gebhart/patrepeval huggingface dataset:
Introduction: spatial origin of murine hematopoietic stem cells (2001)

Hematopoiesis is the developmentally regulated and tissue-specific process of blood cell production. The predominant anatomic site of hematopoiesis changes several times during murine and human ontogeny. Blood and endothelial cells become morphologically identifiable on embryonic day 7.5 (E7.5) in
An access protocol for a wireless home network (2003)

Wireless technology is an attractive option to network devices in the home as it does not require rewiring the home. The media access protocol (MAC) plays a crucial role in allowing multiple devices to transmit and receive on the shared wireless medium and thereby determining the efficiency of a wireless home network (WiHN). It is found that many of the protocols proposed to date like the Distributed Foundation Wireless MAC (DFWMAC) in the IEEE 802.11 standard have poor performance at high data rates (100 Mbps). We modify the slotted-idle sense multiple access protocol and propose a simple and efficient MAC protocol which fits well with the WiHN architecture. We present a queuing analysis and simulation results of the performance of the wireless home network MAC (WiHNMAC) protocol.
Efficacy and Safety of a Switch to Rilpivirine-Based Regimens in Treatment-Experienced HIV-1-Infected Patients: A Cohort Study (2015)

In patients fully suppressed on ART, a switch to an RPV-based regimen should only be considered in the absence of prior virological failure or resistance mutations to nucleoside reverse transcriptase inhibitors and NNRTIs to avoid virological failures.
Discriminative Dimensionality Reduction in Kernel Space (2016)

Modern nonlinear dimensionality reduction (DR) techniques enable an efficient visual data inspection in the form of scatter plots, but they suffer from the fact that DR is inherently ill-posed.Discriminative dimensionality reduction (DiDi) offers one remedy, since it allows a practitioner to identify what is relevant and what should be regarded as noise by means of auxiliary information such as class labels.Powerful DiDi methods exist, but they are restricted to vectorial data only.In this contribution, we extend one particularly promising approach to non-vectorial data characterised by a kernel.This enables us to apply discriminative dimensionality reduction to complex, possibly discrete or structured data.
Centrin in the photoreceptor cells of mammalian retinae (1995)

Photoreceptor cells of vertebrate retinae are highly specialized ciliary cells. Their non-motile ciliated structure is restricted to the so-called connecting cilium at the joint between the light sensitive outer segment and the metabolically active inner segment. Extensive bidirectional intracellular transport between both segments is forced to occur through this tight connecting cilium. In the present study it is shown that the CA2+-binding, phospho-protein centrin is present in mammalian retinae. Western blot and immunoprecipitation reveal that anti-centrin antibodies react with purified photoreceptor cell fractions of retinae in bands at a molecular weight of 20 kDa, the molecular weight of centrins found in other cells. Indirect immunofluorescence analysis of cryosections through retinae of different mammalian species show that centrin is present only in centrosomes and basal bodies but also more extensively at the linkage between the inner and the outer segment of the photoreceptor cells. Immunocytological studies on isolated rod cells and immunoelectron microscopy clearly demonstrate a unique presence of centrin in the connecting cilium of photoreceptor cells. High molecular identity between centrins in lower eukaryotes and mammals indicates that centrin may play a role in cellular motility and/or in microtubule severing in the mammalian retina.
Dithiocarbamates Trigger Differentiation and Induction of CD11c Gene through AP-1 in the Myeloid Lineage (1996)

It has recently been shown that the alteration of the cell-redox status affects the transcription factor expression and activity. Dithiocarbamates (DTCs) are potent antioxidant agents that can switch the expression of genes dependent on the activation of the transcription factors AP-1 and NF kappa B. In this study, we show that these agents triggered the expression of genes involved in myeloid differentiation of the promonocytic U-937 cell line. DTCs promoted differentiation-associated changes that included the surface up-regulation of beta 2-integrins (CD11a-c/CD18), cell growth arrest concomitant with transferrin receptor (CD71) down-modulation, induction of the nonspecific esterase enzyme, and a rapid drop in the mRNA levels of c-myc. A further analysis, focused on the molecular mechanisms leading to the activation of CD11c expression, revealed that the pyrrolidine derivative of DTC (PDTC) increased CD11c mRNA levels and augmented its gene promoter activity. Transfection experiments with reporter constructs harboring different promoter regions of CD11c gene, indicated the presence of a functional DTC-responsive region located between positions -160 and +40 of the promoter. Gel retardation assays revealed that the PDTC-induced DNA-protein complexes were restricted to members of the Fos and Jun families that bound to an AP-1 site located at position -60 from the transcription start site. A role for this site was confirmed by in vitro mutagenesis experiments that indicated the functional importance of this site for the CD11c gene transcriptional activation in response to PDTC. The effect of DTCs on myeloid cell differentiation supports a possible role for these agents in the therapy of some bone marrow-derived malignancies.
Studies of Charged Excitations inπ-Conjugated Oligomers and Polymers by Optical Modulation (1996)

We have studied photogenerated charged excitations in sexithiophene and a variety of $\ensuremath{\pi}$-conjugated polymers by photoinduced absorption (PA) and PA-detected magnetic resonance. We found distinct spin signatures for polarons and bipolarons, which enabled us to separate their contributions to the PA spectrum. In all cases, we find that polarons have two subgap optical transitions, whereas bipolarons have one. Having unambiguously identified the energy levels of polarons and bipolarons, we show that bipolarons are stable photoexcitations, with negative effective correlation energy.
A multiple‐method comparative study using GC–MS, AMDIS and in‐house‐built software for the detection and identification of “unknown” volatile organic compounds in breath (2021)

The human respiratory system is a highly complex matrix that exhales many volatile organic compounds (VOCs). Breath-exhaled VOCs are often "unknowns" and possess low concentrations, which make their analysis, peak digging and data processing challenging. We report a new methodology, applied in a proof-of-concept experiment, for the detection of VOCs in breath. For this purpose, we developed and compared four complementary analysis methods based on solid-phase microextraction and thermal desorption (TD) tubes with two GC-mass spectrometer (MS) methods. Using eight model compounds, we obtained an LOD range of 0.02-20 ng/ml. We found that in breath analysis, sampling the exhausted air from Tedlar bags is better when TD tubes are used, not only because of the preconcentration but also due to the stability of analytes in the TD tubes. Data processing (peak picking) was based on two data retrieval approaches with an in-house script written for comparison and differentiation between two populations: sick and healthy. We found it best to use "raw" AMDIS deconvolution data (.ELU) rather than its NIST (.FIN) identification data for comparison between samples. A successful demonstration of this method was conducted in a pilot study (n = 21) that took place in a closed hospital ward (Covid-19 ward) with the discovery of four potential markers. These preliminary findings, at the molecular level, demonstrate the capabilities of our method and can be applied in larger and more comprehensive experiments in the omics world.
SARS-CoV-2 Antibody Responses in Infection-Naive or Previously Infected Individuals After 1 and 2 Doses of the BNT162b2 Vaccine (2021)

This cohort study examines antibody responses in infection-naive and previously infected individuals after 1 and 2 doses of the BNT162b2 vaccine.
Stage Delay Scheduling (2019)

To increase the resource utilization of datacenters, big data analytics jobs are commonly running stages in parallel which are organized into and scheduled according to the Directed Acyclic Graph (DAG). Through an in-depth analysis of the latest Alibaba cluster trace and our motivation experiments on Amazon EC2, however, we show that the CPU and network resources are still under-utilized due to the unwise stage scheduling, thereby prolonging the completion time of a DAG-style job (e.g., Spark). While existing works on reducing the job completion time focus on either task scheduling or job scheduling, stage scheduling has received comparably little attention. In this paper, we design and implement DelayStage, a simple yet effective stage delay scheduling strategy to interleave the cluster resources across the parallel stages, so as to increase the cluster resource utilization and speed up the job performance. With the aim of minimizing the makespan of parallel stages, DelayStage judiciously arranges the execution of stages in a pipelined manner to maximize the performance benefits of resource interleaving. Extensive prototype experiments on 30 Amazon EC2 instances and complementary trace-driven simulations show that DelayStage can improve the cluster resource utilization by up to 81.8% and reduce the job completion time by up to 41.3%, in comparison to the stock Spark and the state-of-the-art stage scheduling strategies, yet with acceptable runtime overhead.
Use of a Surfactant as a Coal Grinding Additive (1987)

The effect of a cationic surfactant on wet grinding of a raw coal with a 34% ash content was studied in an attrition grinder. It was observed that the surfactant increases the grinding efficiency, leading to an economy in the energy input of as much as 25%, depending on the conditions. It also shifts the selectivity in grinding coal components in favor of the mineral matter. Both effects depend on the fulfillment of two conditions: (i) high slurry density, and (ii) continuous particle size distribution in the feed. An analysis of the results reveals that the surfactant is effective when grinding takes place by shear stresses, supporting the theory due to Rebinder.
Comparison of Pressure-Transient Response in Intensely and Sparsely Fractured Reservoirs (1991)

Summary A comprehensive analytical model is presented to quantify the pressure-transient behavior of a naturally fractured reservoir with a continuous matrix-block-size distribution and interporosity skin. Geologically realistic probability density functions of matrix block size are used to represent reservoirs of varying fracture intensity and uniformity. Drawdown and interference type curves are developed with rectangular probability density functions. The results obtained extend previous dual-porosity models by incorporating fracture spacing variability. In the absence of interporosity skin, intensely and sparsely fractured reservoirs show distinctions in the pressure response. Uniformity of a fractured reservoir also significantly affects pressure responses, irrespective of the degree of fracture intensity. The pressure response in a nonuniformly fractured reservoir with large block-size variability, for example, can exhibit a nonfractured (homogeneous) reservoir response. The results may be used to estimate matrix-block-size variability and the degree of fracture intensity from drawdown and interference well tests.
Requirements for Scalable Adaptive Multicast Framework in Non-GIG Networks (2006)

The Scalable Adaptive Multicast (SAM) Research Group is chartered to
explore and research techniques which improve multicast performance
with respect to dimensions such as number of groups, dynamics of group
membership, dynamics of the network topology, and network resource
constraints. This document describes requirements for SAM framework,
especially for non-GIG environment.
TAN: Temporal Aggregation Network for Dense Multi-Label Action Recognition (2019)

We present Temporal Aggregation Network (TAN) which decomposes 3D convolutions into spatial and temporal aggregation blocks. By stacking spatial and temporal convolutions repeatedly, TAN forms a deep hierarchical representation for capturing spatio-temporal information in videos. Since we do not apply 3D convolutions in each layer but only apply temporal aggregation blocks once after each spatial downsampling layer in the network, we significantly reduce the model complexity. The use of dilated convolutions at different resolutions of the network helps in aggregating multi-scale spatio-temporal information efficiently. Experiments show that our model is well suited for dense multi-label action recognition, which is a challenging sub-topic of action recognition that requires predicting multiple action labels in each frame. We outperform state-of-the-art methods by 5% and 3% on the Charades and Multi-THUMOS dataset respectively.
The Arabidopsis thaliana trehalase is a plasma membrane‐bound enzyme with extracellular activity (2007)

The lack of trehalose accumulation in most plant species has been partly attributed to the presence of an active trehalase. Although trehalose synthesis enzymes are thought to be cytosolic, and previous studies have indicated that trehalase activity is extracellular, the exact location of the enzyme has not yet been established in plant cell. We present evidence that the yet uncharacterised full-length Arabidopsis trehalase is a plasma membrane-bound protein, probably anchored to the membrane through a predicted N-terminal membrane spanning domain. The full-length AtTRE1, when expressed in yeast can functionally substitute for the extracellularly active trehalase Ath1p, by sustaining the growth of an ath1 null mutant strain on trehalose and at pH 4.8. We further demonstrate that AtTRE1 expressed in yeast is plasma membrane-bound as in plant cell. In light of these findings, the regulation of plant cell endogenous trehalose by trehalase is discussed.
Simian Immunodeficiency Virus Replicates to High Levels in Sooty Mangabeys without Inducing Disease (1998)

A serologic survey of primates living in a French zoo allowed identification of three cases of infection with simian immunodeficiency virus in sooty mangabeys (Cercocebus atys) (SIVsm). Viral isolates, which were designated SIVsmFr66, SIVsmFr74, and SIVsmFr85, were obtained after short-term culture of mangabey lymphoid cells. Phylogenetic analysis of gag and env sequences amplified directly from mangabey tissues showed that the three SIVsmFr were genetically close and that they constituted a new subtype within the diverse SIVsm-SIVmac-human immunodeficiency virus type 2 (HIV-2) group. We could reconstruct the transmission events that likely occurred in 1986 between the three animals and evaluate the divergence of SIVsmFr sequences since transmission. The estimated rate of mutation fixation was 6 x 10(-3) substitutions per site per year, which was as high as the rate found for SIVmac infection in macaques. These data indicated that SIVsmFr replicated at a high rate in mangabeys, despite the nonpathogenic character of infection in this host. The viral load evaluated by competitive PCR reached 20,000 viral DNA copies per 10(6) lymph node cells. In addition, productively infected cells were readily detected in mangabey lymphoid tissues by in situ hybridization. The amounts of viral RNA in plasma ranged from 10(5) to 10(7) copies per ml. The cell-associated and plasma viral loads were as high as those seen in susceptible hosts (humans or macaques) during the asymptomatic stage of HIV or SIVmac infections. Thus, the lack of pathogenicity of SIVsm for its natural host cannot be explained by limited viral replication or by tight containment of viral production.
2 HUMAN UMBILICAL CORD AUTOANTIBODIES (HUC-AB). AN IDEAL SCREENING TEST FOR COELIAC DISEASE (CD) (1995)

Sulkanen, S.; Marttinen, A.; Hällström, O.; Laurila, K.; Halttunen, T.; Mäki, M. Author Information
MicroRNAs in the Regulation of NADPH Oxidases in Vascular Diabetic and Ischemic Pathologies: A Case for Alternate Inhibitory Strategies? (2022)

Since their discovery in the vasculature, different NADPH oxidase (NOX) isoforms have been associated with numerous complex vascular processes such as endothelial dysfunction, vascular inflammation, arterial remodeling, and dyslipidemia. In turn, these often underlie cardiovascular and metabolic pathologies including diabetes mellitus type II, cardiomyopathy, systemic and pulmonary hypertension and atherosclerosis. Increasing attention has been directed toward miRNA involvement in type II diabetes mellitus and its cardiovascular and metabolic co-morbidities in the search for predictive and stratifying biomarkers and therapeutic targets. Owing to the challenges of generating isoform-selective NOX inhibitors (NOXi), the development of specific NOXis suitable for therapeutic purposes has been hindered. In that vein, differential regulation of specific NOX isoforms by a particular miRNA or combina-tion thereof could at some point become a reasonable approach for therapeutic targeting under some circumstances. Whereas administration of miRNAs chronically, or even acutely, to patients poses its own set of difficulties, miRNA-mediated regulation of NOXs in the vasculature is worth surveying. In this review, a distinct focus on the role of miRNAs in the regulation of NOXs was made in the context of type II diabetes mellitus and ischemic injury models.
Alumina/alumina ceramic matrix composites as part of the SHEFEX II thermal protection system (2010)

For DLR’s SHEFEX II (Sharp Edge Flight Experiment) campaign multiple TPS panels were fabricated from WHIPOX-type alumina/alumina ceramic matrix composites. These CMCs exhibit favourable properties such as high-temperature oxidation resistance and damage tolerance. A special feature of these CMCs is their inherent transparency for electromagnetic waves, making them attractive as thermal protection for antenna. Scheduled for autumn 2010 SHEFEX II will include an actively controlled atmosphere re-entry at a maximum cruise velocity of Mach 11 where a high thermal load on the TPS protected nose-cap is expected. However, emittance of alumina is low and consequently radiation cooling capability of alumina-based TPS panels is limited. In order to prevent thermal overload, emittance of CMCs is improved by superficial impregnation and coating with an oxidation-resistant “black” CoFe-spinel. Thermal performance and material stability was proofed in an arc-heated wind-tunnel at DLR. It turns out that CoFe-spinel surface modification can reduce CMC temperatures by more than 200 K in a Mach 6 hypersonic flow field. The modified CMC exhibits microstructural stability up to the expected TPS peak temperature of 1300°C. Design, manufacturing and set-up of the WHIPOX-TPS segments of SHEFEX II are presented.
Finding refactorings via change metrics (2000)

Reverse engineering is the process of uncovering the design and the design rationale from a functioning software system. Reverse engineering is an integral part of any successful software system, because changing requirements lead to implementations that drift from their original design. In contrast to traditional reverse engineering techniques ---which analyse a single snapshot of a system--- we focus the reverse engineering effort by determining where the implementation has changed. Since changes of object-oriented software are often phrased in terms of refactorings, we propose a set of heuristics for detecting refactorings by applying lightweight, object-oriented metrics to successive versions of a software system. We validate our approach with three separate case studies of mature object-oriented software systems for which multiple versions are available. The case studies suggest that the heuristics support the reverse engineering process by focusing attention on the relevant parts of a software system.
Acute myeloid leukemia following treatment of hodgkin's disease. A review (1982)

Risk factors were analyzed and searched for possible predictive parameters for the development of acute myeloid leukemia in 216 reported patients previously treated for Hodgkin's disease. The distribution of histologic subtypes and the stage at diagnosis were similar to that of all patients with Hodgkin's disease. Seventy-five percent of the 216 patients in whom acute myeloid leukemia developed had received both radiotherapy and chemotherapy, 15% chemotherapy only, and 10% radiotherapy only. Of those receiving radiotherapy, 66% were given multiple courses or total nodal irradiation. Of the patients receiving chemotherapy, 77% had received more than eight months of single or combination drug therapy; only 4% had not been exposed to alkylating agents. When acute leukemia developed, 78% of the patients showed no clinical or pathologic evidence of residual Hodgkin's disease. A period of pancytopenia preceded the onset of overt leukemia in at least one-third of the patients. Complete or partial remission of the acute leukemia was achieved in 25% of the patients treated with antileukemic chemotherapy. On the basis of these findings, it is deemed advisable to reexamine the intensity of treatment presently being administered to achieve cure of Hodgkin's disease. Unnecessary or unproved programs of combined radiation therapy and chemotherapy should be avoided. An optimal balance between the risks and benefits of treatment needs to be applied.
Fluorescence detection of the movement of single KcsA subunits reveals cooperativity (2008)

The prokaryotic KcsA channel is gated at the helical bundle crossing by intracellular protons and inactivates at the extracellular selectivity filter. The C-terminal transmembrane helix has to undergo a conformational change for potassium ions to access the central cavity. Whereas a partial opening of the tetrameric channel is suggested to be responsible for subconductance levels of ion channels, including KcsA, a cooperative opening of the 4 subunits is postulated as the final opening step. In this study, we used single-channel fluorescence spectroscopy of KcsA to directly observe the movement of each subunit and the temporal correlation between subunits. Purified KcsA channels labeled at the C terminus near the bundle crossing have been inserted into supported lipid bilayer, and the fluorescence traces analyzed by means of a cooperative or independent Markov model. The analysis revealed that the 4 subunits do not move fully independently but instead showed a certain degree of cooperativity. However, the 4 subunits do not simply open in 1 concerted step.