Miracle-dz/UniFAR-FTUs huggingface dataset:
Risk Factors for Recurrence of Immunoglobulin A Nephropathy After Renal Transplantation: Single Center Study

We investigated the risk factors for recurrence of IgA nephropathy after kidney transplantation. Of the 184 recipients of allografts for end‐stage renal disease caused by primary IgA nephropathy at our institution and affiliated hospitals between 1990 and 2005, 70 developed recurrent IgA nephropathy (group 1), while the remaining 114 did not develop recurrent IgA nephropathy (group 2). The diagnosis of recurrent IgA nephropathy was based on case and/or protocol renal biopsies. We examined the risk factors for recurrence of IgA nephropathy by comparing the two groups. In addition, we also investigated the risk factors for graft loss in the patients with recurrent IgA nephropathy. The recipient's age at transplantation was significantly younger in group 1 than in group 2 (33.4 ± 10.4 vs. 36.7 ± 10.7, P = 0.037). No significant influence of the immunosuppressive regimens used was observed on the likelihood of recurrence of IgA nephropathy. In the analysis of the risk factors for graft loss, the mean age of the donor was significantly higher in the patient group with graft loss (59.1 ± 9.5 vs. 53.9 ± 9.0, P = 0.033), and the serum creatinine level at one year after surgery was also significantly higher in the patient group with graft loss (1.62 ± 0.52 vs. 1.34 ± 0.34, P = 0.022). Recipients with recurrent IgA nephropathy after transplantation, especially younger patients, need to be followed up carefully.
Understanding Women’s Choice of Mastectomy Versus Breast Conserving Therapy in Early-Stage Breast Cancer

Objective: To identify factors that influence Saskatchewan women’s choice between breast conserving therapy (BCT) and mastectomy in early-stage breast cancer (ESBC) and to compare and contrast underlying reasons behind choice of BCT versus mastectomy. Methods: Interpretive description methods guided this practice-based qualitative study. Data were analyzed using thematic analysis and presented in thematic maps. Results: Women who chose mastectomy described 1 of the 3 main themes: worry about cancer recurrence, perceived consequences of BCT treatment, or breast-tumor size perception. In contrast, women chose BCT because of 3 different themes: mastectomy being too radical, surgeon influence, and feminine identity. Conclusions: Although individual reasons for choosing mastectomy versus BCT have been discussed in the literature before, different rationale underlying each choice has not been previously described. These results are novel in identifying interdependent subthemes and secondary reasons for each choice. This is important for increased understanding of factors influencing a complicated decision-making process.
Derived categories and Deligne-Lusztig varieties II

This paper is a continuation and a completion of [BoRo1]. We extend the Jordan decomposition of blocks: we show that blocks of finite groups of Lie type in non-describing characteristic are Morita equivalent to blocks of subgroups associated to isolated elements of the dual group. The key new result is the invariance of the part of the cohomology in a given modular series of Deligne-Lusztig varieties associated to a given Levi subgroup, under certain variations of parabolic subgroups. We also show that the equivalence arises from a splendid Rickard equivalence. Even in the setting of [BoRo1], the finer homotopy equivalence was unknown. As a consequence, the equivalence preserves defect groups and categories of subpairs. We finally determine when Deligne-Lusztig induced representations of tori generate the derived category of representations.
Statistical Learning of Domain-Specific Quality-of-Service Features from User Reviews

With the fast increase of online services of all kinds, users start to care more about the Quality of Service (QoS) that a service provider can offer besides the functionalities of the services. As a result, QoS-based service selection and recommendation have received significant attention since the mid-2000s. However, existing approaches primarily consider a small number of standard QoS parameters, most of which relate to the response time, fee, availability of services, and so on. As online services start to diversify significantly over different domains, these small set of QoS parameters will not be able to capture the different quality aspects that users truly care about over different domains. Most existing approaches for QoS data collection depend on the information from service providers, which are sensitive to the trustworthiness of the providers. Some service monitoring mechanisms collect QoS data through actual service invocations but may be affected by actual hardware/software configurations. In either case, domain-specific QoS data that capture what users truly care about have not been successfully collected or analyzed by existing works in service computing. To address this demanding issue, we develop a statistical learning approach to extract domain-specific QoS features from user-provided service reviews. In particular, we aim to classify user reviews based on their sentiment orientations into either a positive or negative category. Meanwhile, statistical feature selection is performed to identify statistically nontrivial terms from review text, which can serve as candidate QoS features. We also develop a topic models-based approach that automatically groups relevant terms and returns the term groups to users, where each term group corresponds to one high-level quality aspect of services. We have conducted extensive experiments on three real-world datasets to demonstrates the effectiveness of our approach.
Human Cytomegalovirus Carries a Cell-Derived Phospholipase A2 Required for Infectivity

ABSTRACT Human cytomegalovirus (HCMV) is known to carry host cell-derived proteins and mRNAs whose role in cell infection is not understood. We have identified a phospholipase A2 (PLA2) activity borne by HCMV by using an assay based on the hydrolysis of fluorescent phosphatidylcholine. This activity was found in all virus strains analyzed and in purified strains. It was calcium dependent and was sensitive to inhibitors of cytosolic PLA2 (cPLA2) but not to inhibitors of soluble PLA2 or calcium-independent PLA2. No other phospholipase activity was detected in the virus. Purified virus was found to contain human cellular cPLA2α, as detected by monoclonal antibody. No homology with PLA2 was found in the genome of HCMV, indicating that HCMV does not code for a PLA2. Decreased de novo expression of immediate-early proteins 1 and 2 (IE1 and IE2), tegument phosphoprotein pp65, and virus production was observed when HCMV was treated with inhibitors of cPLA2. Cell entry of HCMV was not altered by those inhibitors, suggesting the action of cPLA2 was postentry. Together, our results indicate a selective sorting of a cell-derived cPLA2 during HCMV maturation, which is further required for infectivity.
The galectin-3/RAGE dyad modulates vascular osteogenesis in atherosclerosis.

AIMS Vascular calcification correlates with inflammation and plaque instability in a dual manner, depending on the spotty/granular (micro) or sheet-like/lamellated (macro) pattern of calcification. Modified lipoproteins trigger both inflammation and calcification via receptors for advanced lipoxidation/glycation endproducts (ALEs/AGEs). This study compared the roles of galectin-3 and receptor for AGEs (RAGE), two ALEs/AGEs-receptors with diverging effects on inflammation and bone metabolism, in the process of vascular calcification. METHODS AND RESULTS We evaluated galectin-3 and RAGE expression/localization in 62 human carotid plaques and its relation to calcification pattern, plaque phenotype, and markers of inflammation and vascular osteogenesis; and the effect of galectin-3 ablation and/or exposure to an ALE/AGE on vascular smooth muscle cell (VSMC) osteogenic differentiation. While RAGE co-localized with inflammatory cells in unstable regions with microcalcification, galectin-3 was expressed also by VSMCs, especially in macrocalcified areas, where it co-localized with alkaline phosphatase. Expression of galectin-3 and osteogenic markers was higher in macrocalcified plaques, whereas the opposite occurred for RAGE and inflammatory markers. Galectin-3-deficient VSMCs exhibited defective osteogenic differentiation, as shown by altered expression of osteogenic transcription factors and proteins, blunted activation of pro-osteoblastogenic Wnt/β-catenin signalling and proliferation, enhanced apoptosis, and disorganized mineralization. These abnormalities were associated with RAGE up-regulation, but were only in part prevented by RAGE silencing, and were partially mimicked or exacerbated by treatment with an AGE/ALE. CONCLUSION These data indicate a novel molecular mechanism by which galectin-3 and RAGE modulate in divergent ways, not only inflammation, but also vascular osteogenesis, by modulating Wnt/β-catenin signalling, and independently of ALEs/AGEs.
Graphene nanoribbon FETs: Technology exploration and CAD

Graphene nanoribbon FETs (GNRFETs) have emerged as a promising candidate for nanoelectronics applications. This paper summarizes (i) current understanding and prospects for GNRFETs as ultimately scaled, ideal ballistic transistors, (ii) physics-based modeling of GNRFETs to support circuit design and CAD, and (iii) variability and defects in GNRs and their impact on GNRFET circuit performance and reliability.
ViCRAM: visual complexity rankings and accessibility metrics

The World Wide Web (Web) has become the means of distribution and use of information by individuals around the world. However, access to this information by visually impaired people is limited due to the Web's visual complexity. ViCRAM is a project that will relate user's implicit understanding of Web page visual complexity with its layout. Eye tracking methods and knowledge acquisition techniques will be used to elicit sighted people's visual perception. During this project we will also determine whether pages that sighted users identify as visually complex are complex for visually impaired users as well, from a Web accessibility perspective. We aim to develop a heuristic framework that will be used for describing Web page's visual complexity and as guidelines for transcoding a Web page into a less visually complex and more accessible one.
Rheological Control of Lateral Growth of the Tibetan Plateau: Numerical Results

The collision and continued convergence between the Indian and Eurasian plates in the past ~50 million years have raised the Tibetan Plateau, but whether or not, and how, the plateau has grown laterally remains controversial. Here we show that useful insights can be gained by studying lithospheric deformation across the front margins of the Tibetan Plateau. Crossing its northern and eastern sides where the plateau is bounded by the Tarim and Sichuan blocks, the topographic slope is steep and crustal deformation is localized near the margins of the plateau, whereas across northeastern Tibetan Plateau the topographic slope is gentle and crustal deformation is diffuse over a broad transition zone. Using a suite of two‐dimensional viscoplastic finite element models, we reproduced the major features of the two types of plateau margins with different rheological contrasts between the Tibetan Plateau and the bounding Asian blocks. Our results suggest that the bounding Asian blocks with a strong mantle lithosphere, such as the Tarim and the Sichuan Basins, have restricted the lateral growth of the Tibetan Plateau, although limited lateral expansion of the plateau can occur where the upper crust of these bounding blocks are relatively weak. Major lateral growth of the Tibetan Plateau mainly occurred northeastward, where numerous terranes with relatively weak mantle lithosphere are readily deformed and incorporated into the Tibetan Plateau. This growth front has reached the strong Alashan and Ordos blocks. Further lateral growth of the Tibetan Plateau depends on whether or not the Tibetan tectonics can weaken the mantle lithosphere of these Asian blocks.
Disruption of LRRK2 Does Not Cause Specific Loss of Dopaminergic Neurons in Zebrafish

Mutations in LRRK2 are genetically linked to Parkinson's disease (PD) but its normal biological function is largely unknown. Sheng et al. recently reported that deletion of the WD40 domain of LRRK2 in zebrafish specifically causes PD-like loss of neurons and behavior defect. However, our similar early study and recent confirming experiments using the same reagents reported by Sheng et al. failed to reproduce the phenotype of the loss of dopaminergic neurons, although the mRNA of LRRK2 was molecularly disrupted. Our study suggests that function of LRRK2 and its usefulness to generate zebrafish PD model needs further evaluation.
The Cspg2 gene, disrupted in the hdf mutant, is required for right cardiac chamber and endocardial cushion formation.

The heart defect (hdf) mouse is a recessive lethal that arose from a transgene insertional mutation on chromosome 13. Embryos homozygous for the transgene die in utero by embryonic day 10.5 postcoitus and exhibit specific defects along the anterior-posterior cardiac axis. The future right ventricle and conus/truncus of the single heart tube fail to form and the endocardial cushions in the atrioventricular and conus/truncus regions are absent. Because the hdf mouse mutation provided the opportunity to identify a gene required for endocardial cushion formation and for specification or maintenance of the anterior most segments of the heart, we initiated studies to further characterize the phenotype, clone the insertion site, and identify the gene disrupted. Chromosome mapping studies first identified the gene, Cspg2 (versican), as a candidate hdf gene. In addition, an antibody recognizing a glycosaminoglycan epitope on versican was found to be positive by immunohistochemistry in the extracellular matrix of normal wild-type embryonic hearts, but absent in homozygous hearts. Expression analysis of the Cspg2 gene showed that the 6/8, 6/9, and 7/9 Cspg2 exon boundaries were present in mRNA of normal wild-type embryonic hearts but absent in the homozygous mutant embryos. DNA sequence flanking the transgene was used to isolate from a normal mouse library overlapping genomic DNA segments that span the transgene insertion site. The contiguous genomic DNA segment was found to contain exon 7 of the Cspg2 in a position 3' to the transgene insertion site. These four separate lines of evidence support the hypothesis that Cspg2 is the gene disrupted by the transgene insertion in the hdf mouse line. The findings of this study and our previous studies of the hdf insertional mutant mouse have shown that normal expression of the Cspg2 gene is required for the successful development of the endocardial cushion swellings and the embryonic heart segments that give rise to the right ventricle and conus/truncus in the outlet of the looped heart.
Smoking and lung cancer risk in Sri Lankan men: a case-control study

Objectives Tobacco smoking is the strongest risk factor for lung cancer. As the strength of association of smoking and lung cancer in Sri Lanka has not been estimated, a study was conducted to estimate the risk of lung cancer among adult male smokers in the Colombo District. Methods A case control study was carried out among 62 newly diagnosed male lung cancer patients from the Colombo District presenting to National Cancer Institute, Maharagama. Four controls per case were randomly selected from the same Grama Niladhari area matching the age of the cases within 10 years. Absence of lung cancer was clinically confirmed in the controls. Information on smoking, other potential risk factors and confounders were obtained using an interviewer-administered questionnaire. Univariate analysis and logistic regression identified the risk factors. Results After adjustment for confounding variables, ever smokers odds of having lung cancer compared to never smokers OR 10.74 (95% CI 3.54-32.59) . Lower educ ation level (OR=5.61, 95% CI 2.37-13.28), ever exposed to X-rays (OR=2.81, 95% CI 1.14-6.94) and a family history of any cancer (OR=2.83, 95% CI 1.09-7.30) were other significant risk factors. The population attributable risk percent (PAR%) showed that 84.04% of the male lung cancer cases are attributed to smoking. Conclusions Smoking and exposure to X-rays were risk factor for lung cancer among adult males in the Colombo District.
Improving the performance of TCP in structure-less networks with virtual infrastructures

In structure-less (ad-hoc) networks, applying the retransmission rules of a reliable transmission protocol (e.g., TCP) without having a structured rerouting scheme is erroneous. We propose a versatile, virtual infrastructure to stabilize a rerouting scheme where, in essence, the scheme tries to slow down the dynamics of the network from the TTR (time-to-transmit) parameter point of view. Therefore, there is less deviation from the primary settings (set before the start of the session), and, during the session, less updating is required. The proposed virtual infrastructure with the same overhead (initialization and maintenance) enhances the routing protocol and TCP performance. We consider a joint routing and TCP design which is based on a virtual infrastructure. We discuss the necessary modifications on the sender's TCP to turn it to a structure-aware protocol to distinguish physical layer initiated problems from those related to routing. As a result, TCP performs fewer mistakes in recognizing problems within a predefined range of acceptance; meanwhile, less updating is required for TTR.
Dynamic Factor Models with Smooth Loadings for Analyzing the Term Structure of Interest Rates

This discussion paper led to a publication in the 'Journal of Applied Econometrics' , 2014, 29(1), 65-90. We propose a new approach to the modelling of the term structure of interest rates. We consider the general dynamic factor model and show how to impose smoothness restrictions on the factor loadings. We further present a statistical procedure based on Wald tests that can be used to find a suitable set of such restrictions. We present these developments in the context of term structure models, but they are also applicable in other settings. We perform an empirical study using a data set of unsmoothed Fama-Bliss zero yields for US treasuries of different maturities. The general dynamic factor model with and without smooth loadings is considered in this study together with models that are associated with Nelson-Siegel and arbitrage-free frameworks. These existing models can be regarded as special cases of the dynamic factor model with restrictions on the model parameters. For all model candidates, we consider both stationary and nonstationary autoregressive processes (with different numbers of lags) for the latent factors. Finally, we perform statistical hypothesis tests to verify whether the restrictions imposed by the models are supported by the data. Our main conclusion is that smoothness restrictions can be imposed on the loadings of dynamic factor models for the term structure of US interest rates but that the restrictions implied by a number of popular term structure models are rejected.
Application of Neural Networks for the retrieval of forest woody volume from SAR multifrequency data at L and C bands

Abstract This work aims at investigating the potential of L (ALOS/PALSAR) and C (ENVISAT/ASAR) band SAR images in forest biomass monitoring and setting up a retrieval algorithm, based on Artificial Neural Networks (ANN), for estimating the Woody Volume (WV, in m3/ha) from combined satellite acquisitions. The investigation was carried out on two test areas in central Italy, where ground WV measurements were available. An innovative retrieval algorithm based on ANN was developed for estimating WV from L and C bands SAR data. The novelty consists of an accurate training of the ANN with several thousands of data, which allowed the implementation of a very robust algorithm. The RMSE values found on San Rossore area were ≅ 40 m3/ha (L band data only), and 25–30 m3/ha (L with C band). On Molise, by using combined data at L and C bands, RMSE<30m3/ha was obtained.
A Statistical Study of Spatial Variation of Relativistic Electron Precipitation Energy Spectra With Polar Operational Environmental Satellites

The mechanisms that drive relativistic electron precipitation (REP) from the radiation belts can be better understood with a better knowledge of the particle energies involved. National Oceanic and Atmospheric Administration Polar Operational Environmental Satellites, being a network of multiple satellites, can provide multiple point spectral data over a long time period, including the Van Allen Probe's era. The number of energy channels is limited, but the particle detectors on Polar Operational Environmental Satellites have a narrow field of view allowing an investigation of bounce loss cone particles. We use the ratio of count rates in the E3 (>300 keV) and the P6 (>700 keV) channels as a parameter to define spectral hardness. Using this parameter, the spatial variation of spectral hardness of REP events was investigated. It was found that very soft events were mostly found in the dusk‐midnight‐early morning magnetic local time sectors and L∼ 5–7 while the hardest events were located in the postnoon sector peaking at L∼ 4–5. The hardest events peaked at lower L shells, and less than 20% were coincident with low‐energy (30–80 keV) proton precipitation. Further, around 70% of nightside REP coincident with proton precipitation was associated with stretched magnetic field lines indicating that curvature scattering may have been an important driver. Around 62% of nightside REP coincident with proton precipitation associated with relaxed magnetic field lines, suggesting a mechanism other than magnetic field curvature scattering, was highly energetic.
Somatic instability of the expanded GAA repeats in Friedreich’s ataxia

Friedreich’s ataxia (FRDA) is a genetic neurodegenerative disorder caused by transcriptional silencing of the frataxin gene (FXN) due to expansions of GAA repeats in intron 1. FRDA manifests with multiple symptoms, which may include ataxia, cardiomyopathy and diabetes mellitus. Expanded GAA tracts are genetically unstable, exhibiting both expansions and contractions. GAA length correlates with severity of FRDA symptoms and inversely with age of onset. Thus, tissue-specific somatic instability of long GAA repeats may be implicated in the development of symptoms and disease progression. Herein, we determined the extent of somatic instability of the GAA repeats in heart, cerebral cortex, spinal cord, cerebellar cortex, and pancreatic tissues from 15 FRDA patients. Results demonstrate differences in the lengths of the expanded GAAs among different tissues, with significantly longer GAA tracts detected in heart and pancreas than in other tissues. The expansion bias detected in heart and pancreas may contribute to disease onset and progression, making the mechanism of somatic instability an important target for therapy. Additionally, we detected significant differences in GAA tract lengths between lymphocytes and fibroblast pairs derived from 16 FRDA patients, with longer GAA tracts present in the lymphocytes. This result urges caution in direct comparisons of data obtained in these frequently used FRDA models. Furthermore, we conducted a longitudinal analysis of the GAA repeat length in lymphocytes collected over a span of 7–9 years and demonstrated progressive expansions of the GAAs with maximum gain of approximately 9 repeats per year. Continuous GAA expansions throughout the patient’s lifespan, as observed in FRDA lymphocytes, should be considered in clinical trial designs and data interpretation.