Miracle-dz/UniFAR-FTUs huggingface dataset:
The prognostic significance of CD11b+CX3CR1+ monocytes in patients with newly diagnosed diffuse large B-cell lymphoma

Despite their critical roles in angiogenesis and host immunosuppression within the tumor microenvironment, the prognostic significance of myeloid-lineage cells expressing CD11b and CX3CR1 in diffuse large B-cell lymphoma (DLBCL) has not been well studied. We prospectively enrolled newly-diagnosed DLBCL patients at two Korean institutions between May 2011 and Aug 2015. CD11b+CX3CR1+ cells were analyzed by flow cytometry using peripheral blood (PB) and bone marrow (BM) aspirate samples before treatments. Eighty-nine patients (52 males) were enrolled. The median age was 65 years (range, 19–88 years). Thirty-seven patients (42%) were classified as high-intermediate or high risk according to the National Comprehensive Cancer Network International Prognostic Index (NCCN-IPI). Patients were categorized into either high or low PB-/BM-CD11b+CX3CR1+ monocyte group according to the cutoffs identified by the receiver-operating-characteristics analysis (PB, 3.68%; BM, 3.45%). The high PB-CD11b+CX3CR1+ monocyte group was significantly associated with high-intermediate and high risk NCCN-IPI group (P = 0.004). With a median follow-up of 27.7 months (range, 1.7-60.4 months), the low PB-CD11b+CX3CR1+ monocyte group showed significantly better overall survival (OS) than the high PB-CD11b+CX3CR1+ monocyte group (3-year, 92.3% vs. 51.2%, respectively; P < 0.001). In contrast, no significant difference was observed between the high and low BM-CD11b+CX3CR1+ monocyte groups. Among patients with high-intermediate to high risk NCCN-IPI, the high PB-CD11b+CX3CR1+ monocyte group showed significantly worse OS than the low PB-CD11b+CX3CR1+ monocyte group (3-year, 29.3% vs. 80.2%, respectively; P = 0.008). Taken together, PB-CD11b+CX3CR1+ monocyte percentage correlates with the NCCN-IPI risk stratification, which enables identification of subgroups with extremely poor clinical outcomes.
Minimizing communication in rate-optimal software pipelining for stream programs

Stream programming model has been productively applied to a number of important applications domains. Software pipelining is an important code scheduling technique for stream programs. However, the multi-/many-core evolution has presented a new dimension of challenges: that is while searching a best software pipelining schedule how to ensure the communications between processing cores are also minimized? In this paper, we proposed a new solution methodology to address the above problem. Our main contributions include the following. A unified formulation has been proposed that combines the requirement of both rate-optimal software pipelining and the minimization of inter-core communication overhead. This formulation has been developed based on a synchronized dataflow graph model, and is expressed as an integer linear programming problem. A solution testbed has been implemented for the proposed problem formulation on the IBM Cell architecture. This has been realized by extending the Brook stream programming environment with our software pipelining support -- named DFBrook. An experimental study has been conducted to verify the effectiveness of the proposed solution. And a comparison of other scheduling methods has demon-strated the performance superiority of our proposed method.
Torsional resonance mode magnetic force microscopy: enabling higher lateral resolution magnetic imaging without topography-related effects

We present experimental work that reveals the benefits of performing magnetic force microscopy measurements employing the torsional resonance mode of cantilever oscillation. This approach provides two clear advantages: the ability of performing magnetic imaging without topography-related interference and the significant lateral resolution improvement (approximately 15%). We believe that this work demonstrates a significant improvement to a versatile magnetic imaging technique widely used in academia and in industry.
OsJAZ1 Attenuates Drought Resistance by Regulating JA and ABA Signaling in Rice

Jasmonates (JAs) and abscisic acid (ABA) are phytohormones known play important roles in plant response and adaptation to various abiotic stresses including salinity, drought, wounding, and cold. JAZ (JASMONATE ZIM-domain) proteins have been reported to play negative roles in JA signaling. However, direct evidence is still lacking that JAZ proteins regulate drought resistance. In this study, OsJAZ1 was investigated for its role in drought resistance in rice. Expression of OsJAZ1 was strongly responsive to JA treatment, and it was slightly responsive to ABA, salicylic acid, and abiotic stresses including drought, salinity, and cold. The OsJAZ1-overexpression rice plants were more sensitive to drought stress treatment than the wild-type (WT) rice Zhonghua 11 (ZH11) at both the seedling and reproductive stages, while the jaz1 T-DNA insertion mutant plants showed increased drought tolerance compared to the WT plants. The OsJAZ1-overexpression plants were hyposensitive to MeJA and ABA, whereas the jaz1 mutant plants were hypersensitive to MeJA and ABA. In addition, there were significant differences in shoot and root length between the OsJAZ1 transgenic and WT plants under the MeJA and ABA treatments. A subcellular localization assay indicated that OsJAZ1 was localized in both the nucleus and cytoplasm. Transcriptome profiling analysis by RNA-seq revealed that the expression levels of many genes in the ABA and JA signaling pathways exhibited significant differences between the OsJAZ1-overexpression plants and WT ZH11 under drought stress treatment. Quantitative real-time PCR confirmed the expression profiles of some of the differentially expressed genes, including OsNCED4, OsLEA3, RAB21, OsbHLH006, OsbHLH148, OsDREB1A, OsDREB1B, SNAC1, and OsCCD1. These results together suggest that OsJAZ1 plays a role in regulating the drought resistance of rice partially via the ABA and JA pathways.
Configuration Management for Large-Scale Scientific Computing at the UK Met Office

The UK Met Office's flexible configuration management (FCM) system uses existing open source tools, adapted for use with high-performance scientific Fortran code, to help manage evolving code in its large-scale climate simulation and weather forecasting models. FCM has simplified the development process, improved team coordination, and reduced release cycles.
Sealing effectiveness of fissure sealants bonded with universal adhesive systems: influence of different etching modes

Abstract This study compared the sealing effectiveness of fissure sealants bonded to enamel with universal adhesive systems applied in self-etch (SE) or etch-and-rinse (ER) modes. Extracted human molars (n = 216), were randomly assigned into nine groups with respect to etching mode, adhesive system, and the sealant material used (Clinpro/3 M or Giomer-Based BeautiSealant/Shofu): (1) ER + Clinpro (Control); (2) SE/Single Bond Universal (SBU) + ClinPro; (3) ER + SBU + Clinpro; (4) SE/All Bond Universal (ABU) + Clinpro; (5) ER + ABU + Clinpro; (6) SE/Clearfil Universal Bond (CUB) + Clinpro; (7) ER + CUB + Clinpro; (8) SE + BeautiSealant Primer + BeautiSealant; (9) ER/BeautiSealant Primer + BeautiSealant. Following thermocycling (1000X) and storage in 0.5% basic fuchsin, microleakage was evaluated quantitatively on tooth sections using imageJ analysis toolkit, and the data were analyzed statistically. The ER Mode significantly reduced the microleakage of universal adhesives. The following statistical ranking was observed with regard to the sealing effectiveness: ER + SBU + Clinpro = ER + ABU + Clinpro = SE/SBU + Clinpro = ER + CUB + Clinpro > SE/ABU + Clinpro = SE/CUB + Clinpro > ER + BeautiSealant Primer + BeautiSealant = ER + Clinpro (Control) = SE/BeautiSealant Primer + BeautiSealant. While the tested universal adhesives showed less microleakage on pre-etched enamel, the sealing effectiveness of SBU under SE mode was similar to all universal adhesives under ER mode. In both ER and SE modes, the sealing effectiveness of the giomer-based sealant was comparable to the control group.
Linkage analysis in the presence of errors III: marker loci and their map as nuisance parameters.

In linkage and linkage disequilibrium (LD) analysis of complex multifactorial phenotypes, various types of errors can greatly reduce the chance of successful gene localization. The power of such studies-even in the absence of errors-is quite low, and, accordingly, their robustness to errors can be poor, especially in multipoint analysis. For this reason, it is important to deal with the ramifications of errors up front, as part of the analytical strategy. In this study, errors in the characterization of marker-locus parameters-including allele frequencies, haplotype frequencies (i.e., LD between marker loci), recombination fractions, and locus order-are dealt with through the use of profile likelihoods maximized over such nuisance parameters. It is shown that the common practice of assuming fixed, erroneous values for such parameters can reduce the power and/or increase the probability of obtaining false positive results in a study. The effects of errors in assumed parameter values are generally more severe when a larger number of less informative marker loci, like the highly-touted single nucleotide polymorphisms (SNPs), are analyzed jointly than when fewer but more informative marker loci, such as microsatellites, are used. Rather than fixing inaccurate values for these parameters a priori, we propose to treat them as nuisance parameters through the use of profile likelihoods. It is demonstrated that the power of linkage and/or LD analysis can be increased through application of this technique in situations where parameter values cannot be specified with a high degree of certainty.
A Survey on Optical Interconnects for Data Centers

Data centers are experiencing an exponential increase in the amount of network traffic that they have to sustain due to cloud computing and several emerging web applications. To face this network load, large data centers are required with thousands of servers interconnected with high bandwidth switches. Current data center networks, based on electronic packet switches, consume excessive power to handle the increased communication bandwidth of emerging applications. Optical interconnects have gained attention recently as a promising solution offering high throughput, low latency and reduced energy consumption compared to current networks based on commodity switches. This paper presents a thorough survey on optical interconnects for next generation data center networks. Furthermore, the paper provides a qualitative categorization and comparison of the proposed schemes based on their main features such as connectivity and scalability. Finally, the paper discusses the cost and the power consumption of these schemes that are of primary importance in the future data center networks.
Temperature Alters Host Genotype-Specific Susceptibility to Chytrid Infection

The cost of parasitism often depends on environmental conditions and host identity. Therefore, variation in the biotic and abiotic environment can have repercussions on both, species-level host-parasite interaction patterns but also on host genotype-specific susceptibility to disease. We exposed seven genetically different but concurrent strains of the diatom Asterionella formosa to one genotype of its naturally co-occurring chytrid parasite Zygorhizidium planktonicum across five environmentally relevant temperatures. We found that the thermal tolerance range of the tested parasite genotype was narrower than that of its host, providing the host with a “cold” and “hot” thermal refuge of very low or no infection. Susceptibility to disease was host genotype-specific and varied with temperature level so that no genotype was most or least resistant across all temperatures. This suggests a role of thermal variation in the maintenance of diversity in disease related traits in this phytoplankton host. The duration and intensity of chytrid parasite pressure on host populations is likely to be affected by the projected changes in temperature patterns due to climate warming both through altering temperature dependent disease susceptibility of the host and, potentially, through en- or disabling thermal host refugia. This, in turn may affect the selective strength of the parasite on the genetic architecture of the host population.
Vision-motion planning with uncertainty

The authors describe a framework for planning of vision and motion for a mobile robot. For planning in a real world, the uncertainty and the cost of visual recognition are important issues. A robot has to consider a tradeoff between the cost of visual recognition and the effect of information obtained by recognition. A problem is to generate a sequence of vision and motion operations based on sensor information which is an integration of the current information and the predicted next sensor data. The problem is solved by recursive prediction of sensor information and the recursive search of operations. As an example of sensor modeling, a model of stereo vision is described in which correspondence of wrong pairs of features as well as quantization error are considered. Using the framework, a robot can successfully generate a plan for real-world problem. <<ETX>>
Structure of Cell Wall and Extracellular Mannans from Saccharomyces rouxii and Their Relationship to a High Concentration of NaCl in the Growth Medium

Cells of Saccharomyces rouxii (a salt-tolerant yeast) were grown in the presence of two levels of NaCl, 0 and 15%. Mannans obtained from both the cell walls and culture filtrates (extracellular) were examined. Yields based on the dry weight of cells demonstrated that the levels of both cell wall and extracellular mannans were lower when cells were grown in the presence of 15% NaCl. However, the carbohydrate and protein contents of the mannan preparations were not altered. The cell wall mannans obtained from the two growth conditions had similar molecular weights, whereas the extracellular mannans had different molecular weight distributions. Structural analyses showed that the cell wall and extracellular mannans had similar structures. Both had an α1-6-linked backbone to which single mannose and mannobiose units were connected as side chains, predominantly by α1-2 linkages. The mannans also contained mannosyloligosaccharides, mannotriose, mannobiose, and mannose attached to protein through an O-glycosidic bond. The molecular structure of the cell wall mannans remained unchanged at both levels of NaCl. However, in the presence of 15% NaCl, the side chains consisting of a mannobiose unit were slightly reduced.
Resistance of Ribosomal Protein mRNA Translation to Protein Synthesis Shutoff Induced by Poliovirus

ABSTRACT Poliovirus infection induces an overall inhibition of host protein synthesis, although some mRNAs continue to be translated, suggesting different translation requirements for cellular mRNAs. It is known that ribosomal protein mRNAs are translationally regulated and that the phosphorylation of ribosomal protein S6 is involved in the regulation. Here, we report that the translation of ribosomal protein mRNAs resists poliovirus infection and correlates with an increase in p70s6k activity and phosphorylation of ribosomal protein S6.
Calibration of focal length and 3D pose based on the reflectance and depth image of a planar object

The estimation of position and orientation of a Photonic Mixer Device (PMD) camera in a global reference frame is required by many measurement applications based on such systems. PMD cameras produce a depth as well as a reflectance image of low resolution compared to standard optical cameras, so that calibration of the cameras based on the reflectance image alone is difficult. We will present a novel approach for calibrating the focal length and 3D pose of a PMD camera based on the depth and reflectance image of a planar checkerboard pattern. By integrating both sources of information higher accuracies can be achieved. Furthermore, one single image is sufficient for calibrating the focal length as well as the 3D pose from a planar reference object. This is because the depth measurements are orthogonal to the lateral intensity measurements and provide direct metric information.
Detection and Characterisation of the Optic Disk in Glaucoma and Diabetic Retinopathy

The optic nerve head is that region of the retina where nerve fibres and blood vessels pass through the sclera. It is sensitive to changes associated with glaucoma that can occur without other symptoms. Diabetes can also be the cause of changes in the appearance of the retina. The changes from the normal appearance can be diagnostic of the diseases, tracking of the changes in sequential images can be used to assess treatment or the progress of the illness. We are concerned with developing automated techniques of generating quantitative descriptions of the retina that might be used in diagnosis and treatment. Normal and abnormal images were collected from a range of sources, to simulate the mass screening process. Although full colour images were collected, only the green channel was processed as it had the greatest contrast. Blood vessels were removed using morphological techniques. The boundary of the optic disk was estimated using a simple edge detector and the circular Hough transform. Heuristic methods were defined to identify true and false positives. Although we do not expect the optic disk to be circular, this technique identifies it with sufficient accuracy to identify its approximate centre, which is used as the origin of 24 uniformly distributed radial vectors. The images were resampled along these vectors. The resulting image was filtered using the Lee filter and thresholded. In one or other of these images, normal subjects had a region of maximum grey value that extended the full width of the image (at the centre of the optic disk) but did not extend the full height. Using a chi-squared test, the separation of normal and abnormal images using this test was found to be highly significant (p < 0.05, n = 60).
DNA Theory Complexity

Most existing theory re nement systems are not incremental. However, any theory re nement system whose input and output theories are compatible can be used to incrementally assimilate data into an evolving theory. This is done by continually feeding its revised theory back in as its input theory. An incremental batch approach, in which the system assimilates a batch of examples at each step, seems most appropriate for existing theory revision systems. Experimental results with the Either theory re nement system demonstrate that this approach frequently increases e ciency without signi cantly decreasing the accuracy or the simplicity of the resulting theory. However, if the system produces bad initial changes to the theory based on only small amount of data, these bad revisions can \snowball" and result in an overall decrease in performance.
Towards Effective Intra-Flow Network Coding in Software Defined Wireless Mesh Networks

Wireless Mesh Networks (WMNs) have potential to provide convenient broadband wireless Internet access to mobile users. With the emergence of Software-Defined Networking (SDN) paradigm that separates control plane and data plane, WMNs can be easily deployed and managed. In addition, by exploiting the broadcast nature of the wireless medium and the spatial diversity of multi-hop wireless networks, intra-flow network coding has shown a greater benefit in comparison with traditional routing paradigms in data transmission for WMNs. In this paper, we develop a novel OpenCoding protocol, which combines the SDN technique with intra-flow network coding for WMNs. Our developed protocol can simplify the deployment and management of the network and improve network performance. In OpenCoding, a controller working on the control plane makes routing decisions for mesh routers and the hop-by-hop forwarding function is replaced by network coding functions in data plane. Through a simulation study, we show the effectiveness of the OpenCoding protocol in comparison with existing schemes. Our data shows that OpenCoding outperforms both traditional routing and intra-flow network coding schemes.
Controlling for population structure and genotyping platform bias in the eMERGE multi-institutional biobank linked to electronic health records

Combining samples across multiple cohorts in large-scale scientific research programs is often required to achieve the necessary power for genome-wide association studies. Controlling for genomic ancestry through principal component analysis (PCA) to address the effect of population stratification is a common practice. In addition to local genomic variation, such as copy number variation and inversions, other factors directly related to combining multiple studies, such as platform and site recruitment bias, can drive the correlation patterns in PCA. In this report, we describe the combination and analysis of multi-ethnic cohort with biobanks linked to electronic health records for large-scale genomic association discovery analyses. First, we outline the observed site and platform bias, in addition to ancestry differences. Second, we outline a general protocol for selecting variants for input into the subject variance-covariance matrix, the conventional PCA approach. Finally, we introduce an alternative approach to PCA by deriving components from subject loadings calculated from a reference sample. This alternative approach of generating principal components controlled for site and platform bias, in addition to ancestry differences, has the advantage of fewer covariates and degrees of freedom.
Replicating 3D printed structures into hydrogels

Fabricating complicated three-dimensional (3D) hydrogel structures are important in biological studies. Herein, stereolithographic printed acrylate-based masters with different complicated 3D geometry (e.g. dodecahedron and a trifurcating network) were replicated into alginate and gelatin. Alginate was further used as a sacrificial template to fabricate a perfusable microfluidic network in cell-seeded agarose to sustain the cell viability in a large slab of agarose scaffold. With the replication approach, 3D alginate (a photo-insensitive material) constructs with stereolithographic (a photolithographic technology) grade resolution and structural complexity were fabricated.
Referral practices and perceived barriers to timely obstetric care among Ugandan traditional birth attendants (TBA).

OBJECTIVES To assess current beliefs, knowledge and practices of Ugandan traditional birth attendants (TBAs) and their pregnant patients regarding referral of obstructed labors and fistula cases. METHODS Six focus groups were held in rural areas surrounding Kampala, the capital city of Uganda. RESULTS While TBAs, particularly those with previous training, appear willing to refer problematic pregnancies and labors, more serious problems exist that could lessen any positive effects of training. These problems include reported abuse by doctors and nurses, and seeing fistula as a disease caused by hospitals. CONCLUSIONS Training of TBAs can be helpful to standardize knowledge about and encourage timely emergency obstetric referrals, as well as increase knowledge about the causes and preventions of obstetric fistula. However, for full efficacy, training must be accompanied by greater collaboration between biomedical and traditional health personnel, and increased infrastructure to prevent mistreatment of pregnant patients by medical staff.