gebhart/patrepeval huggingface dataset:
Effect of Conditioning Regimen Intensity on CMV Infection in Allogeneic Hematopoietic Cell Transplantation (2009)

Nonmyeloablative conditioning is less toxic and results in initial establishment of mixed hematopoietic T cell chimerism for up to half a year with prolonged presence of host T cell immunity. In this study, we examined whether this translates into differences in the risks and/or severity of cytomegalovirus (CMV) infection and disease. We analyzed data from 537 nonmyeloablative (NM-HCT) and contemporaneous 2489 myeloablative hematopoietic cell transplant (M-HCT) recipients. In CMV seropositive recipients, no difference in the overall hazards of CMV infection at any level (adjusted hazard ratio [adj. HR] 0.9, 95% confidence interval [95% CI]: 0.7-1.0, P = .14) was noted; however, NM-HCT was associated with a lower risk of high-grade CMV infection (adj. HR 0.7, 95% CI: 0.5-0.9, P = .02). CMV disease rates were similar between the groups during the first 100 days after HCT, but NM-HCT recipients had an increased risk of late CMV disease (adj. HR 2.0, 95% CI 1.2-3.4). The increased risk of late CMV disease after NM-HCT was pronounced during the earlier years of the study period, but not detectable in more recent years. Contrary to earlier reports, survival following CMV disease was not reduced after NM-HCT when compared to M-HCT recipients. These results suggest that residual host cells after NM-HCT reduce progression to higher CMV viral load in NM-HCT recipients; however, this effect does not appear to protect against serious complications of CMV. Therefore, CMV prevention strategies in NM-HCT recipients should be similar to those used in M-HCT recipients.
Small-Molecule Inhibitors of p53-MDM2 Interaction: the 2006-2010 Update (2011)

Increasing knowledge of the relationship between p53 and MDM2 has led to development of potential small molecule inhibitors useful for clinical studies. Herein, we discuss the patented (2006-2010) inhibitors of p53-MDM2 interaction. The anticancer agents discussed in this review belong to several different chemical classes including benzodiazepinediones, cis-imidazolines, oxindoles, spiro-oxindoles, and numerous miscellaneous groups. This review also provides comprehensive information on inhibitors of p53-MDM2 interaction that are currently being tested in clinical trials. It is important to note that many of the disclosed inhibitors need further validation to be considered as bona fide inhibitors of p53-MDM2 interaction and some will not be further considered for future studies. On the other hand, JNJ-26854165, a novel tryptamine derivative and RG7112, a cis-imidazoline representative have shown promising results in early phases of trials in cancer patients. AT-219, a spiroindolinone in late stage preclinical studies is a likely candidate to proceed into clinical trials. It remains to be seen how these inhibitors will perform in future clinical studies as single agents and in combination with the currently approved chemotherapeutic agents.
Strain and Temperature Measurement with Fiber Optic Sensors (2025)

Sensors operating on interferometric principles and mounted inside optical fibers have recently been considered for measuring strain and temperature. Indeed, such sensors have successfully been employed for measuring pressure or temperature in fluids. Fiber optics sensors are especially adept for such measurements because sensors immersed in fluids can easily be calibrated by tests. Unfortunately, the use of fiber optic sensors inside solids is not as straightforward. Owing to the complex interactions between the sensor and the surrounding material, the relationship between the sensor output and the parameters of interest, namely the strain and temperature inside the material, cannot be determined by simple tests. And without the appropriate relationships, fiber optic sensors do not provide meaningful information. In general, the relationship providing the bridge between the sensor output and the engineering values of strain and temperature must be established via analytical models. The major aim of this book is to present such models for extrinsic and intrinsic Fabry-Perot sensors and for Bragg grating sensors embedded in or mounted on the surface of isotropic or anisotropic solids or immersed in fluids. The scope of the book is limited to the theory of fiber optic strain and temperature sensors. Accordingly, we have taken as our starting point the demodulated sensor signals. The hardware needed to produce these signals is not discussed. It is presumed that the reader is familiar with and has access to the sensor, light source, light detector and demodulator required for generating signals which can then be analyzed and interpreted by the methods presented in the book. The problem necessitates complex analytical developments. To assist the reader, the significant results are summarized in tables, and numerical examples are given illustrating the calculation procedures.
Measuring enjoyment of physical activity in older adults: invariance of the physical activity enjoyment scale (paces) across groups and time (2011)

The purpose of this study was to validate the Physical Activity Enjoyment Scale (PACES) in a sample of older adults. Participants within two different exercise groups were assessed at two time points, 6 months apart. Group and longitudinal invariance was established for a novel, 8-item version of the PACES. The shortened, psychometrically sound measure provides researchers and practitioners an expedited and reliable instrument for assessing the enjoyment of physical activity.
Hydrogen exchange of the tryptophan residues in bovine α‐lactalbumin studied by uv spectroscopy (1988)

Abstract The effect of Ca 2+ ion on structural fluctuation of a milk Ca 2+ ‐binding protein, α‐lactalbumin, under native conditions was investigated by comparing hydrogen‐exchange reactions of tryptophan residues in the apo‐form without Ca 2+ and in the holo‐form at 1 m M CaCl 2 at pH 7.0 in the presence of 0.1 M Na + . The reactions were followed by measuring time‐dependent absorption changes at 298–300 nm due to the 2 H‐ 1 H exchange of the tryptophan imino protons and were found to be biphasic under all the conditions examined. Two of the four tryptophan protons are insensitive to Ca 2+ concentration and show a relatively fast exchange rate. The other two protons are much more extensively protected (a protection degree of 10 3 –10 5 ) and are markedly affected by the presence of Ca 2+ . Examinations of the temperature dependence and pH dependence of the individual exchange rates have been utilized for elucidating the exchange mechanism. The fast protons show a low activation energy reaction with so‐called EX 2 kinetics. The exchange reaction of the slow protons is accompanied by a high activation energy, and the exchange mechanism of the protons depended on the presence or absence of stabilizing Ca 2+ ions—the EX 1 kinetics for the apo‐protein and the EX 2 kinetics for the holo‐protein at 1 m M Ca 2+ . The exchange reaction in the thermally unfolded state was also found to be biphasic, but the fast phase, which has an exchange rate in the fully exposed state, becomes predominant with decreasing temperature. By taking this fact and using a structural unfolding model of hydrogen exchange, the present results are fully consistent with thermodynamic parameters of the thermal transition and kinetic parameters of refolding reactions induced by concentration jumps of guanidine hydrochloride obtained in previous studies. It is demonstrated that the reaction of the slow protons in the native state is mediated by a transient global unfolding equivalent to the “thermal” unfolding under a native condition and that switching of the exchange mechanism from the EX 1 to EX 2 kinetics results from acceleration of the refolding rate with an increase in Ca 2+ concentration. The transient global unfolding takes place even under a strongly native condition, e.g., at a temperature 20° below the beginning of the thermal transition.
641. The structure of the mannan present in Porphyra umbilicalis (1950)

J. K. N. Jones, J. Chem. Soc., 1950, 3292 DOI: 10.1039/JR9500003292
A characterization of endomorphism algebras (1984)

Synopsis The result that any monoid is isomorphic to some endomorphism monoid is generalized to super-associative systems.
Evolution on the network edge: intelligent devices (2003)

A network's edge is arguably one of its most important areas, because this is where it delivers services to network users-or, from the Internet service provider perspective, to subscribers. Devices at the network's edge classify, prioritize, and mark packets for the rest of the network to understand, and ultimately allow them into the network. Given modern networks' complex internetworking, it is not surprising that developing and maintaining edge devices are tasks that head the agendas of most of today's network equipment manufacturers, carriers, service providers, and network administrators. This article examines key elements of current network edge devices and the network topologies that work best with them. It also discusses Multiprotocol Label Switching (MPLS), a standardized solution that combines the performance and virtual circuit capabilities of data-link-layer switching with the proven scalability of network layer routing used by today's edge devices.
ClosTron-Targeted Mutagenesis (2010)

Members of the genus Clostridium have long been recognised as important to humankind and its animals, both in terms of the diseases they cause and the useful biological processes they undertake. This has led to increasing efforts directed at deriving greater information on their basic biology, most notably through genome sequence. Accordingly, annotated sequences of all of the most important species are now available. However, full exploitation of the data generated has been hindered by the lack of mutational tools that may be used in functional genomic studies. Thus, the number of clostridial mutants generated has until recently been disappointingly small. In particular, the construction of directed mutants using classical homologous recombination-based methods has met with only limited success. Moreover, most of these few mutants were constructed by the unstable integration of a plasmid into the chromosome via a single crossover event. As an alternative, recombination-independent strategies have been devised that are reliant upon a re-targeted group II intron. One element in particular, the ClosTron, provides the facility for the positive selection of insertional mutants. The generation of mutants using the ClosTron is extremely rapid (as little as 10 days) and is highly efficient and reproducible. Furthermore, the insertions made are extremely stable. Its deployment has considerably expanded available options for clostridial functional genomic studies.
Modelling the relationship between peripheral blood pressure and blood volume pulses using linear and neural network system identification techniques (1999)

The relationships between peripheral blood pressure and blood volume pulse waveforms can provide valuable physiological data about the peripheral vascular system, and are the subject of this study. Blood pressure and volume pulse waveforms were collected from 12 normal male subjects using non-invasive optical techniques, finger arterial blood pressure (BP, Finapres: Datex-Ohmeda) and photoelectric plethysmography (PPG) respectively, and captured to computer for three equal (1 min) measurement phases: baseline, hand raising and hand elevated. This simple physiological challenge was designed to induce a significant drop in peripheral blood pressure. A simple first order lag transfer function was chosen to study the relationship between blood pressure (system input) and blood volume pulse waveforms (system output), with parameters describing the dynamics (time constant, tau) and input-output gain (K). Tau and K were estimated for each subject using two different system identification techniques: a recursive parameter estimation algorithm which calculated tau and K from a linear auto-regressive with exogenous variable (ARX) model, and an artificial neural network which was trained to learn the non-linear process input-output relationships and then derive a linearized ARX model of the system. The identification techniques allowed the relationship between the blood pressure and blood volume pulses to be described simply, with the neural network technique providing a better model fit overall (p < 0.05, Wilcoxon). The median falls in tau following the hand raise challenge were 26% and 31% for the linear and neural network based techniques respectively (both p < 0.05, Wilcoxon). This preliminary study has shown that the time constant and gain parameters obtained using these techniques can provide physiological data for the clinical assessment of the peripheral circulation.
A Reflective Information Model for Reusing Software Architecture (2008)

Reusing software architecture, which is a kind of coarse-grained software resources at design time, is always a very difficult problem in the realm of software engineer. We consider that there are two fundamental reasons for this problem: one is the lack of information which supports the process of reusing software architecture; another is the lack of effective reusing approach. So this paper proposes RIM4RSA - reflective information model for reusing software architecture supporting the reuse of architectural level design, which offers the information support for reusing software architecture and its constituents at design time by modeling the meta-information about the base-level to construct a meta-level. Moreover, this paper illustrates the approach to construct meta-level and base-level of the RIM4RSA, and presents the implementation solution of RIM4RSA. At the same time, we put forward an approach for reusing software architecture based on the use of RIM4RSA.
Platelet Activation in the Gyro C1E3 Centrifugal Pump: Comparison with the Terumo Capiox and the Nikkiso HPM‐15 (2000)

The Gyro C1E3 was developed as a cardiopulmonary bypass pump incorporating the sealless double pivot bearing system. In this study, we evaluated platelet activation induced by the Gyro C1E3 in vitro and in comparison to that of other centrifugal pumps. Rates of increase (RI) for beta-thromboglobulin (beta-TG) and platelet factor 4 (PF4) in the Gyro C1E3 were calculated from in vitro data and compared with the rate of increase in the Capiox (Terumo) and HPM-15 (Nikkiso) pumps. Fresh human blood was used, and a flow of 5.0 L/min with a DeltaP (pressure difference between the outlet and inlet of the pump) of 100 mm Hg employed. RI = Deltabeta-TG/DeltaN and DeltaPF4/DeltaN were used where Deltabeta-TG is the increase in beta-TG, DeltaPF4 is the increase in PF4, and DeltaN is the increase in the passing number and where N = Qt/V (t = time, V = priming volume, and Q = flow rate). The mean RI for beta-TG was 0.26 +/- 0. 05 in the Gyro C1E3, 0.20 +/- 0.07 in the Capiox, and 0.15 +/- 0.02 in the HPM-15. The mean RI for PF4 was 0.15 +/- 0.03 in the Gyro C1E3, 0.12 +/- 0.05 in the Capiox, and 0.09 +/- 0.04 in the HPM-15. While there was no difference in RI for beta-TG and PF4 between the Gyro C1E3 and Capiox, RI for beta-TG and PF4 were significantly higher in the Gyro C1E3 than in the HPM-15 (p = 0.006 and 0.029). In vitro evaluation using RI for beta-TG and PF4 showed platelet damage caused by the Gyro C1E3 and the Capiox to be nearly equal while the HPM-15 was less traumatic to platelets than the Gyro C1E3.
CLIBE: Precise Cluster-Level I/O Bandwidth Enforcement in Distributed File System (2018)

A distributed file system (DFS) is a core component to implement big data applications. On the one hand, a DFS is capable of managing a large volume of data with desirable properties that strike the balance between high availability, reliability, and so on. On the other hand, a DFS relies on underlying storage systems (e.g., hard drives, solid state drives, etc.) and suffer from slow read/write operations. In big data era, large-scale data processing applications start to leverage the in-memory processing to improve the performance by reducing the inhibitive cost of I/O operations. However, it is still inevitable to read input data from or write outputs to the storage system. Slow I/O operations are often the main bottleneck of emerging big data applications. In particular, while these applications often use DFSs to store their results for the high availability and reliability, the unmanaged I/O bandwidth contention results in the QoS violation of high priority applications when multiple applications share the same DFS. To enable I/O management and allocation on big-data platforms, we propose a Cluster-Level I/O Bandwidth Enforcement (CLIBE) approach that consists of a cluster-level I/O bandwidth quota manager, multiple node-level I/O bandwidth controllers, and a feedback-based quota reallocator. The quota manager splits and distributes the I/O bandwidth quota of an application to the active nodes that are serving this application. The bandwidth controller on a node ensures that the I/O bandwidth used by an application would not exceed its bandwidth quota on the node. For an application affected by slow or overloaded nodes, the quota reallocator reallocates the idle I/O bandwidth on underloaded nodes to this application to guarantee its throughput. Our experiment on a real-system cluster shows that CLIBE is able to precisely control the I/O bandwidth used by an application at the cluster level, with the deviation smaller than 2.51%.
Ground-wave propagation over an inhomogeneous smooth earth (1949)

The problem of ground-wave propagation over an inhomogeneous smooth earth is discussed in terms of the known solution for a homogeneous earth. The inhomogeneity refers only to changes in the earth constants from place to place, and the problem is idealized by assuming a wave radiated from a vertical dipole over a series of homogeneous annular sections. After a statement of some of the conditions the solution would be expected to obey, including the essential one of reciprocity, some fundamental results of the theory for a homogeneous earth are described in a form directly useful to the argument. The solution is first given for the short-wave limit, where it is complete except in the neighbourhood of a boundary. By an approximate consideration of the energy flow at different heights above the ground, the solution is extended to the case of intermediate wavelengths where the first and last boundaries are in the diffraction region of the transmitting and receiving points respectively. It is then shown that a well-known empirical method yields the same solution when it is made reciprocal by taking the geometric mean of the value it gives and the value that would be obtained with the transmitter and receiver interchanged. This method is formally used to obtain a tentative solution for the effect of the disturbance function in the neighbourhood of a boundary. It leads to the striking suggestion that on passing from a section of one value of conductivity to another of a higher one, there is a recovery in field-strength before the attenuation of the wave becomes characteristic of the new section. On crossing the boundary in the other direction, there is a correspondingly increased drop in field strength before the attenuation takes its new characteristic type. Owing to the lack of sufficiently controlled conditions, most of the existing experimental results are inconclusive with regard to these features at a boundary, but some evidence is given in support of them. Stress is laid on the need for further experiments specifically designed to study the field near a land-sea boundary. The paper deals briefly with the practical application of the method, and gives a specimen field-strength/distance curve for a route consisting of several land and sea sections. It concludes by pointing out that further research is needed, especially with regard to the phase relationships, as the argument has dealt only with field-strength values.
Smooth beamforming for OFDM (2009)

This paper investigates the combination of beamforming and channel state information (CSI) smoothing for OFDM. While both can offer significant performance gains, care must be taken when using both of them at the same time. Two different sets of beamforming weights can produce the same beamforming gains but be unsuitable for CSI smoothing due to sudden changes in the frequency domain. By using orthogonal iterations to compute the beamforming weights, it is shown that a smooth beamformer is produced which is suitable for CSI smoothing at the receiver. An additional benefit of this technique is that the beamforming weights are easy to compute by exploiting the frequency correlation of the channel. The performance is evaluated for an OFDM system based on the IEEE 802.11n draft standard for which the gains are quantified. We also present results obtained from a hardware test bed, which verify the performance of the proposed smooth beamforming technique.
Learning the pattern of epistasis linking genotype and phenotype in a protein (2017)

Understanding the pattern of epistasis – the non-independence of mutations – is critical for relating genotype and phenotype in biological systems. However, the complexity of potential epistatic interactions has limited approaches to this problem at any level. To develop practical strategies, we carried out a comprehensive experimental study of epistasis between all mutations that link two phenotypically distinct variants of the Entacmaea quadricolor fluorescent protein. The data demonstrate significant high-order epistatic interactions between mutations, but also reveals extraordinary sparsity, enabling novel experimental strategies and sequence-based statistical methods for learning the relevant epistasis. The sequence space linking the parental fluorescent proteins is functionally connected through paths of single mutations; thus, high-order epistasis in proteins is consistent with evolution through stepwise variation and selection. This work initiates a path towards characterizing epistasis in proteins in general.
Mel-18, a Polycomb Group Protein, Regulates Cell Proliferation and Senescence via Transcriptional Repression of Bmi-1 and c-Myc Oncoproteins (2006)

Polycomb group (PcG) protein Bmi-1 is an important regulator of cell proliferation. It regulates cellular senescence and proliferation of cells via the transcriptional repression of INK4a/ARF locus and other target genes. Here, we report that Mel-18, a PcG ring finger protein (PCGF) transcriptionally down-regulates Bmi-1. Furthermore, the expression of Bmi-1 and Mel-18 inversely correlates in proliferating and senescent human fibroblasts. Bmi-1 down-regulation by Mel-18 results in accelerated senescence and shortening of the replicative life span in normal human cells. Importantly, using promoter-reporter, chromatin immunoprecipitation, and quantitative real-time primary transcript RT-PCR assays, and an RNA interference approach, we demonstrate that Bmi-1 is a bona fide target of c-Myc oncoprotein. Finally, our data suggest that Mel-18 regulates Bmi-1 expression during senescence via down-regulation of c-Myc. These studies link c-Myc and polycomb function in cell proliferation and senescence.