Miracle-dz/UniFAR-FTUs huggingface dataset:
Graft loss among renal-transplant recipients with early reduction of immunosuppression for BK viremia

AIM To review the incidence of graft loss and acute rejection among renal transplant recipients with early reduction of immunosuppression for BK viremia. METHODS We performed a retrospective analysis of consecutive de-novo kidney-only transplants from January 2009 to December 2012 to evaluate the incidence of Polyoma-virus associated nephropathy (PyVAN). Recipient plasma was screened for BKV DNA via quantitative polymerase chain reaction (PCR) at months 1, 3, 6, 9 and 12 post-transplant and on worsening graft function. Immunosuppression was reduced at ≥ 3-log copies/mL. Those with viremia of ≥ 4-log copies/mL (presumptive PyVAN) underwent renal transplant biopsy. Presumptive PyVAN (PP) and definitive PyVAN (DP; biopsy-proven) were treated by immunosuppression reduction (IR) only. RESULTS Among 319 kidney transplant recipients, the median age was 53 years (range 19-83), 65.8% were male, and 58.9% were white. Biopsy-proven acute rejection was found in 18.5% within 0-168 wk. Death-censored graft loss occurred in 5.3% (n = 17) and graft loss attributable to PyVAN was 0.6% (n = 2). Forty-seven patients were diagnosed with PP (14.7%) and 18 (5.6%) with DP. Graft loss among participants with PyVAN (8.5%) and those without (4.8%) was not significantly different. Deceased donor kidney transplantation (OR = 2.3, 95%CI = 1.1-4.6) and AR (OR = 2.3, 95%CI = 1.2-4.7) were associated with PyVAN in the multivariate analysis. BK viremia between 3 and 4-log copies/mL occurred in 27 patients, all of whom underwent IR. Of these, 16 (59%) never developed PyVAN while 11 (41%) developed PyVAN (4 DP, 7 PP) within a range of 11-39 wk. CONCLUSION Instituting an early reduction of immunosuppression, in the absence of adjunctive antivirals, is effective at preventing PyVAN and may be associated with a lower incidence of graft-loss without a reciprocal increase in the incidence of acute rejection.
Circulating Progenitor Cells Correlate with Memory, Posterior Cortical Thickness, and Hippocampal Perfusion.

BACKGROUND Bone marrow-derived progenitor cells survey the vasculature and home to sites of tissue injury where they can promote repair and regeneration. It has been hypothesized that these cells may play a protective role neurodegenerative and vascular cognitive impairment. OBJECTIVE To evaluate progenitor cell levels in older adults with and without mild cognitive impairment (MCI), and to relate circulating levels to memory, brain volume, white matter lesion volume, and cerebral perfusion. METHOD Thirty-two older adults, free of stroke and cardiovascular disease, were recruited from the community and evaluated for diagnosis of MCI versus cognitively normal (CN). Participants underwent brain MRI and blood samples were taken to quantify progenitor reserve using flow cytometry (CD34+, CD34+CD133+, and CD34+CD133+CD309+ cells). RESULTS Participants with MCI (n = 10) exhibited depletion of all CPC markers relative to those who were CN (n = 22), after controlling for age, sex, and education. Post-hoc age, sex, and education matched comparisons (n = 10 MCI, n = 10 CN) also revealed the same pattern of results. Depletion of CD34+ cells correlated with memory performance, left posterior cortical thickness, and bilateral hippocampal perfusion. Participants exhibited low levels of vascular risk and white matter lesion burden that did not correlate with progenitor levels. CONCLUSIONS Circulating progenitor cells are associated with cognitive impairment, memory, cortical atrophy, and hippocampal perfusion. We hypothesize that progenitor depletion contributes to, or is triggered by, cognitive decline and cortical atrophy. Further study of progenitor cell depletion in older adults may benefit efforts to prevent or delay dementia.
Is it really theoretical? A review of sampling in grounded theory studies in nursing journals.

BACKGROUND Grounded theory is a distinct method of qualitative research, where core features are theoretical sampling and constant comparative analysis. However, inconsistent application of these activities has been observed in published studies. AIM This review assessed the use of theoretical sampling in grounded theory studies in nursing journals. DESIGN An adapted systematic review was conducted. METHOD Three leading nursing journals (2010-2014) were searched for studies stating grounded theory as the method. Sampling was assessed using a concise rating tool. RESULTS A high proportion (86%) of the 134 articles described an iterative process of data collection and analysis. However, half of the studies did not demonstrate theoretical sampling, with many studies declaring or indicating a purposive sampling approach throughout. CONCLUSION Specific reporting guidelines for grounded theory studies should be developed to ensure that study reports describe an iterative process of fieldwork and theoretical development.
D ec 2 01 0 AEI-2010-118 E 7 ( 7 ) symmetry in perturbatively quantised N = 8 supergravity

We study the perturbative quantisation of N = 8 supergravity in a formulation where its E7(7) symmetry is realised off-shell. Relying on the cancellation of SU(8) current anomalies we show that there are no anomalies for the non-linearly realised E7(7) either; this result extends to all orders in perturbation theory. As a consequence, the e7(7) Ward identities can be consistently implemented and imposed at all orders in perturbation theory, and therefore potential divergent counterterms must in particular respect the full non-linear E7(7) symmetry. ∗email: bossard@aei.mpg. de †email: hillmann@ihes.fr ‡email: Hermann.Nicolai@aei.mpg. de
Pollen and Phytolith Evidence for Rice Cultivation and Vegetation Change during the Mid-Late Holocene at the Jiangli Site, Suzhou, East China

Pollen and phytolith analyses were undertaken at the Jiangli site in Suzhou, Jiangsu Province, combined with studies on macrofossils by flotation. The concentration of pollen decreased while the percentage of Poaceae pollen in the profile increased from the late phase of the Majiabang Culture to the Songze Culture suggesting that human impact on the local environment intensified gradually. The discovery of rice paddy implies a relatively advanced rice cultivation in this area during the middle-late Holocene. Other than phytoliths, the high percentage of Oryza-type Poaceae pollen (larger than 40 µm) supplied robust evidence for the existence of rice paddy. Moreover, the fact that the farther from the rice paddy, the lower the concentration and percentage of Poaceae pollen also proves that the dispersal and deposition of pollen is inversely proportional to the distance.
Intestinal perception: mechanisms and assessment

Physiological stimuli in the gut induce regulatory reflexes to accomplish the digestive process, but are normally not perceived. However, under some circumstances, gut stimuli may activate perception pathways and induce conscious sensations. Experimental evidence gathered during the past decade suggests that patients with functional gut disorders and unexplained abdominal symptoms may have a sensory dysfunction of the gut, so that physiological stimuli would induce symptoms. Assessment of visceral sensitivity is still poorly developed, but in analogy to somatosensory testing, differential stimulation of visceral afferents may be achieved by a combination of stimulation techniques, which may help to characterize sensory dysfunctions. Visceral afferent input is modulated by a series of mechanisms at different levels of the brain–gut axis, and conceivably, a dysfunction of these regulatory mechanisms could cause hyperalgesia. The sensory dysfunction in functional patients seems to be associated with altered reflex activity, and both mechanisms may interact to produce the symptoms. Evidence of a gut sensory–reflex dysfunction as a common pathophysiological mechanism in different functional gastrointestinal disorders would suggest that they are different forms of the same process, and that the clinical manifestations depend on the specific pathways affected.
Multi-modal imaging of long-term recovery post-stroke by positron emission tomography and matrix-assisted laser desorption/ionisation mass spectrometry.

RATIONALE Stroke is a leading cause of disability worldwide. Understanding the recovery process post-stroke is essential; however, longer-term recovery studies are lacking. In vivo positron emission tomography (PET) can image biological recovery processes, but is limited by spatial resolution and its targeted nature. Untargeted mass spectrometry imaging offers high spatial resolution, providing an ideal ex vivo tool for brain recovery imaging. METHODS Magnetic resonance imaging (MRI) was used to image a rat brain 48 h after ischaemic stroke to locate the infarcted regions of the brain. PET was carried out 3 months post-stroke using the tracers [18 F]DPA-714 for TSPO and [18 F]IAM6067 for sigma-1 receptors to image neuroinflammation and neurodegeneration, respectively. The rat brain was flash-frozen immediately after PET scanning, and sectioned for matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-MS) imaging. RESULTS Three months post-stroke, PET imaging shows minimal detection of neurodegeneration and neuroinflammation, indicating that the brain has stabilised. However, MALDI-MS images reveal distinct differences in lipid distributions (e.g. phosphatidylcholine and sphingomyelin) between the scar and the healthy brain, suggesting that recovery processes are still in play. It is currently not known if the altered lipids in the scar will change on a longer time scale, or if they are stabilised products of the brain post-stroke. CONCLUSIONS The data demonstrates the ability to combine MALD-MS with in vivo PET to image different aspects of stroke recovery.
8 M ay 2 01 4 Dichroism for Orbital Angular Momentum using Stimulated Parametric Down Conversion

One usage of the term dichroism in optics is to describe the differential loss of monochromatic light in one of two orthogonal polarization states with respect to some reference axis. This definition encompasses the case of both linear and circular dichroism, and also gain and/or loss if one allows for negative absorption. For example, circular dichroism refers to case in which right-handed (RHC) and left-handed circular (LHC) polarizations experience different propagation losses in the dichroic medium. As is well known the RHC and LHC polarized states represent two orthogonal spin angular momentum (SAM) states for the light field. Then another way to express circular dichroism is that it is a dichroism based on the spin angular momentum (SAM) state of the incident light field, or simply dichroism for SAM. The goal of this paper is propose and theoretically investigate stimulated Parametric Down Conversion (PDC) as a means to produce dichroism based on the orbital angular momentum (OAM) of an incident signal field. The nonlinear interaction is shown to provide differential gain between signal states of differing OAM, the peak gain occurring at half the OAM of the pump field. Stimulated PDC involving fundamental and second-harmonic fields carrying OAM has previously been explored both experimentally and theoretically but mainly in the context of the conservation of OAM for the PDC process [1–3] as opposed to creating dichroism for OAM. A recent paper has discussed circular dichroism that has its origin in the OAM of a beam incident on a non-chiral structure [4] whereas here we elucidate a means to produce dichroism that acts on the incident beam OAM directly. The remainder of this paper is organized as follows. Section II describes the geometry and governing equations for our system, and Sec. III presents a simplified analytic theory of stimulated PDC and dichroism for OAM for pump and signal beams that are perfect optical vortices. In Sec. IV numerical results are presented for the case of signal and pump fields that are imperfect
Developmental Changes in Topological Asymmetry Between Hemispheric Brain White Matter Networks from Adolescence to Young Adulthood

Abstract Human brain asymmetries have been well described. Intriguingly, a number of asymmetries in brain phenotypes have been shown to change throughout the lifespan. Recent studies have revealed topological asymmetries between hemispheric white matter networks in the human brain. However, it remains unknown whether and how these topological asymmetries evolve from adolescence to young adulthood, a critical period that constitutes the second peak of human brain and cognitive development. To address this question, the present study included a large cohort of healthy adolescents and young adults. Diffusion and structural magnetic resonance imaging were acquired to construct hemispheric white matter networks, and graph‐theory was applied to quantify topological parameters of the hemispheric networks. In both adolescents and young adults, rightward asymmetry in both global and local network efficiencies was consistently observed between the 2 hemispheres, but the degree of the asymmetry was significantly decreased in young adults. At the nodal level, the young adults exhibited less rightward asymmetry of nodal efficiency mainly around the parasylvian area, posterior tempo‐parietal cortex, and fusiform gyrus. These developmental patterns of network asymmetry provide novel insight into the human brain structural development from adolescence to young adulthood and also likely relate to the maturation of language and social cognition that takes place during this period.
Automated ultrasound edge‐tracking software comparable to established semi‐automated reference software for carotid intima‐media thickness analysis

Many commercial ultrasound systems are now including automated analysis packages for the determination of carotid intima‐media thickness (cIMT); however, details regarding their algorithms and methodology are not published. Few studies have compared their accuracy and reliability with previously established automated software, and those that have were in asymptomatic adults. Therefore, this study compared cIMT measures from a fully automated ultrasound edge‐tracking software (EchoPAC PC, Version 110.0.2; GE Medical Systems, Horten, Norway) to an established semi‐automated reference software (Artery Measurement System (AMS) II, Version 1.141; Gothenburg, Sweden) in 30 healthy preschool children (ages 3–5 years) and 27 adults with coronary artery disease (CAD; ages 48–81 years). For both groups, Bland–Altman plots revealed good agreement with a negligible mean cIMT difference of −0·03 mm. Software differences were statistically, but not clinically, significant for preschool images (P = 0·001) and were not significant for CAD images (P = 0·09). Intra‐ and interoperator repeatability was high and comparable between software for preschool images (ICC, 0·90–0·96; CV, 1·3–2·5%), but slightly higher with the automated ultrasound than the semi‐automated reference software for CAD images (ICC, 0·98–0·99; CV, 1·4–2·0% versus ICC, 0·84–0·89; CV, 5·6–6·8%). These findings suggest that the automated ultrasound software produces valid cIMT values in healthy preschool children and adults with CAD. Automated ultrasound software may be useful for ensuring consistency among multisite research initiatives or large cohort studies involving repeated cIMT measures, particularly in adults with documented CAD.
Efficient Top-k Path Search in Large Knowledge Bases

Top-k keyword search in large knowledge bases is always a very important problem in keyword search area. When it comes to keyword search on large scale knowledge bases, we want to propose an algorithm which is not only effective but also efficient. Efficiency plays such an important role in this research domain which inspired us to consider to us Spark to do parallel computing in the table join phase.
Global Network Inference from Ego Network Samples: Testing a Simulation Approach

Network sampling poses a radical idea: that it is possible to measure global network structure without the full population coverage assumed in most network studies. Network sampling is only useful, however, if a researcher can produce accurate global network estimates. This article explores the practicality of making network inference, focusing on the approach introduced in Smith (2012). The method uses sampled ego network data and simulation techniques to make inference about the global features of the true, unknown network. The validity check here includes more difficult scenarios than previous tests, including those that go beyond the initial scope conditions of the method. I examine networks with a skewed degree distribution and surveys that limit the number of social ties a respondent can list. For each network/survey combination, I take a random ego network sample, run the simulation method, and compare the results to the true values (using measures of connectivity and cohesion). I also test the method on local measures of network structure. The results, on the whole, are encouraging. The method produces good estimates even in cases where the degree distribution is skewed and the survey is strongly restricted. I also find that is it better to not truncate the survey if possible. If the survey must be restricted, the researcher would do well to infer the missing data, rather than use the raw data naively.
Interactive Effects of Indigestible Carbohydrates, Protein Type, and Protein Level on Biomarkers of Large Intestine Health in Rats

The effects of indigestible carbohydrates, protein type, and protein level on large intestine health were examined in rats. For 21 days, 12 groups of six 12-week-old male Wistar rats were fed diets with casein (CAS), or potato protein concentrate (PPC), providing 14% (lower protein level; LP), or 20% (higher protein level; HP) protein, and containing cellulose, resistant potato starch, or pectin. Fermentation end-products, pH, and β-glucuronidase levels in cecal digesta, and ammonia levels in colonic digesta were determined. Cecal digesta, tissue weights, cecal and colon morphology, and colonocyte DNA damage were also analyzed. Digesta pH was lower, whereas relative mass of cecal tissue and digesta were higher in rats fed pectin diets than in those fed cellulose. Cecal parameters were greater in rats fed PPC and HP diets than in those fed CAS and LP diets, respectively. Short-chain fatty acid (SCFA) concentrations were unaffected by protein or carbohydrate type. Total SCFA, acetic acid, and propionic acid concentrations were greater in rats fed LP diets than in those fed HP. Cecal pool of isobutyric and isovaleric acids was greater in rats fed PPC than in those fed CAS diets. PPC diets decreased phenol concentration and increased ammonia concentration in cecal and colonic digesta, respectively. Cecal crypt depth was greater in rats fed PPC and HP diets, and was unaffected by carbohydrates; whereas colonic crypt depth was greater in rats fed cellulose. Myenteron thickness in the cecum was unaffected by nutrition, but was greater in the colon of rats fed cellulose. Colonocyte DNA damage was greater in rats fed LP diets than in those fed HP diets, and was unaffected by carbohydrate or protein type. It was found that nutritional factors decreasing cecal digesta weight contribute to greater phenol production, increased DNA damage, and reduced ammonia concentration in the colon.
Pholder: An Eye-Gaze Assisted Reading Application on Android

Eye-gaze has been used extensively in human computer interface design, web layout design and as assistive technology. We successfully built a reading application with automatic scrolling, using the images captured by the in-build camera to determine the eye-gaze. The application, Pholder, uses the appearance-based method for gaze estimation and tracking of gaze movement directions for scrolling of the screen. We used an innovative technique, using the integration of pixel intensity, for gaze movement estimation which is more robust then other techniques.
Roles of the TRAF6 and Pellino E3 ligases in MyD88 and RANKL signaling

Significance TRAF6 is essential for many biological processes, including the operation of the innate immune system and bone formation. The enzymatic activity of TRAF6, an E3 ubiquitin ligase, is thought to have a pivotal role in triggering these processes. In this paper, we reexamined this assumption by generating mice expressing a catalytically inactive mutant of TRAF6. The bone structure of the mice was normal and a major intracellular signaling pathway of the immune system could still be switched on. We found that other E3 ligases, Pellino1 and Pellino2, could generate the ubiquitin chains needed to switch on immune signaling in human cells expressing catalytically inactive TRAF6. Our findings identify essential roles of TRAF6 that are independent of its enzymatic activity. It is widely accepted that the essential role of TRAF6 in vivo is to generate the Lys63-linked ubiquitin (K63-Ub) chains needed to activate the “master” protein kinase TAK1. Here, we report that TRAF6 E3 ligase activity contributes to but is not essential for the IL-1–dependent formation of K63-Ub chains, TAK1 activation, or IL-8 production in human cells, because Pellino1 and Pellino2 generate the K63-Ub chains required for signaling in cells expressing E3 ligase-inactive TRAF6 mutants. The IL-1–induced formation of K63-Ub chains and ubiquitylation of IRAK1, IRAK4, and MyD88 was abolished in TRAF6/Pellino1/Pellino2 triple-knockout (KO) cells, but not in TRAF6 KO or Pellino1/2 double-KO cells. The reexpression of E3 ligase-inactive TRAF6 mutants partially restored IL-1 signaling in TRAF6 KO cells, but not in TRAF6/Pellino1/Pellino2 triple-KO cells. Pellino1-generated K63-Ub chains activated the TAK1 complex in vitro with similar efficiently to TRAF6-generated K63-Ub chains. The early phase of TLR signaling and the TLR-dependent secretion of IL-10 (controlled by IRAKs 1 and 2) was only reduced modestly in primary macrophages from knockin mice expressing the E3 ligase-inactive TRAF6[L74H] mutant, but the late-phase production of IL-6, IL-12, and TNFα (controlled only by the pseudokinase IRAK2) was abolished. RANKL-induced signaling in macrophages and the differentiation of bone marrow to osteoclasts was similar in TRAF6[L74H] and wild-type cells, explaining why the bone structure and teeth of the TRAF6[L74H] mice was normal, unlike TRAF6 KO mice. We identify two essential roles of TRAF6 that are independent of its E3 ligase activity.