gebhart/patrepeval huggingface dataset:
Focal adhesion features during myofibroblastic differentiation are controlled by intracellular and extracellular factors (2001)

Transforming growth factor beta (TGFbeta), the most established promoter of myofibroblast differentiation, induces ED-A cellular fibronectin and alpha-smooth muscle actin expression in fibroblastic cells in vivo and in vitro. ED-A fibronectin exerts a permissive action for alpha-smooth muscle actin expression. A morphological continuity (called fibronexus), a specialized form of focal adhesion, has been described between actin stress fibers that contain alpha-smooth muscle actin, and extracellular fibronectin, which contains the ED-A portion, in both cultured fibroblasts and granulation tissue myofibroblasts. We have studied the development of these focal adhesions in TGFbeta-treated fibroblasts using confocal laser scanning microscopy, three-dimensional image reconstruction and western blots using antibodies against focal adhesion proteins. The increase in ED-A fibronectin expression induced by TGFbeta was accompanied by bundling of ED-A fibronectin fibers and their association with the terminal portion of alpha-smooth muscle actin-positive stress fibers. In parallel, the focal adhesion size was importantly increased, and tensin and FAK were neoexpressed in focal adhesions; moreover, vinculin and paxillin were recruited from the cytoplasmic pool into focal adhesions. We have evaluated morphometrically the length and area of focal adhesions. In addition, we have evaluated biochemically their content of associated proteins and of alpha-smooth muscle actin after TGFbeta stimulation and on this basis suggest a new focal adhesion classification, that is, immature, mature and supermature. When TGFbeta-induced alpha-smooth muscle actin expression was blocked by soluble recombinant ED-A fibronectin, we observed that the fragment was localised into the fibronectin network at the level of focal adhesions and that focal adhesion supermaturation was inhibited. The same effect was also exerted by the ED-A fibronectin antibody IST-9. In addition, the antagonists of actin-myosin contractility BDM and ML-7 provoked the dispersion of focal adhesions and the decrease of alpha-smooth muscle actin content in stress fibers of pulmonary fibroblasts, which constitutively show large focal adhesions and numerous stress fibers that contain alpha-smooth muscle actin. These inhibitors also decreased the incorporation of recombinant ED-A into fibronectin network. Our data indicate that a three-dimensional transcellular structure containing both ED-A fibronectin and alpha-smooth muscle actin plays an important role in the establishment and modulation of the myofibroblastic phenotype. The organisation of this structure is regulated by intracellularly and extracellularly originated forces.
Intraarticular Findings After Gunshot Wounds Through the Knee (1997)

Patients who sustain a low-velocity gunshot through the knee have soft tissue injuries not visible on plain radiographs in most cases, and therefore operative treatment is warranted. Arthroscopic management of these injuries appears to be a safe and effective method of treatment.
Proceedings of the 2006 ACM SIGPLAN symposium on Partial evaluation and semantics-based program manipulation (2006)

Welcome to the ACM SIGPLAN 2006 Workshop on Partial Evaluation and Program Manipulation! PEPM 2006 is the latest incarnation of a series of workshops and symposia that started in the early 1990s. This year, a concerted effort was made to broaden the scope of PEPM from its roots in program manipulation techniques such as partial evaluation to include a variety of application areas such as program slicing and rule-based transformation systems. A separate category of short tool demonstration papers was solicited to ensure the representation of practical work at the meeting.This proceedings contains 17 high-quality papers (including 4 tool demonstration papers) that were selected by the program committee out of 29 submissions. Each paper was reviewed by at least 3 program committee members, with further input from a small number of external reviewers. The reviewing process was conducted using the OCS system, and final decisions were made during a teleconference. The proceedings also includes 2 invited keynote contributions by James R. Cordy and Thomas Reps.The workshop program is structured along the following main themes: Applications, Analysis, Aspect-Oriented Programming, Transformations, Tool Demonstrations, and Meta-programming.
Partitioning a Polygon Into Small Pieces (2022)

We study the problem of partitioning a given simple polygon $P$ into a minimum number of connected polygonal pieces, each of bounded size. We describe a general technique for constructing such partitions that works for several notions of `bounded size,' namely that each piece must be contained in an axis-aligned or arbitrarily rotated unit square or a unit disk, or that each piece has bounded perimeter, straight-line diameter or geodesic diameter. The problems are motivated by practical settings in manufacturing, finite element analysis, collision detection, vehicle routing, shipping and laser capture microdissection. The version where each piece should be contained in an axis-aligned unit square is already known to be NP-hard [Abrahamsen and Stade, FOCS, 2024], and the other versions seem no easier. Our main result is to develop constant-factor approximation algorithms, which means that the number of pieces in the produced partition is at most a constant factor larger than the cardinality of an optimal partition. Existing algorithms [Damian and Pemmaraju, Algorithmica, 2004] do not allow Steiner points, which means that all corners of the produced pieces must also be corners of $P$. This has the disappointing consequence that a partition often does not exist, whereas our algorithms always produce meaningful partitions. Furthermore, an optimal partition without Steiner points may require $Ω(n)$ pieces for polygons with $n$ corners where a partition consisting of just $2$ pieces exists when Steiner points are allowed. Other existing algorithms [Arkin, Das, Gao, Goswami, Mitchell, Polishchuk and Tóth, ESA, 2020] only allow $P$ to be split along chords (and aim to minimize the number of chords instead of the number of pieces), whereas we make no constraints on the boundaries of the pieces.
The Monotone Iterative Technique for Three-Point Second-Order Integrodifferential Boundary Value Problems with p-Laplacian (2007)

A monotone iterative technique is applied to prove the existence of the extremal positive pseudosymmetric solutions for a three-point second-order -Laplacian integrodifferential boundary value problem.
CD8α+ Dendritic Cells Induce Leukemia-Specific T cell Tolerance (2016)

Abstract Antigen presenting cells (APCs) are critical for the acquisition of tumor-derived antigens and the orchestration of anti-tumor T cell responses. Batf3-dependent CD8α+ and CD103+ dendritic cells (DCs) have been implicated as the critical APCs that initiate and maintain spontaneous CD8+ T cell priming against solid tumors. In contrast, little is known about the APCs that regulate immunity against malignancies of hematopoietic origin. Using a murine model of acute myeloid leukemia (AML) that induces T cell tolerance, we demonstrate that leukemia-derived antigens are exclusively acquired and cross-presented by CD8α+ DCs. In the steady state, CD8α+ DCs rapidly induce leukemia-specific T cell tolerance, which can be prevented upon the activation of these DCs. Together, our data reveal that the same DC lineage can imprint disparate T cell fates in mice with solid verses hematopoietic malignancies. In the context of solid tumors, Batf3-dependent DCs stimulate productive effector responses; however, in AML-bearing mice, CD8α+ DCs actively promote T cell tolerance.
Health state utilities associated with post-surgical Staphylococcus aureus infections (2019)

The preference-based SSI disutilities derived in this study may be used to represent mild and serious SSIs in CUAs assessing and comparing the value of vaccinations that may reduce the risk of SSIs.
33.3: Comparison of Poly‐Si TFT Characteristics Crystallized by a YAG2ω Laser and an Excimer Laser (2004)

Abstract Poly‐Si TFTs were fabricated by both a YAG2ω laser and an excimer laser annealing system using a same TFT manufacturing process, and the electrical characteristics of the TFTs were compared. As a result, it is found that a wider process window can be obtained with the YAG2ω laser annealing system. The possibility of overlapped irradiation is also shown.
60 GHz square open‐loop resonator (SOLR) based on planar Goubau line (PGL) technology (2019)

This study presents the design, fabrication, and measurement of a square open‐loop resonator (SOLR) on high resistivity silicon substrate feed with a planar Goubau line (PGL), which is a very low‐loss transmission line around 60 GHz fabricated through a very simple and low‐cost process. Electromagnetic simulations using ANSYS high frequency structure simulator are performed for the PGL structure, in order to determine the PGL characteristics (impedance, losses and quality factor) versus the line width. The geometrical parameters of the SOLR structure are studied to observe their impact on reflection and transmission properties. An equivalent lumped element circuit is extracted from the distributed planar design to study and optimise the resonating structure using Advanced Design System. This electrical circuit response is successfully compared to the planar electromagnetic structure one, and a parametric study permits to better understand the role of the different circuit elements. Field displays lead to a better understanding of the SOLR behaviour. For measurement purpose of the fabricated structure, a coplanar waveguide‐PGL transition is optimised with 0.9 dB losses. Simulation and measurement results show good performances for filter applications with 1 dB losses and small size at 60 GHz for 10% bandwidth.
Supplementary Table. Select Transition of Care Programs (2020)

Supplementary Table. Highlights from transition of care (TOC) programs: Select pediatric to adult TOC programs from articles written between 2009 and 2019 in the United States and Canada that discussed specific program features.
Influence du microenvironnement sur l'expression des protéines de Staphyloccocus aureus : application pour la prévention vaccinale des mammites bovines (2004)

Staphylococcus aureus provoque chez la vache laitiere des infections mammaires subcliniques et chroniques qui, par leur frequence et leurs pertes economiques, constituent une pathologie majeure pour ces animaux. Il n'y a pas de vaccins contre ces infections. Pour la mise au point d'un vaccin anti-mammite a S. Aureus compose de corps bacteriens, des souches, representatives de celles provoquant des mammites, ont ete cultivees dans differentes conditions. Un proteome pour les proteines cellulaires de S. Aureus a ete defini et des proteines differentiellement exprimees selon la condition de culture ont ete caracterisees. Des genes de facteurs de regulation et de virulence, preferentiellement exprimes selon les souches et les conditions de cultures, ont aussi ete mis en evidence. Apres immunisation de vaches avec differentes preparations vaccinales, la detection des anticorps anti-S. Aureus, la caracterisation des isotypes et la protection induite nous ont permis de choisir une preparation.
PLASTID TRANSFORMATION IN HIGHER PLANTS (2004)

Plastids of higher plants are semi-autonomous organelles with a small, highly polyploid genome and their own transcription-translation machinery. This review provides an overview of the technology for the genetic modification of the plastid genome including: vectors, marker genes and gene design, the use of gene knockouts and over-expression to probe plastid function and the application of site-specific recombinases for excision of target DNA. Examples for applications in basic science include the study of plastid gene transcription, mRNA editing, photosynthesis and evolution. Examples for biotechnological applications are incorporation of transgenes in the plastid genome for containment and high-level expression of recombinant proteins for pharmaceutical and industrial applications. Plastid transformation is routine only in tobacco. Progress in implementing the technology in other crops is discussed.
Quantitative evaluation of alveolar bone resorption on dental panoramic radiographs by standardized dentition image transformation and probability estimation (2016)

Alveolar bone resorption, which can be observed on dental panoramic radiographs (DPRs), is one of the most important signs of the progression of periodontal disease. However, quantitative and consistent evaluation of alveolar bone resorption is labor intense, because of a large number of DPR examinations performed each year. In our previous study, we developed an automated scheme for detection of three lines, corresponding to an occlusion line, an alveolar line and a root apex line, to measure the alveolar bone ratio (ABR), which may be useful to dentists in early detection of periodontal disease. In this study, we propose a new image transformation that maps the tooth region to a standardized dentition image for improved visualization and detection of alveolar crest points by probability estimation. The proposed method was applied to 92 DPRs with 4 degrees of alveolar bone resorption. The ABR measurement obtained by the proposed method was compared with the manual measurement of alveolar bone loss (ABL). In this preliminary investigation, the computer-estimated ABR was moderately correlated with the manual ABL. The result indicates the potential usefulness of the method for early detection and consistent diagnosis of periodontal disease.
Sensitivity and positive predictive value of medicare part B physician claims for rheumatologic diagnoses and procedures (1997)

In specialty practice, Medicare physician claims had high sensitivity and positive predictive value for RA, SLE, OA without specification of anatomic site, and injection or aspiration procedures. The claims had lower sensitivity and predictive value for FM and for OA of the hip. The accuracy of Medicare physician claims for other conditions and in the primary care setting requires further investigation.
A simulation of dynamic task allocation in a distributed computer system (1987)

Distributed processor systems are currently used for advanced, high-speed computation in application areas such as image processing, artificial intelligence, signal processing, and general data processing. The use of distributed and parallel processor computer systems today requires systems designers to partition an application into at least as many functions as there are processors. Spare processors must be allocated and function migration paths must be designed to allow fault tolerant reconfiguration. The parallel process/ parallel architecture control simulation (PPCS) models parallel task allocation on a distributed processor architecture. Parallel task allocation is a first step in designing a dynamic parallel processor operating system that automatically assigns and reassigns application tasks to processors. Advantages of this approach are: dynamic reconfigurability removing the need for spare processing power reserved for failures; the reduced need for fallback and recovery software for fault detection; more optimized partitioning of functions; and better load balancing over available processors. PPCS models various distributed processing configurations, task dependencies, and the scheduling of the tasks onto the processor architecture. The PPCS system implements fifteen different heuristic scheduling algorithms to map a set of tasks onto the processing nodes of a distributed computer. The simulation shows the feasibility of using fast algorithms to heuristically schedule a system of multiple processors allowing dynamic task allocation.
Faculty Opinions recommendation of Directional hearing by linear summation of binaural inputs at the medial superior olive. (2013)

Neurons in the medial superior olive (MSO) enable sound localization by their remarkable sensitivity to submillisecond interaural time differences (ITDs). Each MSO neuron has its own "best ITD" to which it responds optimally. A difference in physical path length of the excitatory inputs from both ears cannot fully account for the ITD tuning of MSO neurons. As a result, it is still debated how these inputs interact and whether the segregation of inputs to opposite dendrites, well-timed synaptic inhibition, or asymmetries in synaptic potentials or cellular morphology further optimize coincidence detection or ITD tuning. Using in vivo whole-cell and juxtacellular recordings, we show here that ITD tuning of MSO neurons is determined by the timing of their excitatory inputs. The inputs from both ears sum linearly, whereas spike probability depends nonlinearly on the size of synaptic inputs. This simple coincidence detection scheme thus makes accurate sound localization possible.
Nervous system involvement in Fabry's disease: Clinicopathological and biochemical correlation (1988)

A detailed neuropathological and biochemical study was performed to evaluate the accumulation of ceramide trihexoside within the central and peripheral nervous systems of 2 patients with Fabry's disease. Luxol fast blue-staining lipid was noted in the leptomeninges and in the choroidal stroma; biochemical studies showed increased quantities of ceramide trihexoside in the cerebrospinal fluid. The permeable blood-brain barrier regions of the central and peripheral nervous systems contained increased quantities of ceramide trihexoside. Some central nervous system nuclei associated with autonomic function were also noted to store lipid. Other areas of increased ceramide trihexoside accumulation included specific cortical and brainstem structures. Possible sources for this selective accumulation of ceramide trihexoside within the central and peripheral nervous system include transport of glycolipid from the systemic vascular network and retrograde transsynaptic glycolipid transport.
Molecular markers in prostate cancer. Part I: predicting lethality (2008)

Assessing the lethality of 'early,' potentially organ-confined prostate cancer (PCa) is one of the central controversies in modern-day urological clinical practice. Such cases are often considered for radical 'curative' treatment, although active surveillance may be equally appropriate for many men. Moreover, the balance between judicious intervention and overtreatment can be difficult to judge. The patient's age, comorbidities, family history and philosophy of self-health care can be weighed against clinical features such as the palpability of disease, the number and percentage of biopsy cores involved with the disease, histological grade, presenting prostate-specific antigen (PSA) and possible previous PSA kinetics. For many years, scientists and physicians have sought additional molecular factors that may be predictive for disease stage, progression and lethality. Usually, claims for a 'new' unique marker fall short of true clinical value. More often than not, such molecular markers are useful only in multivariate models. This review summarizes relevant molecular markers and models reported up to and including 2008.
Durable Clinical Benefit With Nivolumab Plus Ipilimumab in DNA Mismatch Repair–Deficient/Microsatellite Instability–High Metastatic Colorectal Cancer (2018)

Purpose Nivolumab provides clinical benefit (objective response rate [ORR], 31%; 95% CI, 20.8 to 42.9; disease control rate, 69%; 12-month overall survival [OS], 73%) in previously treated patients with DNA mismatch repair-deficient (dMMR)/microsatellite instability-high (MSI-H) metastatic colorectal cancer (mCRC); nivolumab plus ipilimumab may improve these outcomes. Efficacy and safety results for the nivolumab plus ipilimumab cohort of CheckMate-142, the largest single-study report of an immunotherapy combination in dMMR/MSI-H mCRC, are reported. Patients and Methods Patients received nivolumab 3 mg/kg plus ipilimumab 1 mg/kg once every 3 weeks (four doses) followed by nivolumab 3 mg/kg once every 2 weeks. Primary end point was investigator-assessed ORR. Results Of 119 patients, 76% had received ≥ two prior systemic therapies. At median follow-up of 13.4 months, investigator-assessed ORR was 55% (95% CI, 45.2 to 63.8), and disease control rate for ≥ 12 weeks was 80%. Median duration of response was not reached; most responses (94%) were ongoing at data cutoff. Progression-free survival rates were 76% (9 months) and 71% (12 months); respective OS rates were 87% and 85%. Statistically significant and clinically meaningful improvements were observed in patient-reported outcomes, including functioning, symptoms, and quality of life. Grade 3 to 4 treatment-related adverse events (AEs) occurred in 32% of patients and were manageable. Patients (13%) who discontinued treatment because of study drug-related AEs had an ORR (63%) consistent with that of the overall population. Conclusion Nivolumab plus ipilimumab demonstrated high response rates, encouraging progression-free survival and OS at 12 months, manageable safety, and meaningful improvements in key patient-reported outcomes. Indirect comparisons suggest combination therapy provides improved efficacy relative to anti-programmed death-1 monotherapy and has a favorable benefit-risk profile. Nivolumab plus ipilimumab provides a promising new treatment option for patients with dMMR/MSI-H mCRC.
Development of a Decarboxylative Palladation Reaction and Its Use in a Heck‐Type Olefination of Arene Carboxylates. (2003)

The development of a palladium-catalyzed decarboxylative coupling reaction of arene carboxylates with olefinic substrates is described. The optimized procedure for decarboxylative palladation employs Pd(O&lt;sub&gt;2&lt;/sub&gt;CCF&lt;sub&gt;3&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt; as catalyst (0.2 equiv) in the presence of Ag&lt;sub&gt;2&lt;/sub&gt;CO&lt;sub&gt;3&lt;/sub&gt; (3 equiv) in the solvent 5% DMSO-DMF and proceeds at temperatures of 80−120 °C with a wide range of arene carboxylates and alkenes as substrates. The process is proposed to proceed by an initial Ar-S&lt;sub&gt;E&lt;/sub&gt; reaction involving ipso attack of an electrophilic Pd(II) intermediate on an arene carboxylate to form an arylpalladium(II) species with loss of carbon dioxide. This intermediate is then proposed to react with an olefinic substrate by steps common to the Heck coupling process. Reoxidation of the liberated Pd(0) in situ is proposed to establish the catalytic cycle.
Duality-free Methods for Stochastic Composition Optimization (2017)

We consider the composition optimization with two expected-value functions in the form of $\frac{1}{n}\sum\nolimits_{i = 1}^n F_i(\frac{1}{m}\sum\nolimits_{j = 1}^m G_j(x))+R(x)$, { which formulates many important problems in statistical learning and machine learning such as solving Bellman equations in reinforcement learning and nonlinear embedding}. Full Gradient or classical stochastic gradient descent based optimization algorithms are unsuitable or computationally expensive to solve this problem due to the inner expectation $\frac{1}{m}\sum\nolimits_{j = 1}^m G_j(x)$. We propose a duality-free based stochastic composition method that combines variance reduction methods to address the stochastic composition problem. We apply SVRG and SAGA based methods to estimate the inner function, and duality-free method to estimate the outer function. We prove the linear convergence rate not only for the convex composition problem, but also for the case that the individual outer functions are non-convex while the objective function is strongly-convex. We also provide the results of experiments that show the effectiveness of our proposed methods.