and DAPI staining and confirmed by electron microscopy. Flow cytometry analysis of MCF7:5C cells revealed that apoptotic cell population increased gradually from less than 5% in vehicle control to ∼70-80% with 1 nM E2, and that this effect was almost completely blocked by the universal capase inhibitor z-VAD-FMK and fulvestrant. Interestingly, we found that fulvestrant did not induce apoptosis in MCF7:5C cells despite its ability to significantly reduce the growth of these cell, thus suggesting an alternative mechanism for its growth inhibitory effects. Furthermore, western blot analyses revealed that E2 treatment significantly reduced the levels of the anti-apoptotic proteins Bcl-2, Bcl-xl, and Hsp27 but significantly increased the levels of Bax, Bid, and Bak (pro-apoptotic). Overall, these results show that E2 is capable of inducing apoptosis in long-term estrogen-deprived breast cancer cells and that this effect is most likely capase dependent and ER-mediated. This research was supported by the DOD grant DAMD17-001-0386 and the signal transduction grant T32CA70085.
On Constructing Seminal Paper Genealogy (2013)

Let us consider that someone is starting a research on a topic that is unfamiliar to them. Which seminal papers have influenced the topic the most? What is the genealogy of the seminal papers in this topic? These are the questions that they can raise, which we try to answer in this paper. First, we propose an algorithm that finds a set of seminal papers on a given topic. We also address the performance and scalability issues of this sophisticated algorithm. Next, we discuss the measures to decide how much a paper is influenced by another paper. Then, we propose an algorithm that constructs a genealogy of the seminal papers by using the influence measure and citation information. Finally, through extensive experiments with a large volume of a real-world academic literature data, we show the effectiveness and efficiency of our approach.
Ab-initio XRPD structural characterization of coordination polymers: the case of [Ag(C3H3N2CS2)] (2003)

Abstract The crystal structure of the one-dimensional polymer [Ag(C 3 H 3 N 2 CS 2 )] has been determined from conventional X-ray powder diffraction methods, through simulated annealing and Rietveld refinement techniques [Ag(C 3 H 3 N 2 CS 2 )] is monoclinic, P 2 1 / c ; a = 8.409(1), b = 11.740(1), c = 6.721(1) Å, β = 101.86(2)°, V = 649.3(2) Å 3 ; Z = 4; ρ = 2.566 g cm -3 Final R wp , R p and R F agreement factors, for 3100 data points collected in the 8–70° 2θ range, are 0.091, 0.071 and 0.058, respectively Anisotropic peak shapes and high-angle tails for the 0 k 0 (and neighboring) reflections suggest that the polymeric chains, aligned along b , suffer from a partial disorder, in that packing of adjacent molecules does not conform to a rigorous crystalline, truly periodic , tiling.
Risk Factors for the Need of Surgical Necrosectomy After Percutaneous Catheter Drainage in the Management of Infection Secondary to Necrotizing Pancreatitis (2018)

Both mean CT density of NFC and MOF are independent pre- and post-PCD risk factors for the need of necrosectomy after PCD. Post-PCD serum procalcitonin level might be a respondent factor that is correlated with the necessity of necrosectomy.
Unsupervised Deformable Image Registration Using Cycle-Consistent CNN (2019)

Medical image registration is one of the key processing steps for biomedical image analysis such as cancer diagnosis. Recently, deep learning based supervised and unsupervised image registration methods have been extensively studied due to its excellent performance in spite of ultra-fast computational time compared to the classical approaches. In this paper, we present a novel unsupervised medical image registration method that trains deep neural network for deformable registration of 3D volumes using a cycle-consistency. Thanks to the cycle consistency, the proposed deep neural networks can take diverse pair of image data with severe deformation for accurate registration. Experimental results using multiphase liver CT images demonstrate that our method provides very precise 3D image registration within a few seconds, resulting in more accurate cancer size estimation.
Thermochemical aspects of proton transfer in the gas phase (2001)

The beginning of the twentieth century saw the development of new theories of acidity and basicity, which are currently well accepted. The thermochemistry of proton transfer in the absence of solvent attracted much interest during this period, because of the fundamental importance of the process. Nevertheless, before the 1950s, few data were available, either from lattice energy evaluations or from calculations using the emerging molecular orbital theory. Advances in mass spectrometry during the last 40 years allowed studies of numerous systems with better accuracy. Thousands of accurate gas-phase acidities or basicities are now available, for simple atomic and molecular systems and for large biomolecules. The intrinsic effect of structure on the Brønsted basic or acidic properties of molecules and the influence of solvents have been unravelled. In this tutorial, the basics of the thermodynamic principles involved are given, and the mass spectrometric techniques are briefly reviewed. Advances in the design and measurements of gas-phase superacids and superbases are described. Recent studies concerning biomolecules are also evoked.
Nitrogen-Doped Tungsten Carbide-Modified Graphite Felt as a Bifunctional Electrocatalyst for an All-Vanadium Redox Flow Battery (2022)

To enhance the electrochemical capability of graphite felt (GF) electrodes in vanadium redox flow batteries (VRFBs), we prepare nitrogen-doped tungsten carbide nanowires (N-WC NWs), which are grown on the GF surface via a two-step route. In the first step, we use a hydrothermal process using tungstic acid (H2WO4) as a precursor, and the WO3 NWs are deposited on the GF surface. Subsequently, the grown WO3 NWs are simultaneously carbonized and N-doped using melamine as the source of nitrogen and carbon. Compared to pristine GF, the prepared N-WC NWs-GF electrode exhibits an apparent electrocatalytic effect on the VO2+/VO2+ and V3+/V2+ redox reaction. The presence of a negatively charged density on the nitrogen atom encourages the vanadium ions’ absorption. The nanowire structure exposes more active sites for the vanadium ions’ redox reactions. Hence, the prepared N-WC NWs-GF electrode demonstrates the optimal electrochemical activity with energy and voltage efficiencies of 74.8% and 78.9%, respectively, which are much greater than those of the 59.8% and 63.2% attained from pristine GF at 100 mA cm–2. Moreover, the N-WC NWs-GF presented good stability and durability in acidic electrolyte during long-term operations for 100 cycles at a higher current density of 100 mA cm–2.
Femoral Osteotomies for Avascular Necrosis of the Femoral Head (2004)

Avascular necrosis of the femoral head affects 10,000 to 20,000 people every year and often these patients are in their 30s and 40s. The natural history of this disease is important to understand because the rate of femoral head collapse and treatment options are related to multiple factors including the cause of the disease, its stage at initial presentation, and the size and location of the lesion. Various treatment options have been purposed for different stages of avascular necrosis of the femoral head. Nonoperative treatments include protected weightbearing, electrical stimulation, and pharmacologic treatments. Operative treatment includes core decompression with or without grafting, debridement and grafting, osteotomy, fusion, hemiresurfacing, hemiarthroplasty, and total hip arthroplasty. The purpose of the current study was to discuss the history, indications, techniques, and results of proximal femoral osteotomies for the treatment of avascular necrosis of the femoral head.