Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanisms governing the fragmentation of glycerophospholipids containing choline and ethanolamine polar head groups

Glycerophospholipids are the major amphiphilic molecules found in the plasma membrane bilayer of all vertebrate cells. Involved in many biological processes, their huge structural diversity and large concentration scale make their thorough characterization extremely difficult in complex biological matrices. Mass spectrometry techniques are now recognized as being among the most powerful methods for the sensitive and comprehensive characterization of lipids. Depending on the experimental conditions used during electrospray ionization mass spectrometry experiments, glycerophospholipids can be detected as different molecular species (e.g. protonated, sodiated species) when analyzed either in positive or negative ionization modes or by direct introduction or hyphenated mass spectrometry-based methods. The observed ionized forms are characteristic of the corresponding phospholipid structures, and their formation is highly influenced by the polar head group. Although the fragmentation behavior of each phospholipid class has already been widely studied under low collision energy, there are no established rules based on charge-induced dissociation mechanisms for explaining the generation of fragment ions. In the present paper, we emphasize the crucial roles played by ion–dipole complexes and salt bridges within charge-induced dissociation processes. Under these conditions, we were able to readily explain almost all the fragment ions obtained under low-energy collision-induced dissociation for particular glycerophospholipids and lysoglycerophospholipids species including glycerophosphatidylcholines and glycerophosphatidylethanolamines. Thus, in addition to providing a basis for a better comprehension of phospholipid fragmentation processes, our work also highlighted some potentially new relevant diagnostic ions to signal the presence of particular lipid species.
Phase I study of carboplatin combined with pemetrexed for elderly patients with advanced non-squamous non-small cell lung cancer.

OBJECTIVE The primary objective of this study was to evaluate the safety and tolerability of carboplatin plus pemetrexed for elderly patients (≥75 years) with chemotherapy-naïve advanced non-squamous non-small cell lung cancer. METHODS Patients received escalated doses of carboplatin at an area under the concentration-time curve of 4 (Level 1) or 5 (Level 2) plus pemetrexed (500 mg/m(2)) every 3 weeks for a maximum of six cycles. Dose escalation was decided according to whether dose-limiting toxicity occurred in the first cycle of chemotherapy. RESULTS A total of 20 patients (6 at Level 1, 14 at Level 2) were enrolled. No dose-limiting toxicities were observed in patients at Level 1 or the first six patients at Level 2, and therefore the combination of carboplatin at an area under the concentration-time curve of 5 plus pemetrexed at 500 mg/m(2) was considered to be the recommended dose. Among a total of 14 patients in Level 2, only 1 patient experienced dose-limiting toxicity: Grade 3 febrile neutropenia and urticaria. The major toxicities were neutropenia, thrombocytopenia and anemia. Liver dysfunction, fatigue and anorexia were also common, but generally manageable. Six patients showed partial responses, giving the overall response rate of 30%. The median progression-free survival period was 4.8 months (95% confidence interval 2.9-6.7 months). CONCLUSIONS The combination of carboplatin at an area under the concentration-time curve of 5 plus pemetrexed at 500 mg/m(2) was determined as the recommended dose in chemotherapy-naïve elderly patients (≥75 years) with advanced non-squamous non-small cell lung cancer, in view of overall safety and tolerability.
Intranet Boundaries as Guidelines for Systems Integration

Systems integration (SI) has been examined from two main vantage points. External B2B SI focuses on transactional interactions between customers and suppliers in the value chain. Internal intraorganizational SI focuses on structural interactions between functional units of the firm. Both approaches present problems for intranet integrations that serve communities of practice and formal project teams that cross organizational boundaries. This paper examines a few nontransactional intranet integrations, using a model of social actor interactions, affiliations, environments, and identities, to characterize integration types. The analysis identifies an alternative, project-based integration approach that may be more appropriate for intranets shared by interorganizational teams and communities. The model-driven evaluation also demonstrates how practitioners can use pre-integration intranet boundaries as guidelines for selectively implementing transactional, structural, and project-based integration approaches.
Effects of experimentally increased costs of activity during reproduction on parental investment and self-maintenance in tropical house wrens

Life-history theory assumes that organisms trade-off current against future reproduction to maximize fitness. Experimental explorations of the costs of reproduction have not yielded a clear understanding of the nature of these costs but rather point to a complex set of allocation possibilities among several physiological functions and behaviors. We investigated how experimentally increased flight costs affected the trade-off between parental investment and self-maintenance in tropical house wrens, which have relatively high annual survival and multiple breeding opportunities per year. We predicted that handicapped wrens would not increase their energy expenditure but instead decrease their effort to rear young in order to maintain their own body condition. Our results largely supported these predictions: handicapped parents decreased their nestling feeding frequency but did neither alter their field metabolic rate (FMR) nor compromise their body condition as measured by basal metabolic rate (BMR) and several measures of innate immune function. Reduced feeding rates did not affect nestling body mass growth but resulted in decreased structural growth (length of tarsus). The latter result can be explained if parents shifted the type of prey brought to offspring or altered the amount of food brought per trip. The experiment-wide positive correlations among FMR, BMR, and feeding frequency are in agreement with the hypothesis that hard work requires elevated levels of BMR. These correlations, in combination with the absence of a handicap treatment effect on FMR or BMR, do not lend support for predictions from studies in the laboratory that birds compensate hard work during the day by lowering their BMR at night. Considering a complex set of allocation possibilities among several physiological functions and behaviors, we conclude that tropical wrens take out the costs of a handicap largely on their offspring quality not on self-maintenance processes. Copyright 2008, Oxford University Press.
Opportunistic Feedback for Multiuser MIMO Systems With Linear Receivers

A novel multiuser scheduling and feedback strategy for the multiple-input multiple-output (MIMO) downlink is proposed in this paper. It achieves multiuser diversity gain without substantial feedback requirements. The proposed strategy uses per-antenna scheduling at the base station, which maps each transmit antenna at the base station (equivalently, a spatial channel) to a user. Each user has a number of receive antennas that is greater than or equal to the number of transmit antennas at the base station. Zero-forcing receivers are deployed by each user to decode the transmitted data streams. In this system, the base station requires users' channel quality on each spatial channel for scheduling. An opportunistic feedback protocol is proposed to reduce the feedback requirements. The proposed protocol uses a contention channel that consists of a fixed number of feedback minislots to convey channel state information. Feedback control parameters including the channel quality threshold and the random access feedback probability are jointly adjusted to maximize the average throughput performance of this system. Multiple receive antennas at the base station are used on the feedback channel to allow decoding multiple feedback messages sent simultaneously by different users. This further reduces the bandwidth of the feedback channel. Iterative search algorithms are proposed to solve the optimization for selection of these parameters under both scenarios that the cumulative distribution functions of users are known or unknown to the base station
Rhizopogon togasawariana sp. nov., the first report of Rhizopogon associated with an Asian species of Pseudotsuga

Rhizopogon subgenus Villosuli are the only members of the genus known to form an ectomycorrhizal relationship exclusively with Pseudotsuga. The specificity of this host relationship is unusual in that Rhizopogon is broadly associated with several tree genera within the Pinaceae and relationships with a host genus are typically distributed across Rhizopogon subgenera. Naturally occurring specimens of R. subg. Villosuli have been described only from North American collections, and the unique host relationship with Pseudotsuga is demonstrated only for Rhizopogon associated with P. menziesii (Douglas-fir), the dominant species of Pseudotsuga in North America. Species of Pseudotsuga are naturally distributed around the northern Pacific Rim, and Rhizopogon associates of other Pseudotsuga spp. are not yet described. Here we present the results of field sampling conducted in P. japonica forests throughout the Japanese archipelago and describe Rhizopogon togasawariana sp. nov., which occurs in ectomycorrhizal association with P. japonica. Placement of this new species within R. subg. Villosuli is supported by morphological and molecular phylogenetic analysis, and its implications to Pseudotsuga-Rhizopogon biogeography are discussed.
Effects of valence and framing in decision making II: Estimating subjective weighting1

In comparison between choice options, judgments of "How much better is a preferred option? " and "How much worse is a less preferred option? " may differ in their magnitudes. Such discrepancies are called "valence effects. " Previously, Yamagishi and Miyamoto (1996) observed systematic positive valence effects ("Better" exceeding "Worse") in the domain of gains and systematic negative valence effects ("Worse" exceed- ing "Better") in the domain of losses. The current experiment used the directions of valence effects as a tool to assess the decision maker's interpretation of choice tasks under the "framing effect" (Tversky & Kahneman, 1986). Preferences under the framing effect switch from certain options in the domain of gains to uncertain options in the domain of losses. This study examined whether preferences for certain options were associated with positive valence effects, whereas preferences for uncertain options were associated with negative valence effects. Moreover, conditions under which preference reversals under the framing manipulations ceased to occur were examined. The effects of valence showed that framing effects ceased to occur when decision makers maintained consistent task inter- pretations as pertaining to gains or to losses. Most importantly, the pattern of subjective weighting under the valence effects was consistent with previous explanation of valence effects (Yamagishi & Miyamoto, 1996). Possibilities for extending the current findings to understanding related psychological phenomena are discussed.
ASYNCHRONOUS PARALLEL SOLVER FOR HYPERBOLIC

This thesis presents a parallel Space Time Discontinuous Galerkin (SDG) finite element method which makes use of the method’s unstructured mesh generation and localized solution technique to achieve a high level of parallel scalability. Our SDG method is different from most traditional adaptive finite element methods in that the solution process generates fully unstructured spacetime grids that satisfy a special causality constraint ensuring that computations can occur locally on small cluster of spacetime elements. The resulting asynchronous solution scheme offers several desirable features: element-wise conservation of solution quantities, strong stability properties without the need for explicit stabilization, local mesh adaptivity operations and linear complexity in the number of spacetime elements. In this thesis we propose an algorithm that effectively parallelizes the Tent Pitcher algorithm developed by [1] using the POSIX Thread (or Pthread) parallel execution model. Multiple software threads can simultaneously and asynchronously perform patch computations by advancing vertices in time. By enforcing the causality constraint on the time step, we can guarantee that each thread only performs calculations using data computed previously. Additionally, improvements to the adaptivity scheme allow for local mesh refinement and coarsening while maintaining globally conforming triangulation. Numerical tests show that our algorithm achieves high parallel scalability using shared-memory parallelization.
Possible Antiretroviral Therapy‐Warfarin Drug Interaction

Highly active antiretroviral therapy (HAART) for human immunodeficiency virus (HIV) has resulted in significant morbidity and mortality reductions. Lifelong antiretroviral therapy must be incorporated into each patient's medical regimen. Patients with HIV may also have simultaneous chronic medical conditions, resulting in the possibility of complex drug‐drug interactions. We report a possible drug‐drug interaction between HAART and warfarin in two patients, as assessed by the Naranjo adverse drug reaction probability scale and the Drug Interaction probability scale. Both patients' pharmacotherapy regimens included a nonnucleoside reverse transcriptase inhibitor (NNRTI), nevirapine, or a protease inhibitor, nelfinavir or lopinavirritonavir, and two nucleoside analogs. In both patients, high warfarin doses were required to maintain therapeutic international normalized ratios (INRs). Warfarin has two enantiomers, R‐and S‐warfarin, which are substrates primarily of cytochrome P450 (CYP) 3A4 (R‐warfarin), CYP1A2 (R‐warfarin), and CYP2C9 (S‐warfarin). Protease inhibitors and NNRTIs have variable effects on CYP: induction, inhibition, or mixed. The increased warfarin doses required in these two patients may have been caused by induction of CYP3A4 by nevirapine, CYP2C9 by nelfinavir, or CYP2C9 by lopinavir‐ritonavir. Thus, practitioners should prudently monitor INRs in patients receiving warfarin with concomitant HAART that includes either a protease inhibitor or an NNRTI.
A simulation study of human performance deterioration and mental workload

Simulation de la deterioration de la performance humaine et de la charge mentale. Une simulation de la performance humaine et de la charge mentale a ete developpee et en partie validee. Le modele a ete mis en œuvre a l'aide du logiciel MicroSAINT. Il est fonde sur les idees de Card, Moran et Newell. Ses parametres ont ete estimes pour quatre tâches : une tâche de poursuite, une tâche de reaction au choix, une tâche de surveillance et une tâche de calcul mental. Le modele a ete utilise pour predire a la fois le comportement observe pour chacune de ces tâches prises isolement et le comportement de realisation simultanee des quatre tâches. Les resultats de la simulation se revelent compatibles avec un modele de type « canal unique » et laissent penser que la validite d'un tel modele soit susceptible de s'accroitre avec la complexite des situations de travail. A partir de ces resultats, on peut en outre considerer que les sujets adoptent une strategie « raisonnable » de commutation de l'attention d'une tâche a l'autre, quand les sujets sont confrontes a plusieurs tâches simultanees. Enfin, on peut penser que les sujets deploient davantage d'effort quand la pression temporelle est elevee.
Lateral error recovery for media streaming in application-level multicast

We consider media streaming using application-level multicast (ALM) where packet loss has to be recovered via retransmission in a timely manner. Since packets may be lost due to congestion, node failures, and join and leave dynamics, traditional "vertical" recovery approach where upstream nodes retransmit the lost packets is no longer effective. We therefore propose lateral error recovery (LER). In LER, hosts are divided into a number of planes, each of which forms an independent ALM tree. Since error correlation across planes is low, a node effectively recovers its error by "laterally" requesting retransmission from nearby nodes in other planes. We present analysis on the complexity and recovery delay on LER. Using Internet-like topologies, we show via simulations that LER is an effective error recovery mechanism. It achieves low overhead in terms of delivery delay (i.e., relative delay penalty) and physical link stress. As compared with traditional recovery schemes, LER attains much lower residual loss rate (i.e., loss rate after retransmission) under a certain deadline constraint. The performance can be substantially improved in the presence of some reliable proxies.
Analysis of Bacterial Communities in Soil by Use of Denaturing Gradient Gel Electrophoresis and Clone Libraries, as Influenced by Different Reverse Primers

ABSTRACT To assess soil bacterial diversity, PCR systems consisting of several slightly different reverse primers together with forward primer F968-GC were used along with subsequent denaturing gradient gel electrophoresis (DGGE) or clone library analyses. In this study, a set of 13 previously used and novel reverse primers was tested with the canonical forward primer as to the DGGE fingerprints obtained from grassland soil. Analysis of these DGGE profiles by GelCompar showed that they all fell into two main clusters separated by a G/A alteration at position 14 in the reverse primer used. To assess differences between the dominant bacteria amplified, we then produced four (100-membered) 16S rRNA gene clone libraries by using reverse primers with either an A or a G at position 14, designated R1401-1a, R1401-1b, R1401-2a, and R1401-2b. Subsequent sequence analysis revealed that, on the basis of the about 410-bp sequence information, all four primers amplified similar, as well as different (including novel), bacterial groups from soil. Most of the clones fell into two main phyla, Firmicutes and Proteobacteria. Within Firmicutes, the majority of the clones belonged to the genus Bacillus. Within Proteobacteria, the majority of the clones fell into the alpha or gamma subgroup whereas a few were delta and beta proteobacteria. The other phyla found were Actinobacteria, Acidobacteria, Verrucomicrobia, Chloroflexi, Gemmatimonadetes, Chlorobi, Bacteroidetes, Chlamydiae, candidate division TM7, Ferribacter, Cyanobacteria, and Deinococcus. Statistical analysis of the data revealed that reverse primers R1401-1b and R1401-1a both produced libraries with the highest diversities yet amplified different types. Their concomitant use is recommended.
Shortest Path Versus Multihub Routing in Networks With Uncertain Demand

We study a class of robust network design problems motivated by the need to scale core networks to meet increasingly dynamic capacity demands. Past work has focused on one of two models. First, design the network for the known point-to-point peak demands. Second, design the network to support all hose matrices (all matrices not exceeding marginal bounds at the nodes). Both models may be too conservative if additional information on traffic patterns is available. We introduce a capped hose model to explore a range of traffic scenarios, which includes the above two as special cases. It is known that optimal network designs for the hose model are always determined by single-hub routing, and for the fixed-demand model are based on shortest-path routing. We demonstrate that a wider variety of routing templates is required to address the broader spectrum of capped hose matrices. We propose the use of hierarchical multihub routing templates, a generalization of hub and tree routing. Our empirical analysis is based on a heuristic for the resulting robust network design problem. These lead to two important findings: 1) designs based on multihub routing are often preferable to both hub and shortest path; 2) it may be possible for a carrier to sample their traffic in order to determine which type of routing is most cost-effective for their network.
Brainstem projections of neurons located in various subdivisions of the dorsolateral hypothalamic area—an anterograde tract-tracing study

The projections from the dorsolateral hypothalamic area (DLH) to the lower brainstem have been investigated by using biotinylated dextran amine (BDA), an anterograde tracer in rats. The DLH can be divided into 3 areas (dorsomedial hypothalamus, perifornical area, lateral hypothalamic area), and further subdivided into 8 subdivisions. After unilateral stereotaxic injections of BDA into individual DLH subdivisions, the correct sites of injections were controlled histologically, and the distribution patterns of BDA-positive fibers were mapped on serial sections between the hypothalamus and spinal cord in 22 rats. BDA-labeled fibers were observable over 100 different brainstem areas, nuclei, or subdivisions. Injections into the 8 DLH subdivisions established distinct topographical patterns. In general, the density of labeled fibers was low in the lower brainstem. High density of fibers was seen only 4 of the 116 areas: in the lateral and ventrolateral parts of the periaqueductal gray, the Barrington's, and the pedunculopontine tegmental nuclei. All of the biogenic amine cell groups in the lower brainstem (9 noradrenaline, 3 adrenaline, and 9 serotonin cell groups) received labeled fibers, some of them from all, or at least 7 DLH subdivisions, mainly from perifornical and ventral lateral hypothalamic neurons. Some of the tegmental nuclei and nuclei of the reticular formation were widely innervated, although the density of the BDA-labeled fibers was generally low. No definitive descending BDA-positive pathway, but long-run solitaire BDA-labeled fibers were seen in the lower brainstem. These descending fibers joined some of the large tracts or fasciculi in the brainstem. The distribution pattern of BDA-positive fibers of DLH origin throughout the lower brainstem was comparable to patterns of previously published orexin- or melanin-concentrating hormone-immunoreactive fibers with somewhat differences.