Miracle-dz/UniFAR-FTUs huggingface dataset:
Phase I Study of Oncolytic Vaccinia Virus GL-ONC1 in Patients with Peritoneal Carcinomatosis

Purpose: Peritoneal carcinomatosis is common in advanced tumor stages or disease recurrence arising from gastrointestinal cancers, gynecologic malignancies, or primary peritoneal carcinoma. Because current therapies are mostly ineffective, new therapeutic approaches are needed. Here, we report on a phase I study designed to assess safety, MTD, and antitumor activity of intraperitoneal administration of oncolytic vaccinia virus GL-ONC1 in advanced stage peritoneal carcinomatosis patients. Patients and Methods: GL-ONC1 was administered intraperitoneally every 4 weeks for up to four cycles at three different dose levels (107–109 pfu) following a standard 3+3 dose escalation design. GL-ONC1 was infused via an indwelling catheter that enabled repetitive analyses of peritoneal fluid biopsies. The primary study objective was safety of GL-ONC1 according to Common Terminology Criteria for Adverse Events, version 4.0 (CTCAEv4.0). Results: Patients with advanced-stage peritoneal carcinomatosis (n = 7) or advanced peritoneal mesothelioma (n = 2) received 24 doses of GL-ONC1. Adverse events were limited to grades 1–3, including transient flu-like symptoms and increased abdominal pain, resulting from treatment-induced peritonitis. No DLT was reported, and the MTD was not reached. Furthermore, no signs of viral shedding were observed. Importantly, in 8 of 9 study patients, effective intraperitoneal infections, in-patient replication of GL-ONC1, and subsequent oncolysis were demonstrated in cycle 1. All patients developed neutralizing activities against GL-ONC1. Conclusions: GL-ONC1 was well tolerated when administered into the peritoneal cavity of patients with advanced stage peritoneal carcinomatosis. Efficient tumor cell infection, in-patient virus replication, and oncolysis were limited to treatment cycle 1 (ClinicalTrials.gov number, NCT01443260). Clin Cancer Res; 24(18); 4388–98. ©2018 AACR.
The importance of non-regional lymph nodes in assigning risk in primary metastatic prostate cancer.

227Background: Patients diagnosed with non-regional lymph nodes (NRLN) in isolation exhibit a more prolonged clinical course than those with bone or visceral metastases in trial data, but evaluation of survival data in general populations is sparse and their presence doesn’t feature in risk estimations based on tumour volume. Methods: The evaluation and prognostic relevance of NRLN metastasis presenting synchronously with osseous or non-ossesous metastasis in hormone-naive prostate cancer was evaluated using the Surveillance, Epidemiology and End-results (SEER) database. Patients with stage M1a-c PCa diagnosed between 2004 and 2009 were identified and included within the analysis. Kaplan Meier was used to estimate overall (OS) and cancer specific survival (CSS) rates in relation to metastatic distribution. Multivariate cox-regression models were used to identify predictors of OS and CSS. Results: Of 4869 metastatic PCa patients identified, osseous metastasis was the most common finding (65.1%); followed b.
Fast learning of scale‐free networks based on Cholesky factorization

Recovering network connectivity structure from high‐dimensional observations is of increasing importance in statistical learning applications. A prominent approach is to learn a Sparse Gaussian Markov Random Field by optimizing regularized maximum likelihood, where the sparsity is induced by imposing L1 norm on the entries of a precision matrix. In this article, we shed light on an alternative objective, where instead of precision, its Cholesky factor is penalized by the L1 norm. We show that such an objective criterion possesses attractive properties that allowed us to develop a very fast Scale‐Free Networks Estimation Through Cholesky factorization (SNETCH) optimization algorithm based on coordinate descent, which is highly parallelizable and can exploit an active set approach. The approach is particularly suited for problems with structures that allow sparse Cholesky factor, an important example being scale‐free networks. Evaluation on synthetically generated examples and high‐impact applications from a biomedical domain of up to more than 900,000 variables provides evidence that for such tasks the SNETCH algorithm can learn the underlying structure more accurately, and an order of magnitude faster than state‐of‐the‐art approaches based on the L1 penalized precision matrix.
Long term potentiation affects intracellular metalloproteinases activity in the mossy fi ber — CA 3 pathway

a Laboratory of Neuroscience, Department of Biophysics, Wroclaw Medical University, Chalubinskiego 3, 50‐368, Wroclaw, Poland b Department of Animal Molecular Physiology, Zoological Institute, Wroclaw University, Cybulskiego 30, 50‐205, Wroclaw, Poland c Department of Histology and Embryology, Wroclaw Medical University, Chalubinskiego 6A, 50‐368, Wroclaw, Poland d Anatomical Neuropharmacology Unit, Medical Research Council, Mansfield Road, Oxford OX1 3TH, United Kingdom e Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute, Ludwika Pasteura 3, 02‐093, Warsaw, Poland f Department of Molecular and Cellular Neurobiology, Nencki Institute, Ludwika Pasteura 3, 02‐093, Warsaw, Poland
Interference Analysis in Dynamic TDD System Combined or not with Cell Clustering Scheme

Dynamic Time Division Duplex (TDD) has been introduced as a solution to deal with the uplink and downlink traffic asymmetry, mainly observed for dense heterogeneous network deployments. However, the use of this feature requires new interference mitigation schemes capable to handle two additional types of interferences between cells in opposite transmission cycle: downlink to uplink and uplink to downlink interferences. Among them, Cell clustering has been proposed as an efficient solution to minimize inter-cell interferences in opposite transmission directions and somehow responds to the requirements of enhanced Interference Mitigation and Traffic Adaptation (eIMTA) problem. This work is devoted to provide a new analytical approach to model inter-cell interferences and quantify performances of Dynamic TDD system in terms of SINR (Signal to Interferences plus Noise Ratio) distribution. Analytical system performance investigation concerns two scenarios: i) basic Dynamic TDD without any other feature and ii) Dynamic TDD with interference mitigation schemes.
Evaluation of Automatic Formant Trackers

Four open source formant trackers, three LPC-based and one based on Deep Learning, were evaluated on the same American English data set VTR-TIMIT. Test data were time-synchronized to avoid differences due to different unvoiced/voiced detection strategies. Default output values of trackers (e.g. producing 500Hz for the first formant, 1500Hz for the second etc.) were filtered from the evaluation data to avoid biased results. Evaluations were performed on the total recording and on three American English vowels [i:], [u] and [ ] ʌ separately. The obtained quality measures showed that all three LPC-based trackers had comparable RSME error results that are about 2 times the inter-labeller error of human labellers. Tracker results were biased considerably (in average too high or low), when the parameter settings of the tracker were not adjusted to the speaker's sex. Deep Learning appeared to outperform LPC-based trackers in general, but not in vowels. Deep Learning has the disadvantage that it requires annotated training material from the same speech domain as the target speech, and a trained Deep Learning tracker is therefore not applicable to other languages.
Cross-Layer Optimization for Virtual Machine Resource Management

Virtualized systems (e.g., public and private clouds) are playing an increasingly vital role to support the computing of applications from different domains. Existing resource management solutions in such systems typically treat virtual machines (VMs) as black boxes, which presents a hurdle to achieving application-desired Quality of Service (QoS). This paper advocates the cooperation between VM host- and guest-layer schedulers for optimizing the resource management and application performance. It presents an approach to such cross-layer optimization by enabling the host-layer scheduler to feedback resource allocation decisions and adapt guest-layer application configurations. As case studies, the proposed approach is applied to virtualized databases and map services which have challenging dynamic and complex resource demands as well as sophisticated configurations. Specifically, for databases, the proposed approach adapts query executions by tuning the cost model parameters according to the available storage bandwidth and memory capacity. For map services, it adapts the quality of returned map imagery in order to meet the response time target as the workload intensity and available network bandwidth change over time. A prototype of the proposed approach is implemented on Xen and Hyper-V VMs, and evaluated using a TPC-H based database workload and a TerraFly-based map service workload. The results show that with the proposed host-to-guest application adaptation, the TPC-H workload improves its performance by 33.5%, and the TerraFly workload improves the map imagery quality by 40% and always meets its response time target, compared to the schemes without adaptation.
Accurate Face Reconstruction through Anisotropic Fitting and Eye Correction

Fitting a facial template model to 3D-scanner data is a powerful technique for generating face avatars, in particular in the presence of noisy and incomplete measurements. Consequently, there are many approaches for the underlying non-rigid registration task, and these are typically composed from very similar algorithmic building blocks. By providing a thorough analysis of the different design choices, we derive a face matching technique tailored to high quality reconstructions from high resolution scanner data. We then extend this approach in two ways: An anisotropic bending model allows us to more accurately reconstruct facial details. A simultaneous constrained ﬁtting of eyes and eye lids improves the reconstruction of the eye region considerably
Effect of 2 Psoriasis Treatments on Vascular Inflammation and Novel Inflammatory Cardiovascular Biomarkers: A Randomized Placebo-Controlled Trial

Background: Psoriasis is a chronic inflammatory disease associated with dyslipidemia, cardiovascular events, and mortality. We aimed to assess and compare the effect of treatment of moderate-to-severe psoriasis with adalimumab or phototherapy on vascular inflammation and cardiovascular biomarkers. Methods and Results: Randomized, double-blind, trial of adalimumab, phototherapy, and placebo (1:1:1) for 12 weeks, with crossover to adalimumab for 52 weeks total. Outcomes included vascular inflammation by 18F-fluorodeoxyglucose positron emission tomography/computed tomography and biomarkers of inflammation, insulin resistance, and lipoproteins. Ninety-seven patients were randomized, 92 completed the randomized controlled trial portion; 81 entered the adalimumab extension with 61 completing 52 weeks of adalimumab. There was no difference in change in vascular inflammation at week 12 in the adalimumab group (change compared with placebo, 0.64%; 95% confidence interval, −5.84% to 7.12%) or the phototherapy group (−1.60%; 95% confidence interval, −6.78% to 3.59%) or after 52-week adalimumab treatment (0.02% compared with initiation; 95% confidence interval, −2.85% to 2.90%). Both adalimumab and phototherapy decreased inflammation by serum CRP, interleukin-6. Only adalimumab reduced tumor necrosis factor and glycoprotein acetylation at 12 and 52 weeks. Neither had an impact on metabolic markers (insulin, adiponectin, and leptin). Only phototherapy increased high-density lipoprotein-p at 12 weeks. At 52-week of adalimumab cholesterol efflux and high-density lipoprotein-p were reduced. Conclusions: Adalimumab reduced key markers of inflammation including glycoprotein acetylation compared with phototherapy with no effect on glucose metabolism and vascular inflammation, and potential adverse effects on high-density lipoprotein. Glycoprotein acetylation improvement may partially explain the beneficial effects of adalimumab seen in observational studies. Larger studies with more detailed phenotyping of vascular disease should assess the comparative differences in the effects of adalimumab and phototherapy seen in our study. Clinical Trial Registration : URL: https://www.clinicaltrials. gov. Unique identifiers: NCT01866592 and NCT01553058.
Performance of pairwise shape dissimilarity morphometrics on nonmammalian taxa (Insecta: Neuroptera: Mantispidae)

Morphometric dissimilarity metrics aim to quantify the variation between compared specimens such that inferences about their relatedness and alpha taxonomy can be made. Recently, the technique has developed metrics that purport to quantify shape dissimilarity between specimens—employing the use of least squares regression analysis. These metrics have been well applied by studies in the hominin fossil record with an arguably unsubstantiated backing for the technique. Originally postulated was the log10 sem metric which subsequently led to the standard error test of the null hypothesis metric. Following this, the standard deviation of logged ratios (SLR) metric arose as a pairwise dissimilarity metric that constrains the regression to a zero‐intercept, that is, a significant development in the robustness of the technique. This metric was tested on extant primates in order to evaluate its effectiveness alongside the two other metrics. It was shown to be the most reliable for comparisons between specimens of primates, but was unable to discriminate between heterospecific and conspecific comparisons. Arguably, an alternative model organism with which to compare the technique is lacking. This study considers shape dissimilarity metrics with respect to a group of nonmammalian organisms (mantidflies) and tests the metrics against three lines of evidence (morphology, CO1‐DNA, and geographic distribution) that can delimit the species‐level taxonomy for the group. It is shown that the metrics are unable to discriminate between pairwise comparisons of closely related species, resulting in biologically erroneous groupings, and contradicting the groupings derived from morphological, CO1‐DNA, and distributional comparisons. It is thus asserted that the technique is unsuitable for use in alpha taxonomy as an additional line of evidence in mantidflies. It is further supposed that morphometrics in general should be employed with caution in studies of evolutionary history as phylogeny is not the only information contained within morphometric data. J. Morphol. 276:1482–1494, 2015. © 2015 Wiley Periodicals, Inc.
Public health and economic impact of dampness and mold.

UNLABELLED The public health risk and economic impact of dampness and mold exposures was assessed using current asthma as a health endpoint. Individual risk of current asthma from exposure to dampness and mold in homes from W.J. Fisk, Q. Lei-Gomez & M.J. Mendell [(2007) Indoor Air, [corrected] 17, 284-296], and [corrected] asthma risks calculated from additional studies that reported the prevalence of dampness and mold in homes were used to estimate the proportion of US current asthma cases that are attributable to dampness and mold exposure at 21% (95% confidence internal 12-29%). An examination of the literature covering dampness and mold in schools, offices, and institutional buildings, which is summarized in the Appendix, suggests that risks from exposure in these buildings are similar to risks from exposures in homes. Of the 21.8 million people reported to have asthma in the USA, approximately 4.6 (2.7-6.3) million cases are estimated to be attributable to dampness and mold exposure in the home. Estimates of the national cost of asthma from two prior studies were updated to 2004 and used to estimate the economic impact of dampness and mold exposures. By applying the attributable fraction to the updated national annual cost of asthma, the national annual cost of asthma that is attributable to dampness and mold exposure in the home is estimated to be $3.5 billion ($2.1-4.8 billion). Analysis indicates that exposure to dampness and mold in buildings poses significant public health and economic risks in the USA. These findings are compatible with public policies and programs that help control moisture and mold in buildings. PRACTICAL IMPLICATIONS There is a need to control moisture in both new and existing construction because of the significant health consequences that can result from dampness and mold. This paper demonstrates that dampness and mold in buildings is a significant public health problem with substantial economic impact.
Competitive intelligence practices of European firms

ABSTRACT This article presents the results of a survey of competitive intelligence (CI) practices in European firms. In comparing the results to a similar 2006 global study and a 2006 European CI study, it appears that the breadth of applications for CI has grown well beyond competitors to include customer related intelligence, technology, market, etc. Innovation is driving much intelligence activity, in particular research and development (R&D) and new product development decisions. CI is more formalised now in European firms than it was in 2006. The study also found similarities between corporate foresight and CI in terms of objectives (development and maintenance of competitive advantage, help with decision making) and analytical techniques with scenarios being among the more frequently used analytical techniques along with STEEP and other environmental analysis in both corporate foresight studies and the CI study.
KLF 5 mediates the hyper-proliferative phenotype of the intestinal epithelium in mice with intestine-specific endogenous K-RasG 12 D expression

Oncogenic K-Ras activation is a common mutational event in colorectal cancer. We previously showed that transcription factor, Krüppel-like factor 5 (KLF5), contributes to intestinal polyposis in mice with K-Ras activation. At 14 months of age, Villin-Cre/LSL-K-RasG12D mice developed small intestinal and colonic hyperplastic polyps while LSL-K-RasG12D had none. The intestinal crypts of Villin-Cre/LSL-K-RasG12D mice contained a higher number of mitotic figures and increased crypt heights compared to controls. The intestinal epithelium of Villin-Cre/LSL-K-RasG12D mice showed prolific KLF5 expression throughout and above the elongated crypts. In contrast, KLF5 expression was limited to the upper crypt region in the controls. The levels of K-Ras effectors were significantly increased in VillinCre/LSL-K-RasG12D as compared to controls. The Villin-Cre/LSL-K-RasG12D mice showed decreased survival upon treatment with azoxymethane (AOM) as compared to controls. Furthermore, loss of one of Klf5 alleles reduced levels of K-Ras effector proteins and prevented mortality of Villin-Cre/LSL-K-RasG12D mice upon AOM treatment. The Villin-Cre/LSL-K-RasG12D mice spontaneously develop hyperplastic intestinal polyps and display a hyper-proliferative intestinal phenotype with elongated crypts, increased numbers of mitotic figures, elevated expression of KLF5, and other pro-proliferative targets. Induction of colonic tumorigenesis with AOM is detrimental to Villin-Cre/LSL-K-RasG12D mice that is in part dependent of KLF5.
Exact Analytical Formula for the Excess Noise Factor for Mixed Carrier Injection Avalanche Photodiodes

The well-known analytical formula for the excess noise factor associated with avalanche photodiodes (APDs), developed by R. J. McIntyre in 1966, assumes the injection of either an electron or a hole at the edge of the APD's avalanche region. This formula is based on the statistics of the probabilities of carriers gaining and losing energy subject to high electric fields. However, this analytical formula, is not applicable in cases when photons are absorbed inside the avalanche region (even though the physics of the high field transport remains the same), and its use may severely underestimate or overestimate the actual excess noise factor depending on the absorption profile and the hole-to-electron ionization coefficient ratio, k. Here, an easy-to-use exact analytical formula is derived for the excess noise factor of APDs while taking into account a mixed-carrier initiated avalanche multiplication process, which is triggered by a parent electron-hole pair at an arbitrarily specified location within the multiplication region. The derivation relies on analytically solving a special case of a previously reported recursive integral equations [Hayat et al., IEEE Trans. Electron Devices, vol. 39, no. 3, pp. 546–552, Mar. 1992. ], and the result matches the formula reported by McIntyre in 1999 using a different and limited technique. In addition, an expression for the excess noise factor is presented in the case when the location of the parent electron-hole pair within the multiplication region obeys an arbitrary exponential distribution. The results show that in contrast to the case of edge parent-electron injection, when mixed injection is allowed even a small level of hole ionization (e.g., small k ∼ 0.0001) causes the excess noise factor to increase dramatically, depending on the absorption profile as it ranges from narrow to flat within the multiplication region. The theoretical results are validated against experimental results for Si APDs.
Peritoneal cancer index as a predictor of survival in advanced stage serous epithelial ovarian cancer: a prospective study

Objective A numerical score, the peritoneal cancer index (PCI), was developed to reflect the extent of tumor growth in gastric and colorectal cancers and to tailor treatment. This study aimed to examine the value of the PCI score in advanced epithelial ovarian cancer (EOC) regarding completeness of surgical cytoreduction and survival. Methods This was a prospective observational cohort study. Patients with primary serous EOC at International Federation of Gynecology and Obstetrics (FIGO) stages IIIB or higher were included. Patients with FIGO stage IVB as well as those assigned to receive neoadjuvant treatment were excluded from the study. The PCI was obtained and registered intraoperatively. Results In the study period we recruited 96 patients with serous EOC stage IIIB–IVA. A PCI score cut-off value of 13 was calculated using a receiver operator characteristic (ROC) curve, above which worse survival is expected (area under the curve [AUC]=0.641; 95% confidence interval [CI]=0.517–0.765; sensitivity and specificity 80.6%, 45.0%, respectively; p=0.050). A multivariate analysis determined that suboptimal surgical cytoreduction was the only independent predictive factor for recurrence (odds ratio [OR]=7.548; 95% CI=1.473–38.675; p=0.015). A multivariate analysis determined that only suboptimal surgical cytoreduction (hazard ratio [HR]=2.33; 95% CI=0.616–8.795; p=0.005), but not PCI score >13 (HR=1.289; 95% CI=0.329–5.046; p=0.716), was an independent predictive factor for death. Conclusion We conclude from this study that the PCI score is a reliable tool helping to assess the extent of disease in advanced serous EOC patients and may help predicting complete surgical cytoreduction but cannot qualify as a predictor of survival.