Miracle-dz/UniFAR-FTUs huggingface dataset:
Time Course of Pathologic Changes in Kidney Allografts of Positive Crossmatch HLA-Incompatible Transplant Recipients

Background Recipients of incompatible allografts are at increased risk of graft loss. We hypothesized that analysis of sequential biopsies from these grafts could define progression of graft lesions and identify features predictive of progression. Methods We studied the time course of histologic injury in 745 kidney graft biopsies from 129 patients transplanted with a positive crossmatch human leukocyte antigen–incompatible kidney between 2000 and 2010 (follow-up of 1–9 years). Results Graft survival was 98% at 1 year and 80% at 5 years after transplantation. Throughout follow-up, 70% of patients experienced rejection, with 52% showing subclinical rejection in the first year. Cell-mediated rejection was more frequent than antibody-mediated rejection throughout follow-up. Transplant glomerulopathy (TxGN; cg≥1) developed in 47% of patients over the period of the study, as early as 3 months in a few patients. TxGN was preceded by glomerulitis in more than 90% of cases, with a median time interval of 12 months. Glomerulitis and detectable posttransplantation donor-specific antibodies were risk factors for TxGN (P<0.0001 and P<0.05). C4d-negative antibody-mediated rejection manifesting as capillaritis (g≥1 and ptc≥1) with detectable donor-specific antibodies was observed in some recipients (<20%). There was progressively higher average tubulointerstitial scarring (ci+ct) from 3 to 6 to 12 months (P<0.001). Conclusions Despite good graft survival, a significant incidence of biopsy-proven rejection occurred in this subset of closely monitored human leukocyte antigen–incompatible recipients throughout follow-up. Microcirculation inflammation, particularly glomerulitis, irrespective of C4d, is associated with a high risk of development of TxGN at 1 year.
Influence of treatment temperature and duration on selected biological, mechanical, physical and optical properties of thermally modified timber

Abstract The impact of heat-treatment temperature (180, 200, 210, 220 and 240°C) and various heat-treatment durations on selected biological, mechanical, optical and physical properties of thermally modified timber (TMT) was determined. The suitability of different measures for prediction of the treatment intensity was also investigated. Resistance to impact milling (RIM), lightness L*, equilibrium moisture content (EMC), and antiswelling efficiency (ASE) were correlated with corresponding fungal resistance achieved by heat treatments. The results show that the decrease in mass by heat treatments is a suitable measurand to describe the treatment intensity, which is a product of treatment temperature and duration, where the impact of temperature is dominant over the impact of time. The properties examined showed a strong reciprocally proportional relationship with the decrease in mass. Different correlations were found for the various treatment temperatures: the higher the temperature applied, the lower the decrease in mass required for an equivalent improvement in certain wood properties, e.g. biological durability, EMC and dimensional stability. However, mass loss by Poria placenta correlated well with RIM, lightness L*, EMC and ASE of the different heat-treated specimens, depending on the heat-treatment temperature. Consequently, a reliable estimation of improved fungal resistance of TMT, as well as quality control of TMT in general, requires certain process information.
Optimized design of a Human Intranet network

We address the design space exploration of wireless body area networks for wearable and implantable technologies, a task that is increasingly challenging as the number and variety of devices per person grow. Our method efficiently decomposes the problem into smaller subproblems by coordinating specialized analysis and optimization techniques. We leverage mixed integer linear programming to generate candidate network configurations based on coarse energy estimations. Accurate discrete-event simulation is used to check the feasibility of the proposed configurations under reliability constraints and guide the search to achieve fast convergence. Numerical results show that our application-specific approach substantially reduces the exploration time with respect to generic optimization techniques and helps provide clear identification of promising solutions.
Reclaiming Quasi - Monte Carlo Efficiency in Portfolio Value-at-Risk Simulation Through Fourier Transform

QuasiMonte Carlo methods overcome the problem of sample clustering in regular Monte Carlo simulation and have been shown to improve simulation efficiency in the derivatives pricing literature when the price is expressed as a multidimensional integration and the integrand is suitably smooth. For portfolio value-at-risk (VaR) problems, the distribution of portfolio value change is based on the expectation of an indicator function, hence the integrand is discontinuous. The purpose of this paper is to smooth the expectation estimation of an indicator function via Fourier transform so that the faster convergence rate of quasiMonte Carlo methods can be reclaimed theoretically. Under fairly mild assumptions, the simulation of portfolio value-at-risk is fast and accurate. Numerical examples elucidate the advantage of the proposed approach over regular Monte Carlo and quasiMonte Carlo methods.
Evaluating Information in Zero-Sum Games with Incomplete Information on Both Sides

In a Bayesian game some players might receive a noisy signal regarding the specific game actually being played before it starts. We study zero-sum games where each player receives a partial information about his own type and no information about that of the other player and analyze the impact the signals have on the payoffs. It turns out that the functions that evaluate the value of information share two property. The first is Blackwell monotonicity, which means that each player gains from knowing more. The second is concavity on the space of conditional probabilities
Optimal Force–Time Integral for Pulmonary Vein Isolation According to Anatomical Wall Thickness Under the Ablation Line

Background Low contact force and force–time integral (FTI) during catheter ablation are associated with ineffective lesion formation, whereas excessively high contact force and FTI may increase the risk of complications. We sought to evaluate the optimal FTI for pulmonary vein (PV) isolation based on atrial wall thickness under the ablation line. Methods and Results Contact force parameters and FTI during anatomical ipsilateral PV isolation for atrial fibrillation and atrial wall thickness were assessed retrospectively in 59 consecutive patients for their first PV isolation procedure. The PV antrum was divided into 8 segments, and the wall thickness of each segment under the ablation line was determined using multidetector computed tomography. The FTI for each ablation point was divided by the wall thickness of the PV antrum segment where each point was located to obtain FTI/wall thickness. In total, 5335 radiofrequency applications were delivered, and 85 gaps in PV isolation ablation lines and 15 dormant conductions induced by adenosine were detected. The gaps or dormant conductions were significantly associated with low contact force, radiofrequency duration, FTI, and FTI/wall thickness. Among them, FTI/wall thickness had the best prediction value for gaps or dormant conductions by receiver operating characteristic curve analysis. FTI/wall thickness of <76.4 gram‐seconds per millimeter (gs/mm) predicted gaps or dormant conductions with sensitivity (88.0%) and specificity (83.6%), and FTI/wall thickness of <101.1 gs/mm was highly predictive (sensitivity 97.0%; specificity 69.6%). Conclusions FTI/wall thickness is a strong predictor of gap and dormant conduction formation in PV isolation. An FTI/wall thickness ≈100 gs/mm could be a suitable target for effective ablation.
Histamine-releasing activity and bronchoconstricting effects of sisal

Nicholls, P. J., Evans, E. , Valić, F. , and Žuškin, E. (1973). British Journal of Industrial Medicine,30, 142-145. Histamine-releasing activity and bronchoconstricting effects of sisal. Extracts of dry and oiled sisal released histamine from pig and human but not from rat lung tissue. A suspension in Tyrode solution of the oil used for softening the sisal fibres had a pH of 8·1 and also released histamine from pig and human lung. The releasing activity was abolished when the pH of this suspension was adjusted to pH 7·4. As all the sisal extracts were adjusted to pH 7·4 for incubation with lung tissue, the histamine-releasing activity of sisal in vitro is unrelated to the presence of the oil. Significant (P < 0·01) mean reductions over the work shift of ventilatory capacity (PEF and FEV1·0) were recorded in all the workers exposed to airborne sisal dust. These reductions were greater in combers than in drawers and spinners. Sisal collected from combing machines possessed more histamine-releasing activity than material from drawing and spinning machines. These results indicate that histamine release by sisal may be the cause of acute ventilatory capacity changes in sisal exposure.
Weakly Supervised Semantic Parsing with Abstract Examples

Training semantic parsers from weak supervision (denotations) rather than strong supervision (programs) complicates training in two ways. First, a large search space of potential programs needs to be explored at training time to find a correct program. Second, spurious programs that accidentally lead to a correct denotation add noise to training. In this work we propose that in closed worlds with clear semantic types, one can substantially alleviate these problems by utilizing an abstract representation, where tokens in both the language utterance and program are lifted to an abstract form. We show that these abstractions can be defined with a handful of lexical rules and that they result in sharing between different examples that alleviates the difficulties in training. To test our approach, we develop the first semantic parser for CNLVR, a challenging visual reasoning dataset, where the search space is large and overcoming spuriousness is critical, because denotations are either TRUE or FALSE, and thus random programs are likely to lead to a correct denotation. Our method substantially improves performance, and reaches 82.5% accuracy, a 14.7% absolute accuracy improvement compared to the best reported accuracy so far.
ATPase and DNA Helicase Activities of the Saccharomyces cerevisiae Anti-recombinase Srs2*

Saccharomyces cerevisiae SRS2 encodes an ATP-dependent DNA helicase that is needed for DNA damage checkpoint responses and that modulates the efficiency of homologous recombination. Interestingly, strains simultaneously mutated for SRS2 and a variety of DNA repair genes show low viability that can be overcome by inactivating homologous recombination, thus implicating inappropriate recombination as the cause of growth impairment in these mutants. Here, we report on our biochemical characterization of the ATPase and DNA helicase activities of Srs2. ATP hydrolysis by Srs2 occurs efficiently only in the presence of DNA, with ssDNA being considerably more effective than dsDNA in this regard. Using homopolymeric substrates, the minimal DNA length for activating ATP hydrolysis is found to be 5 nucleotides, but a length of 10 nucleotides is needed for maximal activation. In its helicase action, Srs2 prefers substrates with a 3′ ss overhang, and ∼10 bases of 3′ overhanging DNA is needed for efficient targeting of Srs2 to the substrate. Even though a 3′ overhang serves to target Srs2, under optimized conditions blunt-end DNA substrates are also dissociated by this protein. The ability of Srs2 to unwind helicase substrates with a long duplex region is enhanced by the inclusion of the single-strand DNA-binding factor replication protein A.
An autopsied case of V180I Creutzfeldt‐Jakob disease presenting with panencephalopathic‐type pathology and a characteristic prion protein type

A 73‐year‐old Japanese woman showed slowly progressive aphasia, apraxia and dementia. She had no family history of prion disease or dementia. One year later she showed parkinsonism and corticobasal degeneration was initially suspected. On MRI, the left temporal neocortex seemed swollen on T2‐weighted images in the initial stage, and a later high‐signal intensity region was observed in the cerebral cortex in diffusion‐weighted images. The patient developed myoclonus and an akinetic mutism state 15 months and 22 months after onset, respectively. Consecutive electroencephalography revealed no periodic sharp‐wave complexes. Prion protein (PrP) gene analysis revealed a valine to isoleucine point mutation at codon 180, and methionine homozygosity at codon 129. This patient's clinical symptoms and disease course were atypical for Creutzfeldt–Jakob disease (CJD), and a stable state with nasal tube‐feeding lasted several years. She died of respiratory failure at the age of 81, 102 months after the onset. Autopsy revealed widespread spongiform degeneration with weak synaptic‐type PrP deposition, confirming the diagnosis of genetic CJD. Neurons in the cerebral cortex were relatively preserved in number and hypertrophic astrocytosis was generally moderate for such long‐term disease, but cerebral white matter showed diffuse severe myelin pallor with tissue rarefaction suggestive of panencephalopatic‐type pathology. The cerebellar cortex was relatively well preserved with observation of mild spongiform change in the molecular layer, moderate neuron loss in the Purkinje neuron layer, and scattered small plaque‐like PrP deposition. Western blot analysis of protease‐resistant PrP showed a characteristic pattern without a diglycoform band. V180I CJD is an interesting form of genetic CJD with regards to the clinicopathologic, molecular and genetic findings.
Alcohol Effects on Driving Behavior and Performance in a Car Simulator

A fixed-base simulation has been developed to test the effect of alcohol on driving performance. The simulation includes both lateral steering control and a discrete visual detection, recognition, and response task set up to provide the workload and division of attention typical of real world driving. Measurements of both driver control behavior and driver-vehicle performance were obtained for the steering task, and detection and recognition indexes and reaction time were measured on the discrete task. Preliminary results on scanning behavior as measured with an eye-point-of-regard monitor are also presented. Data are given for eighteen drivers, ranging in age from 21-65, at blood alcohol concentrations (BAC) of 0, 0.06, and 0.11. Alcohol causes larger lane and heading deviations, and increases detection and reaction times on the discrete task. Control-behavior measures show that the driver's control gain decreases, but stability margins are maintained under alcohol, while driver remnant increases. Such effects could be due to indifference thresholds and/or intermittent attention in the control task. Both continuous steering control and discrete peripheral ``sign'' response tasks were performed, singly and combined, to investigate the effects of divided attention. Performance on the steering control task was decreased when both tasks were done concurrently, but the sensitivity to alcohol effects was similar. The driving simulation has proven an efficient tool for alcohol research. It has gained acceptance from subjects as a valid approximation of driving, and the various related measurements have proven to be reliable and sensitive to levels of intoxication.
Hepatitis C virus-associated B-cell non-Hodgkin’s lymphomas: what do we know?

Epidemiological studies have shown an increased risk of developing B-cell lymphomas in patients with chronic hepatitis C virus (HCV) infection. There is, however, a great geographic variability and it remains unclear whether additional environmental and genetic factors are involved or whether the international discrepancies represent simply a consequence of the variable prevalence of HCV infection in different countries. Other confounding factors may affect the comparability of the different studies, including the method of HCV assessment, the selection of normal controls, the lymphoma classification used and the year of publication. The most convincing evidence for a causal relationship comes from the observation, mainly limited to some indolent subtypes, of B-cell lymphoma regressions after successful HCV eradication with antiviral treatment. Yet, the molecular mechanism of HCV-induced lymphomagenesis are mainly hypothetical. According to most plausible models, lymphoma growth is a consequence of continuous antigenic stimulation induced by the chronic viral infection. This review will summarize the current knowledge on HCV-associated lymphomas and their management.
Sustainability indicator system and policy processes in Malaysia : a framework for utilisation and learning

Formulation of effective sustainability indicators for national assessment demands a comprehensive understanding of the utilisation, diffusion and dissemination of information in policy processes. To illustrate the dynamic of sustainability assessment within the context of policy processes, this paper uses a case study of national sustainability indicators development in Malaysia. Subsequently, this paper ascribes the limited achievement of national sustainability assessment in Malaysia to four types of constraints: meta-policy issues; technical capacities; communication concerns; and the inherent knowledge gaps within the indicator developer community vis-à-vis their theoretical limitations. It is proposed that such constraints will be encountered in many countries. Drawing from the literature on public policy, this paper outlines a framework for investigating indicator behaviour within policy processes based on well-established concepts such as knowledge utilisation and policy learning. I conclude this paper by elaborating on the corresponding future challenges that must be addressed before effective integration of sustainability indicators within policy systems can occur. q 2004 Elsevier Ltd. All rights reserved.
On the oncogenic properties of chicken embryo lethal orphan virus, an avian adenovirus.

Summary The oncogenicity of chicken embryo lethal orphan virus for newborn hamsters has been confirmed. Tumor incidence was found to be a function of the titer of the virus inoculum. Fifty-four % (7/13) of the hamsters given 109.3 50% lethal dose developed tumors, while only 8% (8/99) of the hamsters given 109.0 50% lethal dose developed tumors. With a single exception, lower virus doses were nononcogenic; one tumor developed among 26 hamsters given virus inactivated from 108.7 to 104.0 50% lethal dose by nitrous acid. Although all the tumors were of mesenchymal origin a variety of sarcomatous types were noted. The latent period varied from 14 to 52 weeks and all but one tumor appeared at the site of injection. Female hamsters appeared more susceptible than males. Indirect immunofluorescence and complement-fixation tests failed to demonstrate antibody in the sera of tumor-bearing hamsters to autologous tumor extracts or to chicken embryo lethal orphan virus-infected chick and hamster embryo cells.
Serum concentrations of markers of TNFalpha and Fas-mediated pathways and renal function in nonproteinuric patients with type 1 diabetes.

BACKGROUND AND OBJECTIVES The aim of our study was to examine serum markers of the TNF and Fas pathways for association with cystatin-C based estimated glomerular filtration rate (cC-GFR) in subjects with type 1 diabetes (T1DM) and no proteinuria. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS The study group (the 2nd Joslin Kidney Study) comprised patients with T1DM and normoalbuminuria (NA) (n = 363) or microalbuminuria (MA) (n = 304). Impaired renal function (cC-GFR <90 ml/min) was present in only 10% of patients with NA and 36% of those with MA. We measured markers of the tumor necrosis factor alpha (TNFalpha) pathway [TNFalpha, soluble TNF receptor 1 (sTNFR1), and 2 (sTNFR2)], its downstream effectors [soluble intercellular and soluble vascular adhesion molecules (sICAM-1 and sVCAM-1), interleukin 8 (IL8/CXCL8), monocytes chemoattractant protein-1 (MCP1), and IFNgamma inducible protein-10 (IP10/CXCL10)], the Fas pathway [soluble Fas (sFas) and Fas ligand (sFasL)], CRP, and IL6. RESULTS Of these, TNFalpha, sTNFRs, sFas, sICAM-1, and sIP10 were associated with cC-GFR. However, only the TNF receptors and sFas were associated with cC-GFR in multivariate analysis. Variation in the concentration of the TNF receptors had a much stronger impact on GFR than clinical covariates such as age and albumin excretion. CONCLUSIONS Elevated concentrations of serum markers of the TNFalpha and Fas-pathways are strongly associated with decreased renal function in nonproteinuric type 1 diabetic patients. These effects are independent of those of urinary albumin excretion. Follow-up studies are needed to characterize the role of these markers in early progressive renal function decline.
Hyperspectral Time Series Analysis of Native and Invasive Species in Hawaiian Rainforests

Abstract: The unique ecosystems of the Hawaiian Islands are progressively being threatened following the introduction of exotic species. Operational implementation of remote sensing for the detection, mapping and monitoring of these biological invasions is currently hampered by a lack of knowledge on the spectral separability between native and invasive species. We used spaceborne imaging spectroscopy to analyze the seasonal dynamics of the canopy hyperspectral reflectance properties of four tree species: (i) Metrosideros polymorpha , a keystone native Hawaiian species; (ii) Acacia koa , a native Hawaiian nitrogen fixer; (iii) the highly invasive Psidium cattleianum ; and (iv) Morella faya , a highly invasive nitrogen fixer. The species specific separability of the reflectance and derivative-reflectance signatures extracted from an Earth Observing-1 Hyperion time series, composed of 22 cloud-free images spanning a period of four years and was quantitatively evaluated using the Separability Index (SI). The analysis revealed that the Hawaiian native trees were universally unique from the invasive trees in their near-infrared-1 (700–1,250 nm) reflectance (0.4 > SI > 1.4). Due to its higher leaf area index, invasive trees generally had a higher near-infrared reflectance. To a lesser extent, it could also be demonstrated that nitrogen-fixing trees were spectrally unique from non-fixing trees. The higher leaf nitrogen content of nitrogen-fixing trees was expressed through slightly increased separabilities in visible and shortwave-infrared reflectance wavebands (SI = 0.4). We also found phenology to be key to spectral separability analysis. As such, it was shown that the spectral separability in the near-infrared-1 reflectance
Mcl-1 determines the Bax dependency of Nbk/Bik-induced apoptosis

B cell lymphoma 2 (Bcl-2) homology domain 3 (BH3)–only proteins of the Bcl-2 family are important functional adaptors that link cell death signals to the activation of Bax and/or Bak. The BH3-only protein Nbk/Bik induces cell death via an entirely Bax-dependent/Bak-independent mechanism. In contrast, cell death induced by the short splice variant of Bcl-x depends on Bak but not Bax. This indicates that Bak is functional but fails to become activated by Nbk. Here, we show that binding of myeloid cell leukemia 1 (Mcl-1) to Bak persists after Nbk expression and inhibits Nbk-induced apoptosis in Bax-deficient cells. In contrast, the BH3-only protein Puma disrupts Mcl-1–Bak interaction and triggers cell death via both Bax and Bak. Targeted knockdown of Mcl-1 overcomes inhibition of Bak and allows for Bak activation by Nbk. Thus, Nbk is held in check by Mcl-1 that interferes with activation of Bak. The finding that different BH3-only proteins rely specifically on Bax, Bak, or both has important implications for the design of anticancer drugs targeting Bcl-2.