gebhart/patrepeval huggingface dataset:
The amino acid sequence of chymopapain from Carica papaya (1990)

Chymopapain is a polypeptide of 218 amino acid residues. It has considerable structural similarity with papain and papaya proteinase omega, including conservation of the catalytic site and of the disulphide bonding. Chymopapain is like papaya proteinase omega in carrying four extra residues between papain positions 168 and 169, but differs from both papaya proteinases in the composition of its S2 subsite, as well as in having a second thiol group, Cys-117. Some evidence for the amino acid sequence of chymopapain has been deposited as Supplementary Publication SUP 50153 (12 pages) at the British Library Document Supply Centre, Boston Spa., Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies may be obtained on the terms indicated in Biochem. J. (1990) 265, 5. The information comprises Supplement Tables 1-4, which contain, in order, amino acid compositions of peptides from tryptic, peptic, CNBr and mild acid cleavages, Supplement Fig. 1, showing re-fractionation of selected peaks from Fig. 2 of the main paper. Supplement Fig. 2, showing cation-exchange chromatography of the earliest-eluted peak of Fig. 3 of the main paper, Supplement Fig. 3, showing reverse-phase h.p.l.c. of the later-eluted peak from Fig. 3 of the main paper, and Supplement Fig. 4, showing the separation of peptides after mild acid hydrolysis of CNBr-cleavage fragment CB3.
A high-throughput phenotypic screen identifies clofazimine as a potential treatment for cryptosporidiosis (2017)

Cryptosporidiosis has emerged as a leading cause of non-viral diarrhea in children under five years of age in the developing world, yet the current standard of care to treat Cryptosporidium infections, nitazoxanide, demonstrates limited and immune-dependent efficacy. Given the lack of treatments with universal efficacy, drug discovery efforts against cryptosporidiosis are necessary to find therapeutics more efficacious than the standard of care. To date, cryptosporidiosis drug discovery efforts have been limited to a few targeted mechanisms in the parasite and whole cell phenotypic screens against small, focused collections of compounds. Using a previous screen as a basis, we initiated the largest known drug discovery effort to identify novel anticryptosporidial agents. A high-content imaging assay for inhibitors of Cryptosporidium parvum proliferation within a human intestinal epithelial cell line was miniaturized and automated to enable high-throughput phenotypic screening against a large, diverse library of small molecules. A screen of 78,942 compounds identified 12 anticryptosporidial hits with sub-micromolar activity, including clofazimine, an FDA-approved drug for the treatment of leprosy, which demonstrated potent and selective in vitro activity (EC50 = 15 nM) against C. parvum. Clofazimine also displayed activity against C. hominis-the other most clinically-relevant species of Cryptosporidium. Importantly, clofazimine is known to accumulate within epithelial cells of the small intestine, the primary site of Cryptosporidium infection. In a mouse model of acute cryptosporidiosis, a once daily dosage regimen for three consecutive days or a single high dose resulted in reduction of oocyst shedding below the limit detectable by flow cytometry. Recently, a target product profile (TPP) for an anticryptosporidial compound was proposed by Huston et al. and highlights the need for a short dosing regimen (< 7 days) and formulations for children < 2 years. Clofazimine has a long history of use and has demonstrated a good safety profile for a disease that requires chronic dosing for a period of time ranging 3-36 months. These results, taken with clofazimine's status as an FDA-approved drug with over four decades of use for the treatment of leprosy, support the continued investigation of clofazimine both as a new chemical tool for understanding cryptosporidium biology and a potential new treatment of cryptosporidiosis.
Supplementary Table 1 from The Splicing Factor PTBP1 Represses <i>TP63 γ</i> Isoform Production in Squamous Cell Carcinoma (2023)

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Chiral Discrimination of α-Chiral Ammonium Ions by Sterically Geared Chiral Tripodal Oxazolines (2010)

” conformation (“1,3,5-up/2,4,6-down” conformation) to avoid otherwise increased steric repulsion between the vicinal substituents of the benzene frame. Use of such sterically bulky subunits within a molecule to enable it to adopt a thermodynamically favored conformation with mini-mum steric interactions has been dubbed as “steric gearing.”
A computational investigation of the properties of a reverse osmosis membrane (2010)

Reverse osmosis (RO) is currently one of the most widely used methods of desalination in the world and rapidly increasing in usage. The membranes used in the RO process play a vital role in determining the effectiveness of the desalination process. In this work, fully atomistic molecular dynamics simulations of one of the most widely employed membranes, namely the FT30 polyamide material, have been carried out in order gain greater understanding of the structure of the system and its interaction with saline solution. The system studied consisted of a solvated membrane layer and a layer of bulk solution, thus allowing the membrane interface to be simulated. The behaviour of water and salt ions in both the bulk solution and membrane has been investigated. It was found that the diffusivities of water and the salt ions were reduced by an order of magnitude within the membrane. Furthermore, umbrella sampling methods have been used in order to determine the free energy surface associated with the salt ions passing through the membrane-solution interface. The present work demonstrates that there is a high degree of variability in the resistance to salt diffusion into the membrane associated with the structure of the water encountered as the ion permeates the membrane. Despite this variability in the free energy gradient, all cases ultimately exhibit a high resistance to ionic diffusion due to charge separation. However, migration of a sodium cation/chloride anion pair fails to substantially lower the barrier to salt diffusion, thus confirming the robust nature of the membrane selectivity for water.
A Study on Flow Boiling in Microchannel With Piranha Pin Fin (2015)

In this paper we reported an advanced structure, the Piranha Pin Fin (PPF), for microchannel flow boiling. Fluid flow and heat transfer performance were evaluated in detail with HFE7000 as working fluid. Surface temperature, pressure drop, heat transfer coefficient and critical heat flux (CHF) were experimentally obtained and discussed. Furthermore, microchannels with different PPF geometrical configurations were investigated. At the same time, tests for different flow conditions were conducted and analyzed. It turned out that microchannel with PPF can realize high-heat flux dissipation with reasonable pressure drop. Both flow conditions and PPF configuration played important roles for both fluid flow and heat transfer performance. This study provided useful reference for further PPF design in microchannel for flow boiling.
New non invasive Doppler technology for carotid stenosis assessment (2013)

Multigate Quality Doppler Profiles (QDP) is a Fast Fourier Transform-based Doppler technology recently integrated in a commercial ultrasound scanner. QDP represents a novel analysis tool, which is able to simultaneously detect and show the velocity components, present in the blood flow of multiple vessels, without any frame rate reduction. The present work describes QDP application to the measurement of Internal Carotid Artery stenosis (i.e. vessel lumen reduction due to plaque formation). Measurements were performed in vitro on a Doppler Phantom and in vivo in comparison to Computed Tomography Angiography. The results confirmed QDP as a proper tool for the NASCET index measurement, more precise and robust than the traditional Ultrasound modalities used so far.
Design Method of Smallest Robust Networks Against Performance Deterioration During Failures (2010)

A telecommunication network should be reliable. However, in many actual networks, there exists the risk that the quality of service drastically deteriorates when the length of paths increases due to a link failure. To get rid of this risk, it is necessary to design a stable network that the maximum increasing ratio of the length of all paths in case of a link failure is small. We proposed the approximation algorithm for the network design problem that constructs such a network by adding some links to a network before. On the other hand, a network design method to construct a network from scratch is also needed. For that purpose, in this paper, we deal with the network design problem that determines a graph with the limited degree, diameter, and maximum increasing ratio of the lengths of all paths in case of an edge deletion. First, we prove that this problem is NP-complete. Next, we propose a heuristic algorithm for this problem and evaluate its performance by the comparison with some actual ISP backbone networks. Our experimental results show that the proposed algorithm worked well on a set of network structures.
The Immunotherapy Landscape in Adrenocortical Cancer (2021)

Adrenocortical carcinoma (ACC) is a rare cancer of the adrenal gland that is frequently associated with excess production of adrenal hormones. Although surgical resection may be curative in early-stage disease, few effective therapeutic options exist in the inoperable advanced or metastatic setting. Immunotherapies, inclusive of a broad array of immune-activating and immune-modulating antineoplastic agents, have demonstrated clinical benefit in a wide range of solid and hematologic malignancies. Due to the broad activity across multiple cancer types, there is significant interest in testing these agents in rare tumors, including ACC. Multiple clinical trials evaluating immunotherapies for the treatment of ACC have been conducted, and many more are ongoing or planned. Immunotherapies that have been evaluated in clinical trials for ACC include the immune checkpoint inhibitors pembrolizumab, nivolumab, and avelumab. Other immunotherapies that have been evaluated include the monoclonal antibodies figitumumab and cixutumumab directed against the ACC-expressed insulin-like growth factor 1 (IGF-1) receptor, the recombinant cytotoxin interleukin-13-pseudomonas exotoxin A, and autologous tumor lysate dendritic cell vaccine. These agents have shown modest clinical activity, although nonzero in the case of the immune checkpoint inhibitors. Clinical trials are ongoing to evaluate whether this clinical activity may be augmented through combinations with other immune-acting agents or targeted therapies.
Guided acoustic wave resonators using an acoustic Bragg mirror (2010)

Lamb wave devices have recently gained an interest for providing narrow bandpass filters in wireless transmission systems. Their cointegration with film bulk acoustic wave resonators is a major advantage, enabling the possibility to provide simultaneously several radio frequency and intermediate-frequency filters in a single fabrication. Similarly, in this work, we report the fabrication of resonators using waves guided in a piezoelectric layer deposited atop a Bragg mirror. Such waves exhibit a behavior close to Lamb waves, thanks to the acoustic isolation provided by the mirror, while being cointegrated along with solidly mounted resonator structures.
Transverse anisotropy of compressive failure in European oak – a digital speckle photography study (2006)

Abstract The mechanical behaviour of European oak ( Quercus robur L.) was studied in radial and tangential compression. Young's modulus and the yield strength were approximately 1.7- and 1.6-fold higher, respectively, in the radial direction. Strain fields were determined by digital speckle photography (DSP). Strains and the effective Poisson ratio could be determined separately in earlywood and latewood during deformation and failure events. In radial compression, strain data showed that rays contributed significantly to the high modulus. In addition, multiseriate ray microbuckling was observed to control yield strength. The microbuckling was localised in the low-density earlywood. In tangential compression, yield strength was controlled by vessel collapse in the low-density regions of the latewood. The strain field data provide direct evidence that the rays are the main micro-structural factor controlling transverse anisotropy in European oak.
Management of regional citrate anticoagulation for continuous renal replacement therapy: guideline recommendations from Chinese emergency medical doctor consensus (2023)

Continuous renal replacement therapy (CRRT) is widely used for treating critically-ill patients in the emergency department in China. Anticoagulant therapy is needed to prevent clotting in the extracorporeal circulation during CRRT. Regional citrate anticoagulation (RCA) has been shown to potentially be safer and more effective and is now recommended as the preferred anticoagulant method for CRRT. However, there is still a lack of unified standards for RCA management in the world, and there are many problems in using this method in clinical practice. The Emergency Medical Doctor Branch of the Chinese Medical Doctor Association (CMDA) organized a panel of domestic emergency medicine experts and international experts of CRRT to discuss RCA-related issues, including the advantages and disadvantages of RCA in CRRT anticoagulation, the principle of RCA, parameter settings for RCA, monitoring of RCA (mainly metabolic acid-base disorders), and special issues during RCA. Based on the latest available research evidence as well as the paneled experts' clinical experience, considering the generalizability, suitability, and potential resource utilization, while also balancing clinical advantages and disadvantages, a total of 16 guideline recommendations were formed from the experts' consensus.
ASSOCIATION OF MHC CLASS I WITH SPONDYLOARTHROPATHIES IN KUWAIT (1996)

This study is the first to assess the prevalence of HLA B27 in Kuwaiti patients with ankylosing spondylitis (AS) or related spondyloarthropathies compared to healthy controls. Positive HLA B27 was found in nine (25.7%) of 35 patients, but only in 22 (4%) of 544 controls (P = 0.000). A significant difference in Cw2 and Cw6 between patients and controls was also found (P < 0.01 and 0.000, respectively), suggesting a linkage disequilibrium between B27 and Cw2 (P < 0.000) in the Kuwaiti population. These findings suggest that B27-positive Kuwaitis are at high risk of developing AS and spondyloarthropathies, especially if they carry Cw2 and Cw6: The importance of HLA Cw loci is becoming increasingly apparent in disease association studies.
EXCISION AND IMMEDIATE REVASCULARIZATION FOR HEPATIC ARTERY PSEUDOANEURYSM FOLLOWING LIVER TRANSPLANTATION (1998)

177 Pseudoaneurysm (PA) of the hepatic artery following liver transplantation is a rare and often fatal complication. It frequently occurs in the face of intra-abdominal infection. Reports in the literature have described ligation as the preferred management of PA in an infected field. We report here on the treatment of 15 patients who developed hepatic artery PA. In our experience, primary excision with immediate revascularization provides superior results to ligation or embolization. Methods: A retrospective review was done to evaluate treatment and outcome of patients with hepatic artery PA following liver transplantation. Between 12/1/89 and 12/31/97, 2073 orthotopic liver transplants were performed at our institution. All patients received immunosuppression based on a standard regimen employing tacrolimus and steroids. In this time period, 15 patients were diagnosed with 16 PA. Treatment consisted of ligation or embolization, or excision and revascularization with autologous or allograft tissue. Treatment was selected at the discretion of the surgeon. Results: The most common cause of PA in these patients was a bile leak (11). Other causes included suture line dehiscence (2), intraparenchymal injuries after liver biopsy (2), and pancreatitis (1). All PA secondary to a bile leak presented within two months of transplant. PA from other causes tended to present late (mean-360 d). 5 patients underwent operative ligation. All died of sepsis an average of 62 d after ligation, despite retransplantation in 3 of them. One patient died of sepsis after embolization of a PA, while one patient remains alive over 4 years after embolization of an intraparenchymal branch of the hepatic artery. In contrast, 8 patients underwent excision and immediate revascularization, including 5 with intraabdominal infection from a bile leak, and 1 with severe pancreatitis. All patients treated with immediate revascularization were subsequently discharged from the hospital with normal liver function. Three of these patients died an average of 831 d after presentation with a PA from unrelated causes. None of the patients required later retransplantation. Conclusions: Most hepatic artery PA occur in the presence of intraabdominal infection. However, our results indicate that excision of the PA with immediate revascularization offers the best survival advantage to the patient.
Resonantly coupled surface plasmon polaritons in the grooves of very deep highly blazed zero-order metallic gratings at microwave frequencies (2001)

Sharp features are observed in the wavelength-dependent reflectivity of very deep highly blazed zero-order metallic gratings at microwave frequencies. These features are attributed to the resonant excitation of self-coupled surface plasmon polaritons in the cavities of such samples. The slat structures may, in a simplistic model, be treated as a class of Fabry–Pérot cavity resonator.
The multiple facets of Peto's paradox: a life-history model for the evolution of cancer suppression (2015)

Large animals should have higher lifetime probabilities of cancer than small animals because each cell division carries an attendant risk of mutating towards a tumour lineage. However, this is not observed--a (Peto's) paradox that suggests large and/or long-lived species have evolved effective cancer suppression mechanisms. Using the Euler-Lotka population model, we demonstrate the evolutionary value of cancer suppression as determined by the 'cost' (decreased fecundity) of suppression verses the 'cost' of cancer (reduced survivorship). Body size per se will not select for sufficient cancer suppression to explain the paradox. Rather, cancer suppression should be most extreme when the probability of non-cancer death decreases with age (e.g. alligators), maturation is delayed, fecundity rates are low and fecundity increases with age. Thus, the value of cancer suppression is predicted to be lowest in the vole (short lifespan, high fecundity) and highest in the naked mole rat (long lived with late female sexual maturity). The life history of pre-industrial humans likely selected for quite low levels of cancer suppression. In modern humans that live much longer, this level results in unusually high lifetime cancer risks. The model predicts a lifetime risk of 49% compared with the current empirical value of 43%.
Large-Angle, Broadband and Multifunctional Gratings Based on Directively Radiating Waveguide Scatterers (2019)

Conventional surface-relief gratings are inefficient at deflecting normally-incident light by large angles. This constrains their use in many applications and limits the overall efficiency of any optical instrument integrating gratings. Here, we demonstrate a simple approach for the design of diffraction gratings that can be highly efficient for large deflection angles, while also offering additional functionality. The gratings are composed of a unit cell comprising a vertically-oriented asymmetric slot-waveguide. The unit cell shows oscillating unidirectional scattering behavior that can be precisely tuned as a function of the waveguide length. This occurs due to interference between multiple modes excited by the incident light. In contrast to metasurface-based gratings with multiple resonant sub-elements, a periodic arrangement of such non-resonant diffracting elements allows for broadband operation and a strong tolerance for variations in angle of incidence. Full-wave simulations show that our grating designs can exhibit diffraction efficiencies ranging from 94% for a deflection angle of 47$^\circ$ to 80% for deflection angle of 80$^\circ$. To demonstrate the multifunctionality of our grating design technique, we have also proposed a flat polarization beamsplitter, which allows for the separation of the two orthogonal polarizations by 80$^\circ$, with an efficiency of 80%.
Catalytic performance of zirconia-supported oxides (Nb2O5, SiO2 and WO3) in ethanol upgrading: influence of acid-base properties (2022)

We present a study of ethanol upgrading on zirconia-based metal oxides including commercial SiO2/ZrO2, WO3/ZrO2, pure zirconia catalysts and a Nb2O5/ZrO2 catalyst obtained by wet impregnation. Chemical composition, crystallographic features, textural and acid-base properties (NH3 and CO2 temperature programmed desorption) were determined. Reactivity of the catalysts was investigated by temperature programmed surface reaction and isothermal catalytic tests. Catalyst performance was strongly dependent on the acid-base properties which favored the ethanol dehydration to ethylene. All modified zirconia-base catalysts yielded C3 and C4 compounds above 623 K. This study consequently emphasizes the preponderant role of both acid and basic site in the formation of higher products from ethanol.
VGFEM with perfectly matched layers (2010)

This paper is organized as follows: In the next Section, we briefly introduce the framework of the vector generalized finite element (VGFEM) developed on the polyhedral elements, and also present the vector spaces for continuous and discontinuous field representations. Then, we formulate the bilinear form of the VGFEM for anisotropic medium. In Results Section, we validate the formulation by doing a cavity mode analysis and then analyze the performance of the VGFEM with perfectly matched layers (PML) by truncating a rectangular waveguide by PML. Finally, we conclude our work with future research directions.