Miracle-dz/UniFAR-FTUs huggingface dataset:
Survival of childhood polycystic kidney disease following renal transplantation: The impact of advanced hepatobiliary disease

Abstract: Childhood PKD encompasses the diagnoses of AR and ADPKD, glomerulocystic disease, and syndromes such as tuberous sclerosis or Jeune's syndrome. Given the fact that a majority of PKD children with ESRD carry the diagnosis of ARPKD, natural history studies assessing the long‐term prognosis of PKD patients following renal transplantation must focus on morbidity and mortality issues related to complications from congenital hepatic fibrosis. Using the NAPRTCS registry, we analyzed the patient and graft survival rates of 203 PKD patients and 7044 non‐PKD patients undergoing renal transplantation between 1987 and 2001. Deceased PKD patients, all with a diagnosis of ARPKD, were further identified and characterized using a special questionnaire submitted to the principal investigators. Overall graft and patient survival rates were not significantly different between PKD and non‐PKD patients. No differences in rates of acute rejection or time to first rejection were noted between PKD and non‐PKD patients. The relative risk of living longer than 3 yr in the PKD patients was not significantly different from non‐PKD patients (RR = 0.70, p = 0.28). Sepsis was identified as a likely factor in the cause of death in nine (64%) ARPKD patients and was comfirmed with a positive blood culture in four patients. Despite similar graft and patient survival rates among PKD and non‐PKD children following renal transplantation, our results suggest that ARPKD transplant recipients appear to be at increased risk for sepsis that may be related to hepatic fibrosis and ascending cholangitis. The utility of early liver transplantation in ARPKD patients with significant hepatobiliary disease is discussed.
Signal Joint T-Cell Receptor Excision Circle Assay in Miniature Swine

Objective: Assays for T cell receptor excision circles (TREC) have been utilized in human, primate, and mouse models as a measure of thymic activity, but no comparable assay has been described in artiodactyls. We describe the development of the porcine signal joint (sj) TREC assay, and provide a likely reason for previous difficulties in its identification in artiodactyls. Design and Methods: Utilizing the homology between the known genomic sequences in sjTREC in human and mouse, polymerase chain reaction (PCR) primers were derived for the putative porcine sjTREC. Primers from the &psgr;J&agr; side of the sjTREC were derived from the known porcine sequence. Results: The sjTREC in two artiodactyls, swine and sheep, was identified using forward primers from the &psgr;J&agr; region, and reverse primers from the putative &dgr;-rec region. Unlike in the detection of primate TRECs, initially the use of similar primers close to the &dgr;-rec failed to yield the sjTREC product. Marching about 800 basepairs into &dgr;-rec, primers derived from a homology region between human and mouse led to the detection of sjTREC. Comparing sjTREC amongst the species revealed highest homology between the two artiodactyls. A quantitative PCR (QPCR) assay of porcine sjTREC was also developed. Conclusion: Identification and analysis of the sjTREC sequences in two artiodactyls suggested why previous attempts at cloning the pig TREC using known sjTREC sequences were unsuccessful. The development of the porcine signal joint TREC assay should enable a more direct quantification of thymic activity in porcine models of transplant biology.
Quadratic Estimation of Success Probability of Greedy Geographic Forwarding in Unmanned Aeronautical Ad-Hoc Networks

Due to the availability of location information in unmanned aerial vehicles (UAVs), we propose to use geographic routing mechanisms as a core forwarding protocol in unmanned aeronautical ad-hoc networks (UAANETs) for the purpose of reducing routing overhead. As a result, this paper investigates the performance of the core forwarding mechanism i.e. the greedy geographic part. Since the forwarding mechanism for dynamic UAANETs with many statistical inter-dependencies is complex, a closed-form model does not exist. Therefore, a quadratic polynomial estimation is proposed for computing the success probability of greedy geographic forwarding based on the results of a set of realistic Monte Carlo simulations. This mathematical model can later be used to predict and evaluate the performance of other greedy-based geographic routing protocols for UAV applications.
Real-Time Energy Storage Management With Renewable Integration: Finite-Time Horizon Approach

We consider the design of cost-effective management of energy storage with renewable integration for load supply. We take a finite time horizon approach and formulate the control optimization problem aimed at minimizing the system cost over a fixed time period. Recognizing the unpredictable and nonstationary stochastic nature of system dynamics, we assume unknown arbitrary dynamics of renewable generation, load, and electricity pricing in formulating our problem. Furthermore, we incorporate detailed battery operation cost into the system cost. Different from the infinite time horizon problems in existing works, the coupling of control decisions over time, due to finite battery capacity, is more challenging to manage. We develop a special technique to tackle the technical challenges in solving the problem. Through problem modification and transformation, we are able to apply Lyapunov optimization to design a real-time control algorithm that relies only on the current system dynamics. The proposed control solution has a closed-form expression and thus is simple to implement. Through analysis, the proposed algorithm is shown to have a bounded performance gap to the optimal noncausal T-slot lookahead control policy. Simulation studies show the effectiveness of our proposed algorithm as compared with two alternative real-time and noncausal algorithms.
Modelling the effects of gravity waves on stratocumulus clouds observed during VOCALS-UK

Abstract. During the VOCALS campaign spaceborne satellite observations showed that travelling gravity wave packets, generated by geostrophic adjustment, resulted in perturbations to marine boundary layer (MBL) clouds over the south-east Pacific Ocean (SEP). Often, these perturbations were reversible in that passage of the wave resulted in the clouds becoming brighter (in the wave crest), then darker (in the wave trough) and subsequently recovering their properties after the passage of the wave. However, occasionally the wave packets triggered irreversible changes to the clouds, which transformed from closed mesoscale cellular convection to open form. In this paper we use large eddy simulation (LES) to examine the physical mechanisms that cause this transition. Specifically, we examine whether the clearing of the cloud is due to (i) the wave causing additional cloud-top entrainment of warm, dry air or (ii) whether the additional condensation of liquid water onto the existing drops and the subsequent formation of drizzle are the important mechanisms. We find that, although the wave does cause additional drizzle formation, this is not the reason for the persistent clearing of the cloud; rather it is the additional entrainment of warm, dry air into the cloud followed by a reduction in longwave cooling, although this only has a significant effect when the cloud is starting to decouple from the boundary layer. The result in this case is a change from a stratocumulus to a more patchy cloud regime. For the simulations presented here, cloud condensation nuclei (CCN) scavenging did not play an important role in the clearing of the cloud. The results have implications for understanding transitions between the different cellular regimes in marine boundary layer (MBL) clouds.
Common time variation of parameters in reduced-form macroeconomic models

Abstract Standard time varying parameter (TVP) models usually assume independent stochastic processes. In this paper, I show that the number of underlying sources of parameters’ time variation is likely to be small, and provide empirical evidence for factor structure amongst TVPs of popular macroeconomic models. In order to test for the presence of low dimension sources of time variation in parameters and estimate their magnitudes, I develop the factor time varying parameter (Factor-TVP) framework and apply it to [Primiceri, G.E. (2005), “Time Varying Structural Vector Autoregressions and Monetary Policy,” The Review of Economic Studies, 72, 821–852] monetary TVP-VAR model. I find that one factor explains most of the variability in VAR coefficients, while the stochastic volatility parameters vary independently. The inclusion of post-“Great Recession” data causes an important change within VAR coefficients and the procedure suggests two factors. The roots of variability in the VAR parameters are likely to have derived from the financial markets and the real sector. The TVP factors have predictive power for a large number of output, investment, and employment series, as well as for the term structure of interest rates.
Following the heart: temperature and salinity effects on heart rate in native and invasive species of blue mussels (genus Mytilus)

SUMMARY The three species of blue mussels, Mytilus trossulus Gould 1850, M. edulis Linnaeus 1758 and M. galloprovincialis Lamarck 1819, have distinct global distribution patterns that are hypothesized to reflect differences in their tolerances of temperature and salinity. We examined effects on heart rate (beats min–1) of acute exposure and acclimation to different combinations of temperature and salinity to test this hypothesis and, in the context of the invasive success of M. galloprovincialis, to gain insights into the factors that may explain the replacement of the temperate Pacific native, M. trossulus, by this Mediterranean Sea invader along much of the California coast. Heart rate of M. trossulus was significantly higher than that of M. galloprovincialis, consistent with evolutionary adaptation to a lower habitat temperature (temperature compensation) in the former species. Heart rates of M. trossulus/M. galloprovincialis hybrids were intermediate between those of the parental species. Following acclimation to 14°C and 21°C, heart rates of all species exhibited partial compensation to temperature. Heart rate increased with rising temperature until a high temperature was reached at which point activity fell sharply, the high critical temperature (Hcrit). Hcrit increased with increasing acclimation temperature and differed among species in a pattern that reflected their probable evolutionary adaptation temperatures: M. galloprovincialis is more heat tolerant than the other two congeners. Ability to sustain heart function in the cold also reflected evolutionary history: M. trossulus is more cold tolerant than M. galloprovincialis. Heart rates for all three congeners decreased gradually in response to acute reductions in salinity until a low salinity (Scrit) was reached at which heart rate dropped precipitously. Scrit decreased with decreasing salinity of acclimation and was generally lowest for M. galloprovincialis. Mortality during acclimation under common garden conditions was greatest in M. trossulus and was highest at high acclimation temperatures and salinities. These intrinsic differences in basal heart rate, thermal and salinity responses, acclimatory capacity, and survivorship are discussed in the contexts of the species' biogeographic patterning and, for the invasive species M. galloprovincialis, the potential for further range expansion along the Pacific coast of North America.
The Circadian Gene NPAS2, a Putative Tumor Suppressor, Is Involved in DNA Damage Response

Apart from regulating sleep and wakefulness, the circadian system may play an important role in other biological processes, including pathways involved in tumorigenesis. Two genetic association studies recently conducted by our lab have shown that a missense mutation in neuronal PAS domain protein 2 (NPAS2), a core circadian gene and transcriptional regulator, is significantly associated with risk of breast cancer and non–Hodgkin's lymphoma. Our current functional analyses provide the first in vitro evidence further demonstrating that cells with RNA interference–mediated depletion of NPAS2 fail to exhibit the expected cell cycle delay in response to mutagen treatment. DNA repair capacity, as measured by the comet assay, is also impaired. Moreover, a pathway-based PCR expression array of genes important for DNA damage signaling showed that knockdown of NPAS2 significantly represses the expression of several cell cycle and DNA repair genes. Thus, NPAS2 may play a role in tumorigenesis by affecting expression of cancer-related genes and could be considered a novel tumor suppressor. (Mol Cancer Res 2008;6(9):1461–8)
Moderate variation of the oncogenic potential among high‐risk human papillomavirus types in gynecologic patients with cervical abnormalities

The oncogenic potential of human papillomavirus (HPV) infection was assessed by following the disease course in 455 patients who had had a routine diagnostic Hybrid Capture HPV test due to squamous cell abnormalities of the uterine cervix as detected by cytology and/or colposcopy. At entry, 308 patients had cytologic atypia classified as P3 by the Papanicolau classification, 168 had a positive high‐risk HPV test, and 23 were infected only with low‐risk HPV. The patients were followed‐up using the patient registry until the endpoint of histologically diagnosed cervical intraepithelial neoplasia (CIN). High‐grade CIN was diagnosed in 75 surgical biopsies. High‐risk HPV infection (relative risk: 76.8 CI95: 23.7–249.5), cytologic atypia (RR: 16.2 CI95: 3.9–66.6), and age above 35 (RR: 1.99 CI95: 1.26–3.16) were independent risk factors for high‐grade CIN, while the viral load did not predict oncogenic progression (P = 0.47). After PCR–RFLP typing, the high‐risk types were classified into groups as follows: (1) types 16 and 18, (2) types 45, 52, and 56, (3) types 31, 33, 35, 51, and 58. The relative risks of high‐grade CIN were 119.1 (CI95: 36.2–390.9) for group 1, 44.4 (CI95: 9.8–201) for group 2, and 39.7 (CI95: 10.9–144.8) for group 3, respectively. The risk ratios between the groups of high‐risk types were found to differ at most by a factor of 2.98 (corrected P value: 0.007) indicating that the oncogenic potential varies moderately within the high‐risk group of HPVs. J. Med. Virol. 71:585–592, 2003. © 2003 Wiley‐Liss, Inc.
Per-Thread Cycle Accounting

Resource sharing unpredictably affects per-thread performance in multithreaded architectures, but system software assumes all coexecuting threads make equal progress. Per-thread cycle accounting addresses this problem by tracking per-thread progress rates for each coexecuting thread. This approach has the potential to improve Quality Of Service (QoS), Service-Level Agreements (SLA), performance predictability, service differentiation, and proportional-share performance on multithreaded architectures.
Stereotypes, Emotions, and Behaviors Toward Lesbians, Gay Men, Bisexual Women, and Bisexual Men

ABSTRACT The utility of the Stereotype Content Model (Fiske, Cuddy, Glick, & Xu, 2002) and the Behaviors from Intergroup Affect and Stereotypes map (Cuddy, Fiske, & Glick, 2007) were examined in the context of heterosexuals’ attitudes toward sexual minorities. Heterosexual adults completed a survey measuring stereotypes, emotions, and behavioral tendencies toward lesbians, gay men, bisexual women, and bisexual men. Stereotype content differed across groups and showed “gendered” and “valenced” effects on emotions and behavioral tendencies. Competence predicted behaviors for men, whereas warmth and competence predicted behaviors for women, and, for the most part, more was better. Admiration and contempt mediated most of these relationships across most subgroups, but pity and envy played smaller roles for some subgroups. Across all groups, competence played a more predictive role than warmth.
Identification of Leishmania‐specific protein phosphorylation sites by LC‐ESI‐MS/MS and comparative genomics analyses

Human pathogenic protozoa of the genus Leishmania undergo various developmental transitions during the infectious cycle that are triggered by changes in the host environment. How these parasites sense, transduce, and respond to these signals is only poorly understood. Here we used phosphoproteomic approaches to monitor signaling events in L. donovani axenic amastigotes, which may be important for intracellular parasite survival. LC‐ESI‐MS/MS analysis of IMAC‐enriched phosphoprotein extracts identified 445 putative phosphoproteins in two independent biological experiments. Functional enrichment analysis allowed us to gain insight into parasite pathways that are regulated by protein phosphorylation and revealed significant enrichment in our data set of proteins whose biological functions are associated with protein turn‐over, stress response, and signal transduction. LC‐ESI‐MS/MS analysis of TiO2‐enriched phosphopeptides confirmed these results and identified 157 unique phosphopeptides covering 181 unique phosphorylation sites in 126 distinct proteins. Investigation of phosphorylation site conservation across related trypanosomatids and higher eukaryotes by multiple sequence alignment and cluster analysis revealed L. donovani‐specific phosphoresidues in highly conserved proteins that share significant sequence homology to orthologs of the human host. These unique phosphorylation sites reveal important differences between host and parasite biology and post‐translational protein regulation, which may be exploited for the design of novel anti‐parasitic interventions.
Estimation of snowfall over the sea of Japan using AMSR-E passive microwave remote sensing observation

Snowfall is an important geophysical parameter and the observation of the spatial and temporal distribution of snowfall can provide valuable information for a wide range of applications including climate change studies and atmospheric modelling. This paper investigates the feasibility to estimates the amount of solid precipitation and the cloud liquid water content over the ocean using AMSR-E passive microwave brightness temperature observations. The parameters are retrieved by minimizing the difference between the observed and modeled brightness temperature. The radiative transfer in the atmosphere is solved using the discrete ordinate method (4 streams) and the Henyey-Greenstein phase function. The scattering effect of the snow particles is calculated using Mie theory and the liquid-equivalent size of the ice particle. Except for the snowfall and the cloud liquid water content, most parameters, which influence the observation are derived from other data sources. The Newton-Raphson method is used to solve the iteration process using observed brightness temperatures at 89 GHz vertical polarization and 36.5 GHz horizontal polarization. The algorithm was applied using data from the Wakasa Bay Experiment 2003 in Japan and the results are compared to snowfall observation derived using a Z-R relationship and data from the Mikuni Doppler radar. Good agreement was achieved for different atmospheric conditions
Providing written information on HIV testing improves patient knowledge but does not affect test uptake

The objective of this study is to determine the effect of providing written information about HIV testing on patient knowledge and test uptake. Patients attending our genitourinary medicine clinic in July 2003 were offered written information about HIV and the test. They were asked to complete a questionnaire which elicited knowledge provided on the leaflet. A control group of individuals were offered verbal discussion only. A total of 382 questionnaires were completed. Individuals given written information were more likely to believe that HIV could not be transmitted by insect bites (P = 0.01), more aware of current treatments and that a negative test would not affect a future mortgage application (P = 0.001). There was no difference in test uptake or reasons for declining a test in both groups. Providing written information on HIV testing increases patient knowledge, but does not affect test uptake.
Pax‐5 is a key regulator of the B cell‐restricted expression of the CD23a isoform

Human CD23 (the low affinity IgE receptor) is a B cell differentiation marker involved in inflammatory responses. Two isoforms (CD23a and CD23b) are known, which differ only in their cytoplasmic domain. Whereas CD23b expression is specifically induced by IL‐4 on B cells and cells of the myeloid lineage, CD23a expression is restricted to B cells. Each isoform is regulated by its own promoter. Pax‐5 is a B‐cell‐restricted transcription factor with an essential role in early and late B cell development. Analyses of the CD23a promoter revealed a Pax‐5‐binding site, which can compete a high affinity Pax‐5‐binding site or directly bind Pax‐5 protein in electrophoretic mobility shift assays. Introducing mutations into this site abrogates the binding. Expression of Pax‐5 in 293 cellsresulted in a seven‐ to tenfold activation of a CD23a core promoter construct. Most importantly, ectopic expression of Pax‐5 in the monocytic cell line U‐937, which regularly expresses only the CD23b isoform, led to CD23a expression after stimulation with IL‐4 and PMA. Our results suggest that Pax‐5 is a key regulator of the B‐cell‐restricted expression of the CD23a isoform.
Technology use, cesarean section rates, and perinatal mortality at Danish maternity wards

Fifty‐eight Danish maternity units, managing 99% of Danish deliveries, participated in a cross sectional study to assess the relationship between use of birth‐related technologies, cesarean section rates and perinatal mortality for births after 35 completed weeks of gestation. A regional technology index (0‐10) was calculated for each maternity unit according to its use of ante and intra partum fetal heart rate monitoring (FHM), hormone analysis (human placental lactogen (HPL) and/or estriol (Ø3)), fetal blood samples (scalp‐pH), intrauterine catheter and umbilical cord‐pH. Maternity units using FHM had a 15% higher cesarean section rate (not planned) than units not using FHM (p<0.05). The referral of potentially complicated deliveries to central units, which at the same time relatively often use FHM, is probably responsible for this association. Trying to encounter this selection bias a technology index was calculated for eight regions in Denmark, weighting the index of each unit in a region according to its number of deliveries. There was no association between the technology index in these eight regions in Denmark and their cesarean section rates. Use of FHM, technology index, and unplanned cesarean section rates in the eight regions were all without significant association to the perinatal mortality in the same regions. For births after the 35th completed week of gestation, this study could not confirm a relationship between different degrees of use of birth‐related technologies and perinatal mortality.