gebhart/patrepeval huggingface dataset:
Fabrication of sonicated chitosan nanofiber mat with enlarged porosity for use as hemostatic materials (2013)

Electrospinning of pure chitosan was employed to obtain a nanofibrous hemostatic material. Owing to the water-solubility of the resulting acidic chitosan nanofibers, the optimum neutralization conditions were identified by testing various alkaline solutions, so that an insoluble material could be achieved. The pore size and thickness of the neutralized chitosan nanofibers mat could be controlled using ultra-sonication. The porosity of the chitosan mat was increased from 79.9% to 97.2% with ultra-sonication treatment for 1 min, and the water absorption time decreased from 110s to 9s. The blood clotting efficiency measured for the sonicated chitosan nanofiber mat was 1.35- and 3.41-fold better than the efficiencies of the Surgicel(®) and chitosan sponge, respectively. In addition, the proliferation of normal human dermal fibroblasts on the sonicated nanofiber mat was found to be 1.4-fold higher than that on the non-sonicated material after 7 days of culture.
The Natural History of Leukocyturia Associated with Indinavir Treatment in HIV+ Individuals (2000)

Urinary complications observed during indinavir treatment of HIV disease are often attributed to indinavir crystalluria. In a prospective study of urinalysis during the first year of indinavir therapy, 5 of 54 asymptomatic HIV+ individuals presented severe leukocyturia (> or =100 cells/HPF) usually accompanying indinavir crystalluria. The clinical course of these 5 individuals, successfully treated for HIV and monitored for an second follow-up year, suggests that recurrence of severe leukocyturia may be an indicator of renal damage, likely tubulointerstitial disease caused by indinavir crystalluria. This is in contrast to the remaining 49 subjects, including those presenting mild leukocyturia, who did not demonstrate any evidence of renal disease. Regular urinalysis is therefore recommended in the clinical management of indinavir-treated individuals to detect early renal damage secondary to indinavir crystalluria and to prevent further renal impairment.
Babesia bovis-Stimulated Macrophages Express Interleukin-1β, Interleukin-12, Tumor Necrosis Factor Alpha, and Nitric Oxide and Inhibit Parasite Replication In Vitro (2000)

The tick-transmitted hemoparasite Babesia bovis causes an acute infection that results in persistence and immunity against challenge infection in cattle that control the initial parasitemia. Resolution of acute infection with this protozoal pathogen is believed to be dependent on products of activated macrophages (Mphi), including inflammatory cytokines and nitric oxide (NO) and its derivatives. B. bovis stimulates inducible nitric oxide synthase (iNOS) and production of NO in bovine Mphi, and chemical donors of NO inhibit the growth of B. bovis in vitro. However, the induction of inflammatory cytokines in Mphi by babesial parasites has not been described, and the antiparasitic activity of NO produced by B. bovis-stimulated Mphi has not been definitively demonstrated. We report that monocyte-derived Mphi activated by B. bovis expressed enhanced levels of inflammatory cytokines interleukin-1beta (IL-1beta), IL-12, and tumor necrosis factor alpha that are important for stimulating innate and acquired immunity against protozoal pathogens. Furthermore, a lipid fraction of B. bovis-infected erythrocytes stimulated iNOS expression and NO production by Mphi. Cocultures of Mphi and B. bovis-infected erythrocytes either in contact or physically separated resulted in reduced parasite viability. However, NO produced by bovine Mphi in response to B. bovis-infected erythrocytes was only partially responsible for parasite growth inhibition, suggesting that additional factors contribute to the inhibition of B. bovis replication. These findings demonstrate that B. bovis induces an innate immune response that is capable of controlling parasite replication and that could potentially result in host survival and parasite persistence.
Alkaline Activation of Blends of Metakaolin and Calcium Aluminate (2007)

The present paper reports the preliminary results obtained and analyzed in the framework of a joint Spanish–Japanese project on the behavior of blends of alkali‐activated metakaolin (MK) and calcium aluminate cement (CAC). In these experiments, the materials were activated with an 8 M solution of NaOH, poured into molds, and subjected to brief thermal curing (2 or 20 h at 85°C). The hardened pastes were tested for mechanical strength and characterized for mineralogy and microstructure by a number of techniques (XRD, FTIR, BSEM, and MAS‐NMR). The results showed that under the above conditions, the Al and Ca in the CAC were taken up into the aluminosilicate formed as the main product of the alkali activation of MK. None of the CAC hydration compounds (CAH 10 ; C 2 AH 8 ; C 3 AH 6 ; AH 3 ) normally formed were detected in any of the cases studied.
Heterogenous Dopamine D2 Receptor Subtype Messenger Ribonucleic Acid Expression in Clinically Nonfunctioning Pituitary Adenomas1 (1998)

Little is known about differences in the expression, localization, and function of the two dopamine D2 receptor subtypes, D2short and D2long (D2s and D2l), in either normal or adenomatous pituitary. We investigated the messenger RNA (mRNA) expression of the D2 receptor (D2R) subtypes in clinically nonfunctioning pituitary adenomas by in situ hybridization using subtype-specific oligonucleotides. The five normal pituitaries studied expressed similar ratios of D2R subtypes mRNA with a predominant expression of the D2l isoform. In 2 of 18 clinically inactive adenomas no D2R mRNA was found, whereas in 16 a heterogeneous expression of D2R isoforms was observed. Six adenomas expressed only the D2l and 2 adenomas only the D2s subtype mRNA; the remaining 8 expressed extremely varying proportions of the two subtypes. The D2R was found only in a subset of the nonfunctioning adenoma cells. In gonadotropin-immunopositive adenomas, the D2R was mainly localized in LH- and FSH-immunopositive cells. Probably because of the heterogeneous D2R subtype expression, suppression of cell proliferation was observed in only 3 of 9 adenoma cell cultures in which the growth inhibitory effect of bromocriptine was studied. Although there is some evidence that the presence of the D2s receptor subtype favors the growth inhibitory response to bromocriptine, further studies with a larger number of inactive adenomas are needed to confirm this speculation.
Experimental study of the eligibility traces in complex valued reinforcement learning (2007)

Effectiveness of eligibility traces in complex valued reinforcement learning is studied. Complex valued reinforcement learning is a new method inspired by complex valued nerual networks. In this study, it is desired that various approaches in the ordinally real valued reinforcement learning are applied to the complex valued reinforcement learning. This paper focuses attention on an experimental study of the eligibility traces. Simulation results infer that there is a possibility of overcoming tight perceptual aliasing with long trace back up.
Structure and expression of human mitochondrial adenylate kinase targeted to the mitochondrial matrix (2001)

The previously isolated cDNA encoding human adenylate kinase (AK) isozyme 3 was recently renamed AK4. Consequently, human AK3 cDNA remains to be identified and we have little information about the functional relationship between human AK3 and AK4. In pursuit of the physiological roles of both the AK3 and AK4 proteins, we first isolated an authentic human AK3 cDNA and compared their expression. Nucleotide sequencing revealed that the cDNA encoded a 227-amino-acid protein, with a deduced molecular mass of 25.6kDa, that shares greater homology with the AK3 cDNAs isolated from bovine and rat than that from human. We named the isolated cDNA AK3. Northern-blot analysis revealed that AK3 mRNA was present in all tissues examined, and was highly expressed in heart, skeletal muscle and liver, moderately expressed in pancreas and kidney, and weakly expressed in placenta, brain and lung. On the other hand, we found that human AK4 mRNA was highly expressed in kidney, moderately expressed in heart and liver and weakly expressed in brain. Western-blot analysis demonstrated expression profiles of AK3 and AK4 that were similar to their mRNA expression patterns in each tissue. Over expression of AK3, but not AK4, in both Escherichia coli CV2, a temperature-sensitive AK mutant, and a human embryonic kidney-derived cell line, HEK-293, not only produced significant GTP:AMP phosphotransferase (AK3) activity, but also complemented the CV2 cells at 42°C. Subcellular and submitochondrial fractionation analysis demonstrated that both AK3 and AK4 are localized in the mitochondrial matrix.
Absolute Configuration of 3,3′-Diphenyl-[2,2′-binaphthalene]-1,1′-diol Revisited (2009)

The experimental vibrational circular dichroism, electronic circular dichroism, and optical rotatory dispersion spectra and corresponding quantum chemical predictions of 3,3'-diphenyl-[2,2'-binaphthalene]-1,1'-diol (VANOL) are used to confirm its absolute configuration as (+)(589)-(aR) or (-)(589)-(aS). A discrepancy in the literature crystal structure has been resolved by determining the X-ray crystal structure of the brucine binaphtholphosphate salt of the (aS)-enantiomer of VANOL.
Artificial intelligence-based histopathology image analysis identifies a novel subset of endometrial cancers with distinct genomic features and unfavourable outcome (2023)

Abstract Endometrial cancer (EC) has four molecular subtypes with strong prognostic value and therapeutic implications. The most common subtype (NSMP; No Specific Molecular Profile) is assigned after exclusion of the defining features of the other three molecular subtypes and includes patients with heterogeneous clinical outcomes. In this study, we employed artificial intelligence (AI)-powered histopathology image analysis to differentiate between p53abn and NSMP EC subtypes and consequently identified a novel sub-group of NSMP EC patients that had markedly inferior progression-free and disease-specific survival (termed ‘p53abn-like NSMP’), in a discovery cohort of 368 patients and an independent validation cohort of 290 patients from another center. Shallow whole genome sequencing revealed a higher burden of copy number abnormalities in the ‘p53abn-like NSMP’ group compared to NSMP, suggesting that this new group is biologically distinct compared to other NSMP ECs. Our work demonstrates the power of AI to detect prognostically different and otherwise unrecognizable subsets of EC where conventional and standard molecular or pathologic criteria fall short, refining image-based tumor classification.
Deep Kernel Learning-Based Channel Estimation in Ultra-Massive MIMO Communications at 0.06-10 THz (2019)

The abundant spectrum resources at the millimeter wave (mm-wave) and Terahertz band (0.06-10 THz) are promising to enable a new paradigm shift in wireless communications to satisfy the demand for higher data rates in the beyond 5G era. Due to limitations of very high propagation attenuations and molecular absorptions at such high frequencies, ultra-massive MIMO (UM MIMO) communications are needed to compensate for the distance limitations, propagation losses, and to achieve higher spatial diversity. However, existing channel estimation algorithms for massive MIMO solutions require excessive computation time and demonstrate high processing complexities, whereas the problem is escalated more when the antenna array size continues to grow in the UM MIMO system. In this paper, a channel estimation method based on deep kernel learning is proposed to address the issues with estimation efficiency and accuracy in the UM MIMO communication system. This nonlinear estimation algorithm is shown to be more efficient compared to classic linear estimation approaches. A numerical comparison is conducted through simulations to show the performance of the proposed solution.
User Characteristics Acquisition from Logs with Semantics. (2007)

Abstract. IVIany current web-based information systems need to adapt to individual user characteristics in order to streamline common tasks and enable users to use them efficiently. In this paper we describe an approach to user characteristics acquisition based on automatic analysis of user behavior thus minimizing the amount of necessary user involvement. We stress the importance of appropriate data collection and propose a novel approach to logging, in which we preserve the semantics of logged evelrts. This has a significant inrpact on the successive log analysis, which focuses on the estimation of user characteristics from user navigation.
Evaluating energy savings in WoL-enabled networks of PCs (2013)

In this paper we present EnergySave, a smart energy-saving system that, by leveraging the consolidated WoL (Wake on LAN) technology, allows the remote wake-up of PCs from a centralized management server, providing easy and secure power management capabilities for local or remote IP-based networks of personal computers (PCs). We also present a lightweight web-based platform implementing the remote management interface as less intrusively as possible. Finally, we model the mathematical saving functions to be used in order to evaluate through simulation the amount of potential energy savings, and hence the whole framework effectiveness, both in the general case and in a real case scenario. Results show that significant savings are achievable provided that the hardware supports the Wake-on-LAN specifications and that proper configuration of the Web server is set-up, allowing the WoL magic packet to travel to the destination hosts and wake them up only when they are really needed.
Lasing characteristics of free-running and Q-switched Cr,Tm,Er:YAG laser operating at 2.694 /spl mu/m (2000)

Summary form only given.Stable room-temperature operation of a flashlamp pumped Cr,Tm,Er:YAG laser operating only at the 2.694 /spl mu/m transition is reported. The optimisation of the Cr, Tm, and Er dopant concentrations, the spectral characteristics of the resonator optics, and the AR coating on the laser rod has resulted in a laser emitting radiation at 2.69 /spl mu/m only irrespective of pump intensity.
High temperature corrosion and electrochemical behavior of HVOF sprayed Inconel 718 coating using an innovative device: HTCMD (2017)

Inconel 718 is one of the most commonly used nickel‐based superalloy materials in petroleum industry due to its high temperature mechanical properties and corrosion resistance. Generally, corrosion resistance assessment of materials at high temperature condition is a challenging task and most of the previous studies in this area were based on estimation of weight‐loss in the sample, which cannot provide accurate results, and it could be very time‐consuming. In this study, a high temperature corrosion measurement device (HTCMD) was used to evaluate electrochemical behavior of HVOF deposited Inconel 718 coating in 3.5 wt% NaCl solution at elevated temperatures. EIS and potentiodynamic polarization results revealed very low corrosion rate of the Inconel 718 coating. Materials characterization by SEM, XRD, and EDS indicated formation of chromium oxide rich unstable passive layer resulted in localized protection of superalloy material that was not sufficient to provide corrosion protection for the entire surface, during the service at high temperature condition.
Abstract B161: PIK3CA mutations H1047R are associated with response to PI3K/AKT/mTOR signaling pathway inhibitors in early-phase clinical trials. (2011)

Abstract Background: Activating mutations in the PIK3CA gene have been identified in many malignancies. Preclinical and early clinical data suggest that these mutations predict response to PI3K/AKT/mTOR inhibitors in subsets of patients. Sensitivity and resistance mutation have not been reported to date. Methods: Patients with diverse cancers referred to the Phase I Clinical Trials Program for targeted therapy starting from October 2008 were analyzed for PIK3CA, and if, possible for KRAS mutations using PCR-based DNA sequencing. Patients with any tumor type and any PIK3CA mutation were treated whenever possible with agents targeting the PI3K/AKT/mTOR signaling pathway. Treatment outcomes with respect to mutation types were analyzed. Results: Overall, 1012 patients were tested and 105 (10%) had PIK3CA mutations. Of the 105 patients with PIK3CA mutations, 66 (median number of prior therapies, 3) were treated on a protocol that included a PI3K/AKT/mTOR pathway inhibitor. Of these 66 patients, 11 (17%) achieved a partial response (PR) and 4 (6%) stable disease ≥ 6 months (SD≥6). The total of SD≥6/PR was 15 (23%). Patients with PIK3CA H1047R mutation (n=16) compared to patients with other PIK3CA mutations (n=50) had higher PR rate (6/16, 37.5% vs. 5/50, 10%; p=0.018), higher rate of SD≥6/PR (7/16, 44% vs. 8/50, 16%; p=0.037), and trend toward longer median progression-free survival (PFS) (5.7 months, 95%CI 0.4–11.0 vs. 2.0 months, 95%CI 1.8–2.2; p=0.064). Patients with a PIK3CA E542K mutation (n=11) compared to others (n=55) trended toward a worse median PFS (1.8 months, 95%CI 1.4–2.2 vs. 2.6 months, 95%CI 1.4–3.8; p=0.058). Of the 66 treated patients with PIK3CA mutations, 55 (83%) had enough tissue for KRAS testing. None of the 16 patients with PIK3CA and simultaneous KRAS mutations in codon 12 or 13 had a PR (0/16, 0% vs. 9/39, 23%; p=0.046) or SD≥6/PR (0/16, 0% vs. 13/39, 33.3%; p=0.011) as compared to patients with PIK3CA, but not KRAS codon 12 or 13 mutations, whereas 2 of 2 (100%) patients with PIK3CA and Q61H KRAS mutation in codon 61 had SD≥6 (n=1) and PR (n=1). Conclusion: Despite the small number of patients, our data suggest that PIK3CA mutations H1047R are associated with response to PI3K/AKT/mTOR inhibitors, whereas codon 12 and 13, but not codon 61 KRAS mutations are associated with resistance. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr B161.
Abstract 298: Tumor-associated lymphatic vessels: Hijacking mechanisms of peripheral tolerance (2012)

Abstract Lymphatic vessels drain fluid, antigens, and immune cells from the periphery to the lymph nodes (LNs). In addition to transporting activated dendritic cells to mount adaptive immune responses in the LN, lymphatic drainage is brings soluble antigens from the periphery to LN-resident immature dendritic cells and B cells. It is also the most common site for cancer metastasis. Despite its importance, the role of tumor-associated lymphatic vessels and their drainage to the LN in regulating host immune responses to the tumor is poorly understood. We show that tumor expression of VEGF-C, the most potent lymphatic growth factor, promotes pro-tumor immune tolerance by several mechanisms. For one, it enhances drainage to the draining LN, where tumor antigens along with suppressive cytokines bathe the LN and could affect B and T cell education there. Second, tumor VEGF-C upregulates CCL21 in the tumor stroma and surrounding lymphatic vessels, which itself promotes T cell infiltration and suppression. Third, VEGF-C drives peritumoral and LN lymphangiogenesis, which can modulate the myeloid cell repertoire towards more suppressive phenotypes. These changes resulted in increased infiltrations of regulatory T cells and myeloid-derived suppressor cells, and increased levels of regulatory cytokines. Interestingly, VEGF-C-expressing tumors were impervious to prior immunization against tumor antigen, unlike control-transfected tumors, which were hindered by the vaccine-induced immune response. Together, these findings suggest that lymphatic drainage serves to maintain peripheral tolerance and that tumors may hijack such mechanisms to escape host immunity. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 298. doi:1538-7445.AM2012-298
Consensus-based somatic variant-calling method correlates FBXW7 mutations with poor prognosis in canine B-cell lymphoma (2020)

Abstract INTRODUCTION Canine Lymphoma (CL) is the most commonly diagnosed malignancy in the domestic dog, with estimates reaching 80,000 new cases per year in the United States. Understanding of genetic factors involved in development and progression of canine B-Cell Lymphoma (cBCL), the most common of the two major subtypes of CL, can help guide efforts to prevent, diagnose, and treat disease in dogs. Such findings also have implications for human Non-Hodgkin Lymphoma (NHL), as pet dogs have recently emerged as an important translational model due to the many shared histopathological, biological, and clinical characteristics between cBCL and NHL. OBJECTIVES We aimed to identify potential driver mutations in cBCL and detect associations between affected genes and differential clinical outcomes. METHODS Using exome sequencing of paired normal and tumor tissues from 71 dogs of various breeds with cBCL, we identified somatic variants with a consensus approach: keeping variants called by both MuTect2 and with high-confidence by VarScan 2. We predicted effects of these variants using SnpEff then measured associations between mutated genes and survival times from clinical data available for 62 cohort dogs using a multivariate Cox Proportional Hazards Model. RESULTS Mutations in FBXW7 , a gene commonly mutated in both human and canine cancers including lymphoma, were associated with shorter overall survival (OS; p=0.01, HR 3.3 [1.4-7.6]). The two most frequently mutated codons of FBXW7 in our cohort correspond to the most frequently mutated codons in human cancers. CONCLUSIONS Our findings show that exome sequencing results can be combined with clinical data to identify key mutations associated with prognosis in cBCL. These results may have implications for precision medicine in dogs and also allow subsets of dogs to serve as models for specific subtypes of human lymphoma. Translational Relevance Identifying tumor biomarkers associated with clinical outcomes has been a major driver in improved success in treating many types of human cancers, including Non-Hodgkin lymphoma (NHL). Since canine B-cell Lymphoma (cBCL) shares many clinically identifiable characteristics with NHL, our detection of recurring mutations in certain genes in cBCL and their association with clinical outcomes stands to benefit both humans and dogs. If common canine lymphoma subtypes show mutational similarity to certain human subtypes, then therapies found to be effective for a subtype in one species may be more likely to improve treatment response in the analogous subtype in the other.