gebhart/patrepeval huggingface dataset:
Violation of cell lineage restriction compartments in the chick hindbrain (1994)

Previous cell lineage studies indicate that the repeated neuromeres of the chick hindbrain, the rhombomeres, are cell lineage restriction compartments. We have extended these results and tested if the restrictions are absolute. Two different cell marking techniques were used to label cells shortly after rhombomeres form (stage 9+ to 13) so that the resultant clones could be followed up to stage 25. Either small groups of cells were labelled with the lipophilic dye DiI or single cells were injected intracellularly with fluorescent dextran. The majority of the descendants labelled by either technique were restricted to within a single rhombomere. However, in a small but reproducible proportion of the cases (greater than 5%), the clones expanded across a rhombomere boundary. Neither the stage of injection, the stage of analysis, the dorsoventral position, nor the rhombomere identity correlated with the boundary crossing. Judging from the morphology of the cells, both neurons and non-neuronal cells were able to expand over a boundary. These results demonstrate that the rhombomere boundaries represent cell lineage restriction barriers which are not impenetrable in normal development.
Rho-Kinase 1/2 Inhibition Prevents Transforming Growth Factor-β-Induced Effects on Pulmonary Remodeling and Repair (2021)

Transforming growth factor (TGF)-β-induced myofibroblast transformation and alterations in mesenchymal-epithelial interactions contribute to chronic lung diseases such as chronic obstructive pulmonary disease (COPD), asthma and pulmonary fibrosis. Rho-associated coiled-coil-forming protein kinase (ROCK) consists as two isoforms, ROCK1 and ROCK2, and both are playing critical roles in many cellular responses to injury. In this study, we aimed to elucidate the differential role of ROCK isoforms on TGF-β signaling in lung fibrosis and repair. For this purpose, we tested the effect of a non-selective ROCK 1 and 2 inhibitor (compound 31) and a selective ROCK2 inhibitor (compound A11) in inhibiting TGF-β-induced remodeling in lung fibroblasts and slices; and dysfunctional epithelial-progenitor interactions in lung organoids. Here, we demonstrated that the inhibition of ROCK1/2 with compound 31 represses TGF-β-driven actin remodeling as well as extracellular matrix deposition in lung fibroblasts and PCLS, whereas selective ROCK2 inhibition with compound A11 did not. Furthermore, the TGF-β induced inhibition of organoid formation was functionally restored in a concentration-dependent manner by both dual ROCK 1 and 2 inhibition and selective ROCK2 inhibition. We conclude that dual pharmacological inhibition of ROCK 1 and 2 counteracts TGF-β induced effects on remodeling and alveolar epithelial progenitor function, suggesting this to be a promising therapeutic approach for respiratory diseases associated with fibrosis and defective lung repair.
Immunomodulatory peptides attenuate local and systemic inflammation in a murine DSS-colitis model (2009)

Cxcl2, and Cxcl3), and MMPs that participate in the remodeling of extracellular matrices (e.g., MMP3, MMP9, and MMP13) were all markedly increased in the colons of DSS-treated WT mice relative to untreated WT mice and DSS-treated mMCP-6-null mice.ELISA and/or immunohistochemistry analyses revealed changes in the corresponding protein levels of many of these differentially expressed transcripts.CONCLUSIONS: mMCP-6 is a critical mediator in the DSS model of murine experimental colitis, and this tryptase acts upstream of many of those factors implicated in IBD.The accumulated data raise the possibility that mast cell hTryptase-1 has prominent adverse roles in patients with IBD.
Case 4-2016 (2016)

A 58-year-old woman presented during the summer with fever, neck swelling, and an ulcerated lesion on the forehead. Imaging of the neck showed enlarged, centrally hypodense lymph nodes with infiltration of the surrounding fat. Tests were performed, and a diagnosis was made.
ChemInform Abstract: Biocompatibility and Drug Delivery Systems (2010)

Abstract Review: 45 refs.
DDoS defense by offense (2010)

This article presents the design, implementation, analysis, and experimental evaluation of speak-up , a defense against application-level distributed denial-of-service (DDoS), in which attackers cripple a server by sending legitimate-looking requests that consume computational resources (e.g., CPU cycles, disk). With speak-up, a victimized server encourages all clients, resources permitting, to automatically send higher volumes of traffic . We suppose that attackers are already using most of their upload bandwidth so cannot react to the encouragement. Good clients, however, have spare upload bandwidth so can react to the encouragement with drastically higher volumes of traffic. The intended outcome of this traffic inflation is that the good clients crowd out the bad ones, thereby capturing a much larger fraction of the server's resources than before. We experiment under various conditions and find that speak-up causes the server to spend resources on a group of clients in rough proportion to their aggregate upload bandwidths, which is the intended result.
Activity of native vs. synthetic promoters inBrucella (2008)

Brucellosis caused by Brucella species is reportedly the most common zoonotic infection worldwide. The bacterial pathogen is also classified by the Centers for Disease Control and Prevention as a category (B) pathogen that has the potential for development as a bioweapon. Although eight genomes of Brucella have been sequenced, little information is available regarding the regulation of gene expression and promoter activity in Brucella spp. We therefore constructed a set of broad-host-range vectors expressing the lacZ reporter gene from various promoters. Four groups of promoters (Brucella native, antibiotic resistant, bacteriophage and synthetic promoters) were tested in vivo and in vitro in Brucella suis. The highest level of heterologous gene expression was achieved with synthetic hybrid trc promoter carrying the adenine-rich upstream element. Furthermore, this demonstrates the usefulness of synthetic promoters for enhanced level of gene expression in Brucella spp.
GPS Signal-in-Space Integrity Performance Evolution in the Last Decade (2012)

Knowledge of the Global Positioning System (GPS) signal-in-space (SIS) anomalies in history has a great importance for not only assessing the general performance of GPS SIS integrity but also validating the fundamental assumption of receiver autonomous integrity monitoring (RAIM): at most one satellite fault at a time. The main purpose of this paper is to screen out all potential SIS anomalies in the last decade by comparing broadcast ephemerides and clocks with precise ones. Validated broadcast navigation messages are generated from 397,044,414 navigation messages logged by on average 410 International GNSS Service (IGS) stations during the period 6/1/2000-8/31/2010. Both IGS and National Geospatial-Intelligence Agency (NGA) precise ephemerides/clocks are used as truth references. Finally, 1256 potential SIS anomalies are screened out. These anomalies show an improving SIS integrity performance in the last decade, from tens or hundreds of anomalies per year before 2003 to on average two anomalies per year after 2008. Moreover, the fundamental assumption of RAIM is valid because never have two SIS anomalies or more occurred simultaneously since 2004.
A work-optimal deterministic algorithm for the asynchronous certified write-all problem (2003)

In their SIAM J. on Computing paper [27] from 1992, Martel et al. posed a question for developing a work-optimal deterministic asynchronous algorithm for the fundamental load-balancing and synchronization problem called Certified Write-All. In this problem, introduced in a slightly different form by Kanellakis and Shvartsman in a PODC'89 paper [17], p processors must update n memory cells and then signal the completion of the updates. It is known that solutions to this problem can be used to simulate synchronous parallel programs on asynchronous systems with worst-case guarantees for the overhead of a simulation. Such simulations are interesting because they may increase productivity in parallel computing since synchronous parallel programs are easier to reason about than asynchronous ones are.This paper presents a solution to the question of Martel et al. Specifically, we show a deterministic asynchronous algorithm for the Certified Write-All problem. Our algorithm has O(n + p4 log n) work, which is optimal for a non-trivial number of processors p ≤ (n/log n)1/4. In contrast, all known deterministic algorithms require superlinear in n work when p = n1/r, for any fixed r ≥ 1. Our algorithm generalizes the collision principle used by the algorithm T that was introduced by Buss et al. [7].
Quantitative Evaluation of Porosity in Aluminum Die Castings by Fractal Analysis of Perimeter (2008)

In the die-casting process, the formation of pores in components is unavoidable. This porosity has a harmful effect on the strength and pressure tightness of die castings. To eliminate the porosity in components, its predominant cause has to be identified as being due to either shrinkage or gas. In practice, however, it is frequently difficult to tell the difference between porosity due to shrinkage and that due to gas from observing die castings. Accurate identification enables die casters to take corrective action. To identify the porosity accurately and to take corrective action in the die-casting process, the quantitative estimation of the morphology of pores such as their shape or spatial distribution can be a source of useful information. In this study, two types of fractal analyses are proposed to characterize the porosity in terms of the shape of individual pores and the spatial distribution of multiple pores. It is shown that these are indicators of whether the predominant cause of the porosity is shrinkage or gas. These parameters are expected to indicate the action that should be taken to manufacture pore-free die castings.
Effect of added Cu on disorder-order transformation of L1/sub 0/-FePt (2002)

The L1/sub 0/-FePt ordered phase is formed at lower annealing temperature by addition of Cu. FePtCu films start ordering at 300/spl deg/C or a lower temperature, whereas FePt and FePtAg films are still disordered alloys after annealing at 300/spl deg/C. The results of X-ray diffraction indicate that FePt and the added Cu form an FePtCu ternary alloy, whereas FePtAg decomposes into FePt and Ag phases in the disorder-order transformation. From thermodynamic considerations, it is concluded that reduction of the ordering temperature of FePt is due to the formation of an FePtCu solid solution.
Positive in vivo heterologous gene regulation by electric pulses delivery with metallothionein I gene promoter (2005)

This time-control of the expression of a therapeutic gene by physical stimuli could be of value in the context of gene regulation for gene therapy.
Neurosurgical Care of the Geriatric Patient (2014)

Chronic subdural hematomas (SDHs) are common in the elderly. Patients with chronic SDHs that produce symptoms can be treated effectively and safely by multiple means. Aneurysms affect older patients just as they do younger ones. Stroke is characterized by the sudden loss of blood circulation to an area of the brain, resulting in a corresponding loss of neurologic function. The endovascular treatment of acute intracranial (IC) thrombosis is advancing rapidly. The major barrier to success in this area appears to be the rapidity with which treatment can be instituted. Normal pressure hydrocephalus (NPH) is predominantly a disease of the elderly. Along with odontoid fractures, vertebral body compression fractures are extremely common in the elderly population. Facial pain can be a challenging problem to both diagnose and treat. The most common and treatable form is trigeminal neuralgia (TGN).
Magnetic resonance elastography predicts advanced fibrosis in patients with nonalcoholic fatty liver disease: A prospective study (2014)

MRE is accurate in predicting advanced fibrosis and may be utilized for noninvasive diagnosis of advanced fibrosis in patients with NAFLD.
Igusa class polynomials, embeddings of quartic CM fields, and arithmetic intersection theory (2010)

Bruinier and Yang conjectured a formula for an intersection number on the arithmetic Hilbert modular surface, CM(K).T_m, where CM(K) is the zero-cycle of points corresponding to abelian surfaces with CM by a primitive quartic CM field K, and T_m is the Hirzebruch-Zagier divisors parameterizing products of elliptic curves with an m-isogeny between them. In this paper, we examine fields not covered by Yang's proof of the conjecture. We give numerical evidence to support the conjecture and point to some interesting anomalies. We compare the conjecture to both the denominators of Igusa class polynomials and the number of solutions to the embedding problem stated by Goren and Lauter.
Sensor calibration based on external stimulus actuation (2005)

We have developed an on-line sensor calibration scheme that employes a additional single source as the external stimulus that creats differential sensor readings used for calibration. The key idea of our approach is to use an actuator to produce differential simultaneous excitement of all sensors over a number of time frames while the environment the sensors are deployed in is relatively inactive. The sensor calibration functions are derived in such a way that all sensors (or a group of sensors) agree on the effect of the actuator in the most consistent way. More specifically, we utilizes the maximal likelihood principle and a nonlinear system optimization solver to derive the calibration functions of arbitrary complexity and accuracy. The approach has the following noble properties: i) it is maximally localized in that each sensor only needs to communicate with one other sensor in order to be calibrated; ii) the number of time steps that are required for calibration is very low. Therefore, the approach is both communication and time efficitent. We present two variants of the approach: i) one where only two neighboring sensors have to communicate in order to conduct calibration; ii) one that utilizes an integer linear programming (ILP) formulation to provably minimize the required number of packets that must be sent for calibration. We evaluate the techniques using traces from light sensors recorded by in-field deployed sensors, and statistical evaluations are conducted in order to obtain the interval of confidence to support all the results.
Is the EWS/FLI-1 fusion transcript specific for Ewing sarcoma and peripheral primitive neuroectodermal tumor? A report of four cases showing this transcript in a wider range of tumor types. (1996)

The presence of t(11;22)(q24;q12) is often considered diagnostic of Ewing sarcoma and peripheral primitive neuroectodermal tumor. We report four cases, all of which possessed this translocation as detected by reverse transcriptase polymerase chain reaction and confirmed by sequencing with or without fluorescent in situ hybridization, but none of which were Ewing sarcoma or peripheral primitive neuroectodermal tumor by histological criteria. Two were polyphenotypic tumors and two were mixed embryonal and alveolar rhabdomyosarcomas. Only one case was positive for MIC2 by immunohistochemistry and only in a rare cell. Two cases (one polyphenotypic tumor and one rhabdomyosarcoma) had double minute chromosomes with > 100 copies of the MDM2 gene. The presence of the t(11;22)(q24;ql2) translocation should probably not be considered diagnostic of Ewing sarcoma and peripheral primitive neuroectodermal tumor in the absence of supporting histological evidence. The presence of this translocation in Ewing sarcoma and peripheral primitive neuroectodermal tumor has been taken as evidence that these two tumors are related. Extending this relationship to include some polyphenotypic tumors and some rhabdomyosarcomas may not be justified unless additional evidence is gathered. Pathologists and oncologists will need to decide whether treatment regimens for tumors are better based on phenotype rather than genotype when these two profiles are seemingly in conflict.
Quasienantiomers and Quasiracemates: New Tools for Identification, Analysis, Separation, and Synthesis of Enantiomers (2005)

The old adage "never mix pure organic compounds" holds in spades for enantiomers. After going to all the trouble to make enantiopure molecules, who in their right mind would ever mix them to make a racemate? Quasienantiomers are almost enantiomers, but not quite. Yet unlike enantiomers, the interest is not so much in separating them but in mixing them to make quasiracemates. This backwards thinking opens new possibilities for identification, analysis, separation and synthesis of enantiomers. A short history is provided, the terms are defined and illustrated, and recent applications of quasienantiomers, quasiracemates and related species are reviewed.
ChemInform Abstract: Synthesis of the Angiotensin Converting Enzyme Inhibitor (‐)‐A58365A via an Isomuenchnone Cycloaddition Reaction. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
GPNLPerf: Robust 4d Non-rigid Motion Correction for Myocardial Perfusion Analysis (2016)

Since the introduction of wide cone detector systems, CT myocardial perfusion has been an area of increased interest, for which non-rigid registration [NRR] is a key step to further analysis. We propose a novel motion management pipeline for perfusion data, GPNLPerf (Group-wise, non-local, NRR for perfusion analysis) centering on group-wise NRR using non-local spatio-temporal constraints. The proposed pipeline deals with the NRR challenges for 4D perfusion data and results in generating clinically relevant perfusion parameters. We demonstrate results on 9 dynamic perfusion exams comparing results quantitatively with ANTs NRR and also show qualitative results on perfusion maps.
Straightforward Pentafluorosulfanylation for Molecular Design (2023)

Pentafluorosulfanylation is a powerful boost of molecular properties for many applications. In order to leverage its full potential, a direct and high-yielding synthetic strategy is in great demand. We report here how the discovery of a direct pentafluorosulfanylation of thiolated arenes led to a generalized synthetic approach toward aryl– and heteroaryl pentafluorosulfanyl (SF5) compounds from various common building blocks. The combination of onium halides with silver(II) fluoride (AgF2) provided drastically enhanced oxidative fluorination conditions that enabled the single-step conversion of various thiophenol derivatives to SF5-compounds in high yields and broad scope. The particularly high reaction rate is accounted to an onium fluoroargentate(II)-mediated fluorination mechanism. The recycling potential of inorganic silver byproducts furthermore offers an avenue into industrial-scale production.
Facile Access to 3,5‐Dihalogenated Pyrazoles by Sydnone Cycloaddition and their Versatile Functionalization by Pd‐Catalyzed Cross‐Coupling Processes (2011)

Abstract The 1,3‐dipolar cycloaddition of diversely N ‐substituted 4‐iodosydnones with 3‐halopropiolates produces easily separable mixtures of dihalogenated pyrazolylcarboxylic esters at a preparative scale level, with the 3,5‐dihalogenopyrazole regioisomers always predominating. Further decarboxylation of the major isomers provided the corresponding 3,5‐dihalogenopyrazoles with a free C‐4 position. These were found to be valuable scaffolds for the elaboration of unsymmetrically 1,3,5‐trisubstituted pyrazole derivatives by site‐selective Pd‐catalyzed cross‐coupling reactions. Notably, the flexible and site‐selective introduction of different (hetero)aryl, vinyl, or alkyl substituents at the C‐5 and C‐3 positions of the pyrazole core could be achieved through sequential Suzuki‐type reactions with various boron compounds. Furthermore, the Suzuki coupling sequence could be amenable to a one‐pot procedure that enables rapid generation of the targeted compounds.
Vitronectin Inhibits Blood Platelet Aggregation (1993)

The effect of vitronectin on platelet aggregation has been investigated. Vitronectin inhibited both thrombin- and ADP-induced platelet aggregation in a dose-dependent manner. A monoclonal antibody (MoAb) to vitronectin increased thrombin-induced platelet aggregation. This effect of the MoAb was not mediated via the platelet Fc-receptor, suggesting that the antibody directly counteracted the inhibitory effect of vitronectin on platelet aggregation. Like some other adhesive proteins such as fibrinogen, fibronectin, and von Willebrand factor, vitronectin contains the amino-acid sequence Arg-Gly-Asp (RGD) which enables binding to the platelet membrane glycoprotein complex IIb/IIIa (GPIIb/IIIa). The results of this study indicate that vitronectin can modulate the function of fibrinogen on platelet aggregation by interfering with the binding of fibrinogen to GPIIb/IIIa in activated platelets.
Continuous versus bolus intermittent loop diuretic infusion in acutely decompensated heart failure: a prospective randomized trial (2014)

ClinicalTrials.gov NCT01441245. Registered 23 September 2011.
Differential effect of CTLA4Ig on murine graft-versus-host disease (GVHD) development: CTLA4Ig prevents both acute and chronic GVHD development but reverses only chronic GVHD (1996)

The role of costimulation was examined in an in vivo model of alloantigen-driven Th1 or Th2 cytokine responses, the parent-into-F1 model of acute or chronic graft-vs-host disease (GVHD), respectively. The soluble fusion protein, murine CTLA4Ig, which blocks engagement of CD28 by its natural ligand B7-1 and B7-2, was administered either early, at the time of GVHD induction, or delayed, after the establishment of Th1 or Th2 effector responses (day 7). Early administration of CTLA4Ig prevented the development of both acute and chronic GVHD by preventing the activation of donor T cells, i.e., by blocking characteristic Th1 or Th2 cytokine production and blocking memory marker up-regulation on donor T cells. Delayed CTLA4Ig administration was unable to alter acute GVHD but did reverse chronic GVHD as evidenced by normalization of serum autoantibody levels, normal host B cell numbers and MHC class II expression, reduced donor T cell expression of CD40 ligand, and reduced numbers of donor CD4+ memory T cells. The percentage of donor memory cells was not altered by delayed CTLA4Ig. We conclude that in this model, alloantigen-driven Th1 or Th2 responses are equally susceptible to costimulatory blockade at the onset of disease; however, once effector mechanisms become established, only Th2-driven responses have a requirement for further costimulation for the continued expansion of CD4+ T cells. These data suggest that humoral, lupus-like autoimmunity requires continuous T cell help for B cells, and agents that interrupt this process may be beneficial.
Multi-Agent Low-Dimensional Linear Bandits (2020)

We study a multi-agent stochastic linear bandit with side information, parameterized by an unknown vector $θ^* \in \mathbb{R}^d$. The side information consists of a finite collection of low-dimensional subspaces, one of which contains $θ^*$. In our setting, agents can collaborate to reduce regret by sending recommendations across a communication graph connecting them. We present a novel decentralized algorithm, where agents communicate subspace indices with each other and each agent plays a projected variant of LinUCB on the corresponding (low-dimensional) subspace. By distributing the search for the optimal subspace across users and learning of the unknown vector by each agent in the corresponding low-dimensional subspace, we show that the per-agent finite-time regret is much smaller than the case when agents do not communicate. We finally complement these results through simulations.