gebhart/patrepeval huggingface dataset:
VISTA: Virtual ImmunoSTAining for pancreatic disease quantification in murine cohorts (2020)

Abstract Mechanistic studies of pancreatic disease progression using animal models require objective and quantifiable assessment of tissue changes among animal cohorts. Disease state quantification, however, relies heavily on tissue immunostaining, which can be expensive, labor- and time-intensive, and all too often produces uneven staining that is prone to variable interpretation between experts and inaccurate quantification. Here we develop a fully automated semantic segmentation tool using deep learning for the rapid and objective quantification of histologic features using hematoxylin and eosin (H&amp;E) stained pancreatic tissue sections acquired from murine pancreatic cancer models. The tool was successfully trained to segment and quantify multiple histopathologic features of pancreatic pre-cancer evolution, including normal acinar structures, the ductal phenotype of acinar-to ductal metaplasia (ADM), dysplasia, and the expanding stromal compartment. Disease quantifications produced by our computational tool were highly correlated to the results obtained by immunostaining markers of normal and diseased tissue (DAPI, amylase, and cytokeratins; correlation score= 0.9, 0.95, and 0.91, respectively) and were able to accurately reproduce immunostain patterns. Moreover, our tool was able to distinguish ADM from dysplasia, which are not reliably distinguished by immunostaining, and avoid the pitfalls of uneven or poor-quality staining. Using this tool, we quantified the changes in histologic feature abundance for murine cohorts with oncogenic Kras-driven disease at 2 months and 5 months of age (n=12, n=13). The calculated changes in histologic feature abundance were consistent with biological expectations, showing an expansion of the stromal compartment, a reduction of normal acinar tissue, and an increase in both ADM and dysplasia as disease progresses (p= 2e-6, 6e-7, 4e-4, and 3e-5, respectively). These results demonstrate the tool’s efficacy for accurate and rapid quantification of multiple histologic features using an objective and automated platform. Our tool promises to rapidly accelerate and improve the quantification of altered pancreatic disease progression in animal studies.
A correlation-based model prior for stereo (2004)

All non-trivial stereo problems need model priors to deal with ambiguities and noise perturbations. To meet requirements of increasingly demanding tasks such as modeling for rendering, a proper model prior should impose preference on the true scene structure, while avoiding artificial bias such as fronto-parallel. We introduce a geometric model prior based on a novel technique we call kernel correlation. Maximizing kernel correlation is shown to be equal to distance minimization in the M-estimator sense. As a model prior, kernel correlation is demonstrated to have good properties that can result in renderable, very smooth and accurate depth map. The results are evaluated both qualitatively by view synthesis and quantitatively by error analysis.
Cover Feature: New Opportunities in the Valorization of Technical Lignins (ChemSusChem 4/2021) (2021)

The Cover Feature shows how lignins and cellolignins (cellulose-containing lignins) are paving the way to successful biorefineries. These variations of renewable raw materials have been largely overlooked as potential candidates for high-value applications. In this Review, we highlight the importance of valorizing these lignins to make sugar-based biorefineries economically viable. Current biorefinery designs need to be optimized towards the integrated use of all products in high-value applications, rather than focusing only on bioethanol, biofuels, or sugars. More information can be found in the Review by M. Y. Balakshin et al.
An EPR Study of Two-Electron Sensitization by Fragmentable Electron Donors (2005)

Fragmentable electron donors (FEDs) are molecules designed to undergo bond fragmentation after capturing the hole created by photoexposure of silver halide. By design, the radical remaining after fragmentation is a potent reductant expected to be capable of injecting an electron into the conduction band of the silver halide. Thus, the addition of a FED to the AgX surface should allow the creation of two electrons for each photon absorbed by the substrate. Photographic studies have confirmed that the addition of FEDs can increase the photosensitivity of AgX materials. In this work, EPR spectroscopy was employed to study the processes of hole capture, donor fragmentation, and secondary electron injection by FEDs in AgBr dispersions. To do so, we used AgBr microcrystals doped with diamagnetic transition metal complexes that act as deep electron traps. For samples exposed to actinic light at 15 K, secondary electron injection was detected as an increase in the EPR signal from electrons trapped at the dopant upon annealing the samples above 50 K. Organic radical intermediates and self-trapped hole centers were the other paramagnetic species monitored in this study. The results presented here confirm that the FED sensitization mechanisms originally proposed by Gould et al. take place at silver halide surfaces and result in additional electrons in the silver halide conduction band.
Classification of hyperspectral images based on conditional random fields (2015)

A significant increase in the availability of high resolution hyperspectral images has led to the need for developing pertinent techniques in image analysis, such as classification. Hyperspectral images that are correlated spatially and spectrally provide ample information across the bands to benefit this purpose. Conditional Random Fields (CRFs) are discriminative models that carry several advantages over conventional techniques: no requirement of the independence assumption for observations, flexibility in defining local and pairwise potentials, and an independence between the modules of feature selection and parameter leaning. In this paper we present a framework for classifying remotely sensed imagery based on CRFs. We apply a Support Vector Machine (SVM) classifier to raw remotely sensed imagery data in order to generate more meaningful feature potentials to the CRFs model. This approach produces promising results when tested with publicly available AVIRIS Indian Pine imagery.
Response after 12 Weeks of Adalimumab Therapy in Patients with Crohnʼs Disease Who Were Nonresponders at Week 4 (2008)

Purpose: The fully human, anti-TNF monoclonal antibody adalimumab (ADA) is approved for treatment of adults with Crohn's disease (CD). In clinical trials, 52–58% of patients responded to ADA by Week 4.1,2 However, some patients require additional time to respond. Physicians may benefit from additional data on the length of an adequate trial of ADA for their patients. Methods: This analysis assessed the efficacy of ADA at Week 12 among patients who did not respond after 4 weeks using data from CHARM and the open-label extension (OLE) of GAIN. In CHARM, following a 4-week induction period in which all patients received OL ADA 80/40 mg at Weeks 0/2, patients were randomized to placebo, ADA 40 mg every other week (eow), or ADA 40 mg weekly. In GAIN, patients who failed infliximab were randomized to ADA 160/80 mg or placebo induction at Weeks 0/2. After 4 weeks, patients could enroll in an OLE trial in which they received ADA 40 mg eow. Clinical response (CR-70) and remission (CDAI < 150) rates at Week 12 were evaluated for 1) CHARM patients who were randomized to blinded ADA 40 mg eow and did not achieve a CR-70 response at Week 4 and 2) GAIN patients who received OL ADA 40 mg eow after being randomized to blinded ADA 160/80-mg induction dose and not achieving a CR-70 response at Week 4. Results: In CHARM, 260 patients were initially randomized to blinded ADA 40 mg eow. Among 88 patients who did not respond (CR-70) at Week 4, 60% achieved CR-70 and 28% achieved remission by Week 12. By Week 12, 82% and 57% of patients who were randomized to eow (including Week 4 responders and nonresponders) achieved CR-70 and remission, respectively. In GAIN, 159 patients were initially randomized to ADA 160/80 mg; 150 with non-missing CDAI entered the OLE. Among 69 patients who did not respond (CR-70) at Week 4, 67% receiving OL ADA eow achieved CR-70 and 25% achieved remission by Week 12. Combining responders and nonresponders (N = 150), most patients achieved CR-70 response (85%) and remission (45%) by Week 12. Conclusion: Most initial Week-4 nonresponders benefited from continued treatment with ADA 40 mg eow through Week 12, with almost two-thirds achieving CR-70 response and more than one-fourth achieving remission. Continuing ADA therapy for up to 12 weeks in patients not responding to initial induction dosing yielded incremental benefits in clinical response. This research was funded by Abbott Laboratories, Abbott Park, IL.
Zinc-Graphite (2001)

[7440-66-6] Zn (MW 65.39) InChI = 1S/Zn InChIKey = HCHKCACWOHOZIP-UHFFFAOYSA-N (very highly activated form of zinc, able to convert halides into organozinc species under mild conditions;2, 3 eliminates α-oxy halides to alkenes4) Solubility: insol in all common solvents; compatible with THF and other ethereal solvents. Preparative Methods: Potassium–Graphite Laminate is prepared by reaction between Potassium metal and degassed graphite at 150 °C. When cool the potassium graphite is suspended in THF. Zinc Chloride is added and a very vigorous reaction ensues before the THF is heated to reflux to ensure complete reaction. Zinc/silver–graphite is prepared by the addition of 10 mol % Silver(I) Acetate to the zinc chloride mixture. These preparations have only been reported on a 15 mmol scale; because molten potassium is used and the reduction of zinc chloride is highly exothermic, great caution should be exercised in any scale-up.3, 5 Handling, Storage, and Precautions: the reagent consists of highly active metal particles; it should be handled under argon and used immediately after preparation.
Special situations (2009)

This chapter explores special situations in dialysis, including dialysis in the elderly, assisted PD, managing diabetic patients on dialysis, surgery in dialysis patients, myeloma and renal failure, pain management in end-stage kidney disease (ESKD), difficulty of pain management in renal patients, managing pain, analgesic drugs, pain at the end of life, pregnancy in dialysis patients, travelling and holidays, plasmapheresis, immunoadsorption techniques, and indications for immunoadsorption.
Evaluation of a Lipopeptide Immunogen as a Therapeutic in HIV Type 1-Seropositive Individuals (2000)

A 32-amino acid HIV-1 Gag immunogen was assessed for its ability to augment existing virus-specific CTL responses in chronically HIV-1-infected individuals. The immunogen was an HIV-1 synthetic lipopeptide conjugate composed of an N-palmitoyl-S-[2,3-bis(palmitoyloxy)-(2R)-propyl-N-(R)-cysteinyl] group covalently coupled to a synthetic 32-amino acid Gag peptide containing at least 5 CTL epitopes known to be restricted by HLA-A33, -B8, -B27, -B35, and -Bw62. This potential immunotherapeutic was first determined to be safe in six HIV-1-seropositive subjects, with no adverse clinical effects noted during a 182-day period after administration of a dose of 350 microg. The immunogenicity of this lipopeptide conjugate was then assessed in a pilot study in nine HIV-1-seropositive volunteers with peripheral blood CD4+ lymphocyte counts of >500/microl. Three groups of individuals were studied: HLA-selected subjects who received 350 microg of the immunogen on days 0, 28, and 56 (four subjects); HLA-selected subjects who received a placebo according to a similar inoculation schedule (three subjects); and HLA-mismatched subjects who received the experimental immunogen (two subjects). All subjects were monitored for 26 weeks. After treatment, PBLs from two of the four HLA-selected subjects who received the experimental immunogen showed a transient increase in Gag peptide-specific bulk CTL activity. None of the placebo-vaccinated or vaccinated HLA-mismatched subjects showed any change in bulk Gag peptide-specific CTL activity. However, no consistent decrease in plasma HIV-1 RNA levels was noted in any of the subjects. The present study illustrates that this peptide formulation may not be a sufficiently potent immunogen to significantly augment HIV-1-specific CTLs and to decrease virus load in HIV-1-seropositive individuals.
Mars Oxygen ISRU Experiment (MOXIE)—Preparing for human Mars exploration (2022)

MOXIE [Mars Oxygen In Situ Resource Utilization (ISRU) Experiment] is the first demonstration of ISRU on another planet, producing oxygen by solid oxide electrolysis of carbon dioxide in the martian atmosphere. A scaled-up MOXIE would contribute to sustainable human exploration of Mars by producing on-site the tens of tons of oxygen required for a rocket to transport astronauts off the surface of Mars, instead of having to launch hundreds of tons of material from Earth's surface to transport the required oxygen to Mars. MOXIE has produced oxygen seven times between landing in February 2021 and the end of 2021 and will continue to demonstrate oxygen production during night and day throughout all martian seasons. This paper reviews what MOXIE has accomplished and the implications for larger-scale oxygen-producing systems.
mtDNA depletion‐like syndrome in Wilson disease (2020)

This study underlines the relevance of targeting the copper-mitochondrial DNA pool in the treatment of WD separate from the established copper-induced oxidative stress-mediated damage.
Local over-expression of prolactin in differentiating mouse mammary gland induces functional defects and benign lesions, but no carcinoma (2006)

Experimental, clinical, and epidemiological data support the growth-promoting role of endocrine prolactin (PRL) in mammary tumors. PRL is also produced by the breast, where it is now recognized to act as a growth/survival factor via autocrine/paracrine mechanisms. Recent transgenic (Tg) mouse models have revealed the pro-oncogenic effect of PRL over-expression in virgin mammary glands. To address the question whether PRL tumorigenicity was maintained on differentiated mammary glands, we generated mammary-specific Tg mice expressing human (h)PRL under the control of the milk whey acidic protein promoter, which directs autocrine hPRL over-expression in late gestation throughout lactation. Minimal levels of transgene expression were detected in the mammary glands of virgin animals, which at best induced partial ductal branching and lobulo-alveolar structures in older nulliparous females. As expected, expression of mammary hPRL dramatically increased at the end of first pregnancy, and from this point it never returned to baseline, although it peaked at each gestation/lactation cycle. Over-expression of hPRL that starts when the gland is already well into the differentiation process led to various morphological mammary alterations, including abnormally differentiated epithelium, atropy of the myoepithelial layer, dilated ducts, cysts, and lymphocytic infiltrates. These phenotypes tended to worsen with successive pregnancies, also reflecting cumulative damage of failure of involution. Although some older, multiparous females developed benign tumors (papillomas and metaplasias), none of the animals studied developed mammary carcinomas. In addition, we noticed that half of the Tg females exhibited lactation defects, leading to significantly increased pup mortality. This phenotype was due neither to failure of milk production nor to modification of its protein content, but rather it was correlated to lipid enrichment of the milk, which, in combination with profoundly altered morphology of the gland, led to impaired milk extrusion through the nipple. In summary, these data show that over-expression of autocrine hPRL in a differentiating mammary gland induces dramatic functional and morphological defects, but not carcinoma. This deserves further investigations on the emerging concept that autocrine PRL may have different effects on pathological development of the mammary gland depending on the differentiation state of the latter.
Super Low Viscosity ATF; AW-2 (2018)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Reducing loss torque in automatic transmissions (ATs) is a key factor in improving fuel economy. A promising approach is to reduce the viscosity of the Automatic Transmission Fluid (ATF) so as to minimize churning loss. Aisin AW and JXTG Nippon Oil &amp;amp; Energy Corporation have developed a super low viscosity ATF, called “AW-2”, which has approximately 50% lower kinematic viscosity at 40 °C compared to the conventional ATF “AW-1”. It is generally understood that if the viscosity of an ATF is too low, it can have a negative impact on the fatigue life of components such as gears and bearings, and possibly lead to increased wear or seizure. AW-2 was designed to solve these problems via the application of two key technologies. The first is a high performance base oil with a low traction coefficient, which translates to low viscosity under high pressure conditions. This decreases the shear resistance between sliding surfaces under elastohydrodynamic lubrication (EHL) conditions, which contributes in improving the fatigue life of bearings and other components. The second is an ester type base oil with high polarity. It was found that the amount of ester base oil used has a major influence on fatigue life. The adsorption of esters onto metal surfaces is thought to improve lubricity in severe lubrication conditions. Durability tests were performed in a wide range of conditions, using gear and bearing components and actual transmission units, and it was confirmed that AW-2 outperforms AW-1, despite its super low viscosity. Furthermore, AW-2 reduced loss torque in the transmission by approximately 10% compared to AW-1.&lt;/div&gt;&lt;/div&gt;
Problema de Alocação de Controladores SDN: Uma Análise do Custo em Redes de Backbone (2016)

O problema de alocação de controladores em Redes Definidas por Software (SDN) é um desafio em aberto por ser um problema de alocação NPCompleto análogo aos problemas clássicos de recobrimento de rede. Para solucionar esse problema, nós propomos um modelo matemático baseado em Programação Linear que realiza a distribuição de controladores SDN minimizando o custo de alocação de todos os controladores. Para validar nossa proposta foram estimados os custos de recobrimento de 112 redes de backbone. Em seguida foram analisadas quais características são determinantes no custo de implantação de controladores SDN de acordo com as características de cada rede.
Abstract 4601: Punctuated evolution of prostate cancer genomes. (2013)

Abstract The analysis of exonic DNA from prostate cancers has identified recurrently mutated genes, but the spectrum of alterations across the entire genome has not been profiled extensively in this disease. We sequenced the genomes of 55 primary prostate tumors and matched normal tissues to catalogue somatic alterations and to study how they accumulate during oncogenesis and progression. By implementing an algorithm to identify genomic alterations that arise together, we found abundant sets of DNA rearrangements and deletions that may occur simultaneously in a single cell. This phenomenon, which we term “chromoplexy," frequently accounts for the dysregulation of prostate cancer genes including PTEN, NKX3-1, TP53 and CDKN1B. The somatic fusion of TMPRSS2 and ERG, which occurs in approximately half of prostate cancers, predominantly arises with additional genomic rearrangements in the context of chromoplexy. We further demonstrate that TMPRSS2-ERG fusion-positive tumors display a unique profile of chromoplexy, with complex chains of rearrangements that may fuse DNA from four or more distinct chromosomes. In prostate cancer and other neoplasms, chromoplexy induces considerable genomic derangement in a series of relatively few events. In several instances, multiple cancer genes from non-contiguous regions of the genome appear to be disrupted simultaneously by this process, suggesting a model of punctuated progression during cancer evolution. By characterizing the clonal hierarchy of genomic lesions in prostate tumors, we constructed a path of oncogenic events along which chromoplexy drives prostate carcinogenesis. Citation Format: Sylvan C. Baca, Davide Prandi, Michael S. Lawrence, Juan Miguel Mosquera, Alessandro Romanel, Yotam Drier, Kyung Park, Naoki Kitabayashi, Theresa Y. MacDonald, Eliezer Van Allen, Gregory V. Kryukov, Jean-Philippe Theurillat, T. David Soong, Elizabeth Nickerson, Daniel Auclair, Ashutosh Tewari, Himisha Beltran, Robert C. Onofrio, Gunther Boysen, Candace Guiducci, Christopher E. Barbieri, Kristian Cibulskis, Andrey Sivachenko, Scott L. Carter, Douglas Voet, Gordon Saksena, Michelle R. Cipicchio, Kristin Ardlie, Philip W. Kantoff, Michael F. Berger, Stacey B. Gabriel, Todd R. Golub, Matthew Meyerson, Eric S. Lander, Olivier Elemento, Gad Getz, Francesca Demichelis, Mark A. Rubin, Levi A. Garraway. Punctuated evolution of prostate cancer genomes. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4601. doi:10.1158/1538-7445.AM2013-4601
New, Virtually Wall-Less Cannulas Designed for Augmented Venous Drainage in Minimally Invasive Cardiac Surgery (2016)

At the well-accepted pump inlet pressure of -80 mm Hg, the new, thinner, virtually wall-less, braided cannulas provide unmatched venous drainage in vivo. Early clinical analyses have confirmed these findings.
In situ study of T-cell subpopulations in cutaneous T-cell lymphoma: Diagnostic criteria (1984)

The T-cell subpopulations present in skin biopsy specimens from 91 patients with cutaneous T-cell lymphoma (CTCL) and from 19 patients with benign lymphocytic infiltrates of the skin were examined in situ to define criteria for the differentiation of benign from malignant lymphocytic infiltrates. The monoclonal antibodies OKT 1 (pan T-cell), BE 3 (pan T-cell), OKT 4 (helper/inducer T-cell), OKT 6 (cortical thymocyte and Langerhans' cell), OKT 8 (suppressor T-cell), and OKT 10 (pan thymocyte) were used in direct or indirect immunoperoxidase reactions. Sections were examined at high magnification, and the distribution and percentage of cells reactive with each antibody were assessed. Three main patterns of staining were observed in the CTCL patients: (1) 64% of the biopsy specimens showed that 60% of the cells present in the dermis were T-cells that were OKT 1+ and BE 3+ and there was an even distribution of the different T-cell subpopulations, with 54% being OKT 4+ and 8% OKT 8+; (2) 21% patients showed selective loss of OKT 1 antigen, and 80% of these also showed loss of BE 3 antigen; and (3) 15% patients showed large numbers of OKT 8+ cells (range, 50%-90%) but the percentages of OKT 1+ and OKT 4+ cells were within the ranges seen in Group 1, indicating the presence of a population of T-cells simultaneously expressing OKT 4 (helper/inducer) and OKT 8 (suppressor) reactivity. In 95% of the CTCL patients, 3.5% OKT 6+ cells were present in the dermal infiltrate, and in 92% of patients, 3% OKT 10+ cells were present. Comparing sections from CTCL and benign dermatoses, no single diagnostic feature was identified, but helpful differentiating features were: (1) the even, rather than nodular, distribution of the T-cell subpopulation; (2) the selective loss of OKT 1 and BE 3 antigens; (3) the presence of T-cells simultaneously expressing OKT 4 and OKT 8 antigens; and (4) the presence of OKT 10+ cells.