Miracle-dz/UniFAR-FTUs huggingface dataset:
A retrospective, matched paired analysis comparing bendamustine containing BeEAM versus BEAM conditioning regimen: results from a single center experience

Abstract The combination of carmustine, etoposide, aracytin, and melphalan(BEAM) conditioning regimen in autologous stem-cell transplantation (ASCT) is widely used in patients with relapsed/refractory non-Hodgkin lymphoma (NHL) and Hodgkin lymphoma. It is also an option in patients with very-high risk aggressive NHL in first complete remission (CR). Recently, a phase Ib–II feasibility study using bendamustine replacing carmustine (BCNU) was reported. We report herein a safety and efficacy analysis of bendamustine-EAM (BeEAM) with a control BEAM counterpart paired cohort (1/2). One hundred and two patients were analyzed. Overall survival (OS) and progression-free survival (PFS) were not reached and seemed to be comparable between both groups. However, grade III or greater diarrhea was significantly higher in BeEAM patients (44 vs. 15%, p = .002). The median number of days with fever >38 °C was significantly higher in BeEAM group (5.5 vs. 2, p < .001). This case-control study suggests that BeEAM followed by ASCT using bendamustine at 100 mg/m2/d is effective but has a different toxicity profile than the BEAM regimen.
Endothelin‐1‐ and isoproterenol‐induced differential protein expression and signaling pathway in HL‐1 cardiomyocytes

It is well known that the two chemical compounds endothelin‐1 (ET‐1) and isoproterenol (ISO) can individually induce cardiac hypertrophy through G protein‐coupled receptors in cardiomyocytes. However, the cardiac hypertrophy signaling pathway activated by ET‐1 and ISO is not well defined. Therefore, we investigated the protein expression profile and signaling transduction in HL‐l cardiomyocyte cells treated with ET‐1 and ISO. Following separation of the cell lysates by using 2‐DE and silver staining, we identified 16 protein spots that were differentially expressed as compared to the controls. Of these 16 spots, three changed only after treatment with ET‐1, whereas four changed only after treatment with ISO, suggesting that these two stimuli could induce different signaling pathways. In order to reveal the differences between ET‐1‐ and ISO‐induced signaling, we studied the different events that occur at each step of the signaling pathways, when selected biocomponents were blocked by inhibitors. Our results indicated that ET‐1 and ISO used different pathways for phosphorylation of glycogen synthase kinase‐3β (GSK3β). ET‐1 mainly used the mitogen‐activated protein kinase and phosphatidylinositol‐3‐kinase/AKT pathways to activate GSK3β, whereas under ISO stimulation, only the phosphatidylinositol‐3‐kinase/AKT pathway was required to trigger the GSK3β pathway. Furthermore, the strength of the GSK3β signal in ISO‐induced cardiac hypertrophy was stronger than that in ET‐1‐induced cardiac hypertrophy. We found that these two agonists brought about different changes in the protein expression of HL‐1 cardiomyocytes through distinct signaling pathways even though the destination of the two signaling pathways was the same.
Efficient Bayesian Model Averaging in Factor Analysis

Although factor analytic models have proven useful for covariance structure modeling and dimensionality reduction in a wide variety of applications, a challenging problem is uncertainty in the number of latent factors. This article proposes an efficient Bayesian approach for model selection and averaging in hierarchical models having one or more factor analytic components. In particular, the approach relies on a method for embedding each of the smaller models within the largest possible model. Bayesian computation can proceed within the largest model, while moving between sub-models based on posterior model probabilities. The approach represents a type of parameter expansion, as one always samples within an encompassing model, incorporating extra parameters and latent variables when a smaller model is true. This results in a highly efficient stochastic search factor selection algorithm (SSFS) for identifying good factor models and performing model-averaged inferences. The approach is illustrated using simulated examples and a toxicology application.
Dbp5p, a cytosolic RNA helicase, is required for poly(A)+ RNA export

The DBP5 gene encodes a putative RNA helicase of unknown function in the yeast Saccharomyces cerevisiae. It is shown here that Dbp5p is an ATP‐dependent RNA helicase required for polyadenylated [poly(A)+] RNA export. Surprisingly, Dbp5p is present predominantly, if not exclusively, in the cytoplasm, and is highly enriched around the nuclear envelope. This observation raises the possibility that Dbp5p may play a role in unloading or remodeling messenger RNA particles (mRNPs) upon arrival in the cytoplasm and in coupling mRNP export and translation. The functions of Dbp5p are likely to be conserved, since its potential homologues can be found in a variety of eukaryotic cells.
Role of Copper Oxide Layer on Pool Boiling Performance With Femtosecond Laser Processed Surfaces

Copper pool boiling surfaces are tested for pool boiling enhancement due to femtosecond laser surface processing (FLSP). FLSP creates self-organized micro/nanostructures on metallic surfaces and creates highly wetting and wicking surfaces with permanent surface features. In this study two series of samples were created. The first series consists of three flat FLSP copper surfaces with varying microstructures and the second series is an open microchannel configuration with laser processing over the horizontal surfaces of the microchannels. These microchannels range in height from 125 microns to 380 microns. Each of these surfaces were tested for pool boiling performance. It was found that all the processed surfaces except one resulted in a decrease in critical heat flux and heat transfer coefficient compared to an unprocessed surface. It was found that the laser fluence parameter had a significant role in whether there was an increase in CHF or HTC. A cross sectioning technique was employed to study the different layers of the microstructure and to understand how FLSP could have a negative effect on the CHF and HTC. It was found that a thick oxide layer forms during the FLSP process of copper in an open-air atmosphere. The thickness and uniformity of the oxide layer is highly dependent on the laser fluence. A low fluence sample results in an inconsistent oxide layer of nonuniform thickness and subsequently an increase in CHF and HTC. A high laser fluence sample results in a uniformly thick oxide layer which increases the thermal resistance of the sample and allows for a premature CHF and decrease in HTC.
Genetic Variants on 3q21 and in the Sp8 Transcription Factor Gene (SP8) as Susceptibility Loci for Psychotic Disorders: A Genetic Association Study

Background Recent genome-wide association studies (GWASs) investigating bipolar disorder (BD) have detected a number of susceptibility genes. These studies have also provided novel insight into shared genetic components between BD and schizophrenia (SCZ), two major psychotic disorders. To examine the replication of the risk variants for BD and the pleiotropic effect of the variants associated with BD, we conducted a genetic association study of single nucleotide polymorphisms (SNPs) that were selected based upon previous BD GWASs, which targeted psychotic disorders (BD and SCZ) in the Japanese population. Methods Forty-eight SNPs were selected based upon previous GWASs. A two-stage analysis was conducted using first-set screening (for all SNPs: BD = 1,012, SCZ = 1,032 and control = 993) and second-set replication samples (for significant SNPs in the screening analysis: BD = 821, SCZ = 1,808 and control = 2,149). We assessed allelic association between BD, SCZ, psychosis (BD+SCZ) and the SNPs selected for the analysis. Results Eight SNPs revealed nominal association signals for all comparisons (Puncorrected<0.05). Among these SNPs, the top two SNPs (associated with psychosis: Pcorrected = 0.048 and 0.037 for rs2251219 and rs2709722, respectively) were further assessed in the second-set samples, and we replicated the signals from the initial screening analysis (associated with psychosis: Pcorrected = 0.0070 and 0.033 for rs2251219 and rs2709722, respectively). The meta-analysis between the current and previous GWAS results showed that rs2251219 in Polybromo1 (PBRM1) was significant on genome-wide association level (P = 5×10−8) only for BD (P = 9.4×10−9) and psychosis (P = 2.0×10−10). Although the association of rs2709722 in Sp8 transcription factor (SP8) was suggestive in the Asian population (P = 2.1×10−7 for psychosis), this signal weakened when the samples size was increased by including data from a Caucasian population (P = 4.3×10−3). Conclusions We found 3p21.1 (including PBRM1, strong linkage disequilibrium made it difficult to pinpoint the risk genes) and SP8 as risk loci for BD, SCZ and psychosis. Further replication studies will be required for conclusive results.
Selective Interactions of UPIa and UPIb, Two Members of the Transmembrane 4 Superfamily, with Distinct Single Transmembrane-domained Proteins in Differentiated Urothelial Cells (*)

The transmembrane 4 (TM4) superfamily contains many important leukocyte differentiation-related surface proteins including CD9, CD37, CD53, and CD81; tumor-associated antigens including CD63/ME491, CO-029, and SAS; and a newly identified metastasis suppressor gene R2. Relatively little is known, however, about the structure and aggregation state of these four transmembrane-domained proteins. The asymmetrical unit membrane (AUM), believed to play a major role in stabilizing the apical surface of mammalian urothelium thus preventing it from rupturing during bladder distention, contains two TM4 members, the uroplakins (UPs) Ia and Ib. In association with two other (single transmembrane-domained) membrane proteins, UPII and UPIII, UPIa and UPIb form 16-nm particles that naturally form two-dimensional crystalline arrays, thus providing unique opportunities for studying membrane structure and function. To better understand how these proteins interact to form the 16-nm particles, we analyzed their nearest neighbor relationship by chemical cross-linking. We show here that UPIa and UPIb, which share 39% of their amino acid sequence, are cross-linked to UPII and UPIII, respectively. We also show that UPIa has a propensity to oligomerize, forming complexes that are stable in SDS, and that UPII can be readily cross-linked to form homodimers. The formation of UPII homodimers is sensitive, however, to octyl glucoside that can solubilize the AUMs. These data suggest that there exist two types of 16-nm AUM particles that contain UPIa/UPII or UPIb/UPIII, and support a model in which the UPIa and UPII occupy the inner and outer domains, respectively, of the UPIa/UPII particle. This model can account for the apparent “redundancy” of the uroplakins, as the structurally related UPIa and UPIb, by interacting with different partners, may play different roles in AUM formation. The model also suggests that AUM plaques with different uroplakin compositions may differ in their assembly, and in their abilities to interact with an underlying cytoskeleton. Our data indicate that two closely related TM4 proteins, UPIa and UPIb, can be present in the same cell, interacting with distinct partners. AUM thus provides an excellent model system for studying the targeting, processing, and assembly of TM4 proteins.
Personality and Other Lifelong Influences on Older‐Age Health and Wellbeing: Preliminary Findings in Two Scottish Samples

Recent observations that personality traits are related to later–life health and wellbeing have inspired considerable interest in exploring the mechanisms involved. Other factors, such as cognitive ability and education, also show longitudinal influences on health and wellbeing, but it is not yet clear how all these early–life factors together contribute to later–life health and wellbeing. In this preliminary study, we assessed hypothesised relations among these variables across the life course, using structural equation modelling in a sample assessed on dependability (a personality trait related to conscientiousness) in childhood, cognitive ability and social class in childhood and older age, education, and health and subjective wellbeing in older age. Our models indicated that both health and subjective wellbeing in older age were influenced by childhood IQ and social class, via education. Some older–age personality traits mediated the effects of early–life variables, on subjective wellbeing in particular, but childhood dependability did not show significant associations. Our results therefore did not provide evidence that childhood dependability promotes older–age health and wellbeing, but did highlight the importance of other early–life factors, particularly characteristics that contribute to educational attainment. Further, personality in later life may mediate the effects of early–life factors on health and subjective wellbeing. © 2016 The Authors. European Journal of Personality published by John Wiley & Sons Ltd on behalf of European Association of Personality Psychology
Autonomic Resource Allocation in Virtualized Data Centers

Virtualization has been widely adopted in data centers for improving efficiency and flexibility. Multiple applications are co-hosted in virtualized data centers. In order to meet the Service Level Agreements (SLA), how to allocate resources for multiple applications is an important and challenging task, especially when dealing with fluctuating workloads and complex server applications. Virtual Machine Monitor provides fine-grained resource allocation and live migration. In this paper, we develop RTCOIN-Qclouds, a response time-aware, cost-aware and interference-aware control framework that tunes resource allocation, which ensures a high level of meeting the SLAs. Every physical machine's resources are assigned to multiple virtual machines which run on it based on application's response time, rather than traditional methods based on resource utilization. Virtual machine migration allows data centers to rebalance workloads across physical machines. However, migration actions may lead to performance impact during the migration process. Current virtualization techniques do not provide effective performance isolation between virtual machines (VMs). Specially, hidden contention for physical resources impacts performance differently in different virtual machines. As to the problem of selecting which virtual machines to be migrated, we consider migration cost. As to the problem of selecting which physical machine to be placed, we consider performance interference. Furthermore, we experimentally validate the effectiveness of response time-aware resource allocation in our framework using microbenchmarks.
Adolescent Parricide and Psychopathy

Most cases of juvenile parricide are believed to be the result of child abuse, yet the vast majority of abused children do not kill their parental abusers. This study explored the role of psychopathy in 10 adolescent parricide offenders tried in adult court who were referred for pretrial psychiatric evaluation. In addition, psychopathological findings, crime-related behaviors, and judicial outcomes are described. Diagnostic and Statistical Manual of Mental Disorders diagnoses, most commonly posttraumatic stress disorder, and chronic, severe child abuse were prevalent. Psychopathic traits were not found to have played a role in the traumatized youths’ parricidal behavior. Killings occurred in the family homes, usually through a surprise attack with parent-owned firearms. There was an average of 1.7 victims per event, with fathers being the most likely victim. Bodies were commonly covered or wrapped and moved postmortem. Confessions were often incredible in quality. One half received sentences of 40+ years, and the modal sanction was a life sentence, despite 90% premorbidly described as good youth. Further studies of adolescent parricide are needed to better understand this unusual population.
Robust greedy deep dictionary learning for ECG arrhythmia classification

This work proposes a new deep learning method which we call robust deep dictionary learning RDDL. RDDL is suitable for learning representations from signals corrupted with sparse but large outliers such as artifacts and noise that are more heavy tailed than Gaussian distributions. Such outliers are common in biomedical signals e.g. EEG and ECG. RDDL learns multiple levels of non-linear dictionaries for representing the data. Instead of the standard Euclidean cost function that is usually employed in dictionary learning, we propose a robust l1-norm cost function. In order to achieve sparse representation, an l1-norm is imposed on the learned representation. The ‘depth’ arises from the fact that multiple levels of dictionaries are learnt. The full formulation is solved in a greedy fashion, one layer at a time. To study the extent of usefulness of RDDL, we first benchmark it with two wellknown deep learning tools — the stacked denoising autoencoder and the deep belief network methods; experiments are carried out on benchmark deep learning datasets — MNIST, CIFAR-10 and SVHN. In all cases, our method yields the best results. Then the proposed method is used for learning representations of ECG data (containing arficacts) and for their classification using the MIT-BIH arrhythmia classification database. We compare it with traditional techniques as well as on deep learning tools. Our method yields the best results.
Invasion of novel habitats uncouples haplo‐diplontic life cycles

Baker's Law predicts uniparental reproduction will facilitate colonization success in novel habitats. While evidence supports this prediction among colonizing plants and animals, few studies have investigated shifts in reproductive mode in haplo‐diplontic species in which both prolonged haploid and diploid stages separate meiosis and fertilization in time and space. Due to this separation, asexual reproduction can yield the dominance of one of the ploidy stages in colonizing populations. We tested for shifts in ploidy and reproductive mode across native and introduced populations of the red seaweed Gracilaria vermiculophylla. Native populations in the northwest Pacific Ocean were nearly always attached by holdfasts to hard substrata and, as is characteristic of the genus, haploid–diploid ratios were slightly diploid‐biased. In contrast, along North American and European coastlines, introduced populations nearly always floated atop soft‐sediment mudflats and were overwhelmingly dominated by diploid thalli without holdfasts. Introduced populations exhibited population genetic signals consistent with extensive vegetative fragmentation, while native populations did not. Thus, the ecological shift from attached to unattached thalli, ostensibly necessitated by the invasion of soft‐sediment habitats, correlated with shifts from sexual to asexual reproduction and slight to strong diploid bias. We extend Baker's Law by predicting other colonizing haplo‐diplontic species will show similar increases in asexuality that correlate with the dominance of one ploidy stage. Labile mating systems likely facilitate colonization success and subsequent range expansion, but for haplo‐diplontic species, the long‐term eco‐evolutionary impacts will depend on which ploidy stage is lost and the degree to which asexual reproduction is canalized.
A Stateless and Light-Weight Bandwidth Management Mechanism for Elastic Traffic

Unbounded growth in the number of active flows can lead to severe service quality degradation to existing flows in a network . To guarantee minimum service quality for individual flows, specially for multimedia traffic, it is necessary to estimate and bound the number of active flows in the network. Prior work on estimating the number of active flows has been difficult without maintaining per-flow state. In this paper, we propose a light weight (not requiring per flow state) mechanism to estimate the number of active flows. This estimate is then used to determine the probability of admitting a new flow into the network with the goal of preventing extreme degradation of throughput to existing flows. The key idea here is that the number of active flows can be inferred from the frequency at which a newly arriving packet is part of the same flow as a randomly selected packet in the buffer. Since this scheme relies on information already available in the buffer, no per-flow state is maintained in the network. This mechanism requires very little per-packet processing, even less than a forwarding table lookup. Simulation results show that the proposed scheme can stabilize an overloaded network by bounding the number of active flows without significantly impairing link utilization. This scheme also gives good performance when buffer sizes are small and when the network has a mix of TCP and UDP traffic.
On a generalization of the Constantin–Lax–Majda equation

We present evidence on the global existence of solutions of De Gregorio's equation, based on numerical computation and a mathematical criterion analogous to the Beale–Kato–Majda theorem. Its meaning in the context of a generalized Constantin–Lax–Majda equation will be discussed. We then argue that a convection term, if set in a proper form and in a proper magnitude, can deplete solutions of blow-up.
Arabidopsis RhoGDIs Are Critical for Cellular Homeostasis of Pollen Tubes1[OPEN]

In planta GDIs for ROP GTPases support pollen germination and tube growth. Rhos of plants (ROPs) play a key role in plant cell morphogenesis, especially in tip-growing pollen tubes and root hairs, by regulating an array of intracellular activities such as dynamic polymerization of actin microfilaments. ROPs are regulated by guanine nucleotide exchange factors (RopGEFs), GTPase activating proteins (RopGAPs), and guanine nucleotide dissociation inhibitors (RhoGDIs). RopGEFs and RopGAPs play evolutionarily conserved function in ROP signaling. By contrast, although plant RhoGDIs regulate the membrane extraction and cytoplasmic sequestration of ROPs, less clear are their positive roles in ROP signaling as do their yeast and metazoan counterparts. We report here that functional loss of all three Arabidopsis (Arabidopsis thaliana) GDIs (tri-gdi) significantly reduced male transmission due to impaired pollen tube growth in vitro and in vivo. We demonstrate that ROPs were ectopically activated at the lateral plasma membrane of the tri-gdi pollen tubes. However, total ROPs were reduced posttranslationally in the tri-gdi mutant, resulting in overall dampened ROP signaling. Indeed, a ROP5 mutant that was unable to interact with GDIs failed to induce growth, indicating the importance of the ROP-GDI interaction for ROP signaling. Functional loss of GDIs impaired cellular homeostasis, resulting in excess apical accumulation of wall components in pollen tubes, similar to that resulting from ectopic phosphatidylinositol 4,5-bisphosphate signaling. GDIs and phosphatidylinositol 4,5-bisphosphate may antagonistically coordinate to maintain cellular homeostasis during pollen tube growth. Our results thus demonstrate a more complex role of GDIs in ROP-mediated pollen tube growth.