Miracle-dz/UniFAR-FTUs huggingface dataset:
Correlation Between SUVmax and CT Radiomic Analysis Using Lymph Node Density in PET/CT-Based Lymph Node Staging

In patients with lung cancer (LC), malignant melanoma (MM), gastroenteropancreatic neuroendocrine tumors (GEP NETs), and prostate cancer (PCA), lymph node (LN) staging is often performed by 18F-FDG PET/CT (LC and MM), 68Ga-DOTATOC PET/CT (GEP NET), and 68Ga-labeled prostate-specific membrane antigen PET/CT (PCA) but is sometimes not accurate because of indeterminate PET findings. To better evaluate malignant LN infiltration, additional surrogate parameters, especially in cases with indeterminate PET findings, would be helpful. The purpose of this study was to evaluate whether SUVmax in the PET examination might correlate with semiautomated density measurements of LNs in the CT component of the PET/CT examination. Methods: After approval by the institutional review board, 1,022 LNs in the PET/CT examinations of 148 patients were retrospectively analyzed (LC: 327 LNs of 40 patients; MM: 224 LNs of 33 patients; GEP NET: 217 LNs of 35 patients; and PCA: 254 LNs of 40 patients). PET/CT was performed before surgery, biopsy, chemotherapy, or internal or external radiation therapy, according to the clinical schedule; patients with prior chemotherapy or radiation therapy were excluded. SUVmax analyses were based on uptake 60 min after tracer injection, and volumetric CT histogram analyses were based on the unenhanced CT images of the PET/CT scan. Results: PET findings were considered positive or negative on the basis of SUVmax in the LN compared with that in the blood pool; histologic confirmation was not available. Of the 1,022 LNs, 331 were PET-positive (3 times the SUVmax of the blood pool), 86 were PET-indeterminate (1–3 times the SUVmax of the blood pool), and 605 were PET-negative (less than the SUVmax of the blood pool). PET-positive LNs had significantly higher CT densities than PET-negative LNs, irrespective of the type of cancer. Conclusion: CT density measurements of LNs in patients with LC, MM, GEP NET, and PCA correlated with18F-FDG uptake, 68Ga-DOTATOC uptake, and 68Ga-PSMA uptake, respectively, and might therefore serve as an additional surrogate parameter for differentiating between malignant and benign LNs. The use of a 7.5–Hounsfield unit CT density threshold to differentiate between malignant and benign LN infiltration and 20 Hounsfield units to exclude benign LN processes might be possible in clinical routine and would be especially helpful for PET-indeterminate LNs.
STAC‐A2 on Intel architecture: evolving from scalar code to heterogeneous applications

STAC‐A2™ is a compute and memory intensive industry benchmark in the field of market risk analysis. The benchmark specifications were created by the Securities Technology Analysis Center (STAC®), and are based on the inputs collected from the leading trading companies, universities, and high performance computing vendors. The specifications describe models that represent realistic market risk analysis workloads. In this paper, we discuss the development steps that lead to the competitive performance of the STAC‐A2 benchmark executed on systems consisting of Intel® Xeon® processors and an Intel® Xeon Phi™ coprocessor. We show the importance of the utilization of all parallel resources available on Intel architectures to achieve maximum performance. We demonstrate that the offload extension supported by Intel® Composer XE minimizes the efforts required to create accelerated applications by using only C/C++ language. With Intel's latest implementation of the STAC‐A2 benchmark, we were able to achieve a significant (800%) performance gain by using a heterogeneous approach running on two Intel Xeon E5‐2699 v3 processors and a single Intel® Xeon Phi™ 7120A card, compared with earlier version running on only two Intel Xeon E5‐2697 v2 processors. Copyright © 2016 John Wiley & Sons, Ltd.
Colony immunoblot assay for the detection of staphylococcal toxic shock syndrome toxin 1 (TSST-1) with anti-TSST-1 F(ab')2 fragments

Toxic shock syndrome toxin 1 (TSST-1), an exoprotein of Staphylococcus aureus, is strongly implicated in the pathogenesis of TSS. Detection of TSST-1, however, is often hindered in immunoassays because of the cosecretion of protein A, a genetic trait which appears to be coordinately expressed with other exoproteins in S. aureus. We developed a colony immunoblot assay for rapid screening of TSST-1-producing S. aureus using TSST-1-specific rabbit F(ab')2 fragments. The sensitivity and specificity of this method were compared with those of a quantitative noncompetitive enzyme-linked immunosorbent assay (ELISA) for 34 S. aureus isolates (17 TSS-associated and 17 non-TSS-associated isolates). Cosecreted protein A in culture supernatants was evaluated by a quantitative competitive ELISA. The results clearly indicated the superiority of F(ab')2 fragments in eliminating nonspecific reactivity of protein A in the colony immunoblot assay. The sensitivity of the immunoblot with TSST-1-specific F(ab')2 was similar to that with whole immunoglobulin G (94 versus 82%, respectively; P = 0.601, Fisher's exact test), but the specificity was markedly improved (94 versus 59%, respectively; P = 0.039). Among TSST-1-negative isolates (as determined by ELISA), strains which gave false-positive results in the immunoglobulin G immunoblot assay produced higher amounts of protein A than strains which gave true-negative results (P = 0.08, Mann-Whitney rank sum test, one tailed). Among strains positive for TSST-1, the level of TSST-1 detected in culture supernatants correlated inversely with the amount of protein A secreted (rs = -0.64; P less than 0.01, Spearman rank correlation). These findings validate the utility of a rapid screening method for the detection of TSST-1-producing S. aureus and support the concept of coordinate secretion of exoproteins in S. aureus.
Effects of dietary history on energy metabolism and physiological parameters in C57BL/6J mice

• What is the central question of this study? Do intake patterns of diets with a different energy content have a lasting effect on body weight persistence? • What is the main finding and its importance? After switches between semi‐purified diets differing only in the fat‐to‐sugar ratio, the last consumed diet determined the energy intake, energy expenditure, body weight, body fat stores, circulating hormones and metabolites in C57BL/6J mice. In contrast with persistent effects observed in studies using diets with different ingredients, suggesting diet‐induced set points, this study shows that body weight and metabolic parameters ‘settle’ based on current energetic input and output. This supports the settling point theory and underlines the importance of the choice of diet in physiological studies.
Variability in performance: identifying early signs of future cognitive impairment.

OBJECTIVE The current study examined whether year-to-year variability in cognitive performance differ between individuals cognitively unimpaired and individuals who subsequently develop dementia. METHOD Analyses included a case-control sample of Baltimore Longitudinal Study of Aging (BLSA; mean [M] age = 69.90, standard deviation [SD] = 8.92) participants. One hundred and 35 clinically diagnosed demented participants were matched with 135 nondemented participants based on age at initial testing and sex. Cognitive performance was examined using measures of memory, executive function, attention, language, and global mental status performance. Cognitive performance was examined from baseline to 5 years before cognitive impairment (M, assessments = 3.03, SD = 2.80). RESULTS As compared with unimpaired individuals, individuals diagnosed with dementia had greater variability on measures of attention, executive function, language, and semantic memory at least 5 years before the estimated onset of cognitive impairment, which may be indicative of maladaptive cognitive functioning. The dementia cases, however, had less variability on visual memory than the unimpaired group, which may suggest that these cases had more difficulty learning. CONCLUSIONS These results demonstrate that performance variability indexed over annual or biennial visits may be useful in identifying early signs of subsequent cognitive impairment.
Trade Liberalization and its Effects on the Economic Growth of Bangladesh: An Empirical Analysis

The objective of this paper is to assess the effectiveness of the trade policy on Bangladesh economy between the periods 1990 to 2010. This research analyzes the achievements of the economy regarding the important variables such as growth of GDP, export, import, exchange rate, terms of trade, and foreign reserve after the trade liberalization in 1990s. The study demonstrates that the inward policy of the trade liberalization reduces the import while the forward policy increases the employment, production, and export. Finally, liberalization policy improves overall economic indicators as GDP per capita, FDI, and remittances have been growing up since pre-liberalization. The study shows that both export and import have increased noticeably since liberalization, with import rising faster than export in the period immediately after liberalization.
Propoxyphene and norpropoxyphene: Influence of diet and fluid on plasma levels

The influence of various test meals and ingested fluid volumes on the bioavailability and pharmacokinetics of propoxyphene and its major metabolite norporpoxyphene has been studied in healthy human subjects. The absorption of drug was delayed by all test meals, but the overall efficiency of absorption was either not affected or was slightly increased. Increased fluid volume intake decreased propoxyphene bioavailability. Plasma levels of metabolite correlated well with levels of unchanged drug, particularly in the first 2 hr after dosing, but were not markedly influenced by treatments.
A Dynamic Capabilities Perspective of High-Growth Firms: Organizational Aspects

Abstract Drawing on interviews conducted at five Hungarian high-growth firms (HGFs), this paper discusses how dynamic capabilities shape the outcome of HGFs’ efforts to meet the managerial challenges posed by rapid growth. HGFs are investigated in the context of a relatively under-researched country: Hungary. The research demonstrates that dynamic capabilities have strong explanatory power for the surveyed companies’ achievements, in a similar manner to what is established in the literature on HGFs in advanced economies. The micro-mechanisms of DC’ deployment is explored by investigating the organizational solutions implemented at the surveyed firms in response to emerging growth-related problems. These responses were found to be similar across the sample. The recurrent growth-related reconfiguration of organizational structures and introduction of various organizational innovations were the result of systematically developed DC and non-abating organizational learning.
Flexible and Robust Methods for Rare‐Variant Testing of Quantitative Traits in Trios and Nuclear Families

Most rare‐variant association tests for complex traits are applicable only to population‐based or case‐control resequencing studies. There are fewer rare‐variant association tests for family‐based resequencing studies, which is unfortunate because pedigrees possess many attractive characteristics for such analyses. Family‐based studies can be more powerful than their population‐based counterparts due to increased genetic load and further enable the implementation of rare‐variant association tests that, by design, are robust to confounding due to population stratification. With this in mind, we propose a rare‐variant association test for quantitative traits in families; this test integrates the QTDT approach of Abecasis et al. [Abecasis et al., ] into the kernel‐based SNP association test KMFAM of Schifano et al. [Schifano et al., ]. The resulting within‐family test enjoys the many benefits of the kernel framework for rare‐variant association testing, including rapid evaluation of P‐values and preservation of power when a region harbors rare causal variation that acts in different directions on phenotype. Additionally, by design, this within‐family test is robust to confounding due to population stratification. Although within‐family association tests are generally less powerful than their counterparts that use all genetic information, we show that we can recover much of this power (although still ensuring robustness to population stratification) using a straightforward screening procedure. Our method accommodates covariates and allows for missing parental genotype data, and we have written software implementing the approach in R for public use.
Assessing the effectiveness of business incubators in fostering SMEs: evidence from China

The number of business incubators (BIs) in China has grown at an astonishing pace through the decades since their establishment. We investigated the effectiveness of China's business incubators as a government tool of cultivating small-medium sized enterprises (SMEs) by relating their service offerings to SMEs' performance. Using data on China's 120 state-level business incubators from 2008 to 2012 and data on the metropolises that host them, we find no evidence that infrastructure support contributes to intellectual property generation or venture capital acquisition. The results suggest a modest contribution of BIs' business assistance to SMEs' access to venture capital. Moreover, the findings confirm that professional technical assistance is valuable for SMEs' growth in the Chinese context. Additionally, we find that incubator's age and number of tenants are significantly positively correlated with the incubator firms' performance.
Clinical trials in neuro-oncology

Clinical trials are prospective scientific studies involving human participants and form the basis for identifying new treatments for diseases like brain tumors. A clinical trial should be designed to provide definitive results for a study question. Therefore, investigators should understand the principles underlying the design, execution and analysis of clinical trials. In addition to the application of basic principles germane to the design of all clinical trials, studies in neuro-oncology also involve unique challenges in case definition, selection of endpoints and definition of response. This review begins with enumeration of the basic principles of clinical trial design including reduction of bias and variability, and concludes with a review of study design factors of particular relevance for neuro-oncology.
Detection and Identification of Theileria Infection In Sika Deer (Cervus nippon) In China

Abstract: The sika deer (Cervus nippon) is a first-grade state-protected animal in China and designated a threatened species by the World Conservation Union. To detect hemoparasite infection of sika deer, blood samples were collected from 24 animals in the Hubei Province Deer Center. Genomic DNA was extracted, and the V4 hypervariable region encoding 18S rRNA was analyzed by reverse line blot hybridization assay. PCR products hybridized with Babesia/Theileria genus-specific probes but failed to hybridize with any of the Babesia or Theileria species-specific probes, suggesting the presence of a novel, or variant, species. Here 18S rRNA and internal transcribed spacer (ITS) genes were amplified, cloned, and sequenced from 7 isolates. Alignment and BlastN of the cloned sequences revealed high similarities to the homologous 18S rRNA genes and ITS genes of Theileria cervi (AY735122), Theileria sp. CNY1A (AB012194), and Theileria sp. ex Yamaguchi (AF529272). Phylogenetic analysis based on the 18S rRNA gene and ITS sequences showed that all cloned sequences were grouped within the Theileria clade. Phylogeny based on the 18S rRNA gene divided the organisms into 2 groups. Group 1 was closest to Theileria sp. ex Yamaguchi (AF529272), and group 2 was distinct from all other identified Theileria and Babesia species. These results suggest the existence of Theileria sp. infection in sika deer in China. To our knowledge, this is the first report of cervine Theileria sp. in China.
Modality-Switching in the Simon Task: The Clash of Reference Frames

The representation of spatial information related to an event can influence behavior even when location is task-irrelevant, as in the case of Stimulus–Response (S-R) compatibility effects on the Simon task. However, unlike single-modality situations, which are often used to study the Simon effect, in real-life scenarios various sensory modalities provide spatial information coded in different coordinate systems. Here, we address the expression of S-R compatibility effects in mixed-modality contexts, where events can occur in 1 of various sensory modalities (i.e., vision, touch or audition). The results confirm that, in single-modality cases, Simon effects in vision are expressed in an external spatial frame of reference, while touch information is coded anatomically. Remarkably, when mixing visual and tactile trials in an unpredictable way, the Simon effect disappeared in vision whereas tactile Simon effects remained expressed in their own (anatomical) frame of reference. Mixing visual and auditory stimuli did not obliterate the visual Simon effect and S-R compatibility effects in an external reference frame were evident for both modalities. The extinction of visual Simon effects as a result of mixing visual and tactile modalities can be interpreted as a consequence of the dynamic reorganization of the weights associated to the different sources of spatial information at play.
A chicken model of pharmacologically-induced Hirschsprung disease reveals an unexpected role of glucocorticoids in enteric aganglionosis

The enteric nervous system originates from neural crest cells that migrate in chains as they colonize the embryonic gut, eventually forming the myenteric and submucosal plexus. Failure of the neural crest cells to colonize the gut leads to aganglionosis in the terminal gut, a pathological condition called Hirschsprung disease (HSCR) in humans, also known as congenital megacolon or intestinal aganglionosis. One of the characteristics of the human HSCR is its variable penetrance, which may be attributable to the interaction between genetic factors, such as the endothelin-3/endothelin receptor B pathway, and non-genetic modulators, although the role of the latter has not well been established. We have created a novel HSCR model in the chick embryo allowing to test the ability of non-genetic modifiers to alter the HSCR phenotype. Chick embryos treated by phosphoramidon, which blocks the generation of endothelin-3, failed to develop enteric ganglia in the very distal bowel, characteristic of an HSCR-like phenotype. Administration of dexamethasone influenced the phenotype, suggesting that glucocorticoids may be environmental modulators of the penetrance of the aganglionosis in HSCR disease.
Using Physiome standards to couple cellular functions for rat cardiac excitation–contraction

Scientific endeavour is reliant upon the extension and reuse of previous knowledge. The formalization of this process for computational modelling is facilitated by the use of accepted standards with which to describe and simulate models, ensuring consistency between the models and thus reducing the development and propagation of errors. CellML 1.1, an XML‐based programming language, has been designed as a modelling standard which, by virtue of its import and grouping functions, facilitates model combination and reuse. Using CellML 1.1, we demonstrate the process of formalized model reuse by combining three separate models of rat cardiomyocyte function (an electrophysiology model, a model of cellular calcium dynamics and a mechanics model) which together make up the Pandit–Hinch–Niederer et al. cell model. Not only is this integrative model of rat electromechanics a useful tool for cardiac modelling but it is also an ideal framework with which to demonstrate both the power of model reuse and the challenges associated with this process. We highlight and classify a number of these issues associated with combining models and provide some suggested solutions.
Intercurrent infection predicts mortality in patients with late hepatic artery thrombosis listed for liver retransplantation

Liver retransplantation for late hepatic artery thrombosis (HAT) is considered the treatment of choice for select patients. Nevertheless, there is a paucity of data to aid decision making in this setting. The aims of this single‐center study of patients listed for late HAT were (1) to determine variables associated with wait‐list mortality, (2) to describe survival after retransplantation, and (3) to determine variables associated with mortality after retransplantation. Seventy‐eight patients were diagnosed with late HAT (incidence = 3.9%). Of the 49 patients listed for retransplantation, 9 died on the waiting list and 36 were retransplanted. The estimated 1‐year survival after listing for retransplantation was 53.7%. Only multidrug‐resistant (MDR) bacteria–positive cultures were predictive of wait‐list mortality (P = 0.01). After retransplantation, the estimated 1‐ and 5‐year patient survival was 71.9% and 62.5%, respectively. Increasing Model for End‐Stage Liver Disease score (overall P = 0.007), MDR bacteria–positive cultures (P = 0.047), and continued antibiotic therapy (P = 0.001) at the time of retransplantation were risk factors for post retransplant death. In conclusion, patients who undergo liver retransplantation for late HAT have satisfactory outcomes. However, the presence of active infection and MDR bacteria–positive cultures should be taken into account when risk stratifying such patients. Liver Transpl, 2012. © 2012 AASLD.
Methylselenol, a Selenium Metabolite, Plays Common and Different Roles in Cancerous Colon HCT116 Cell and Noncancerous NCM460 Colon Cell Proliferation

Methylselenol is hypothesized to be a critical selenium metabolite for anticancer action, and differential chemopreventive effects of methylselenol on cancerous and noncancerous cells may play an important role. In this study, the submicromolar concentrations of methylselenol were generated by incubating methionase with seleno-L methionine, and colon-cancer-derived HCT-116 cells and noncancerous colon NCM460 cells were exposed to methylselenol. Methylselenol exposure inhibited cell growth and led to an increase in G1 and G2 fractions with a concomitant drop in S-phase and an induction of apoptosis in HCT116, but to a much lesser extent in NCM460 colon cells. Similarly, the examination of mitogen-activated protein kinase (MAPK) and cellular myelocytomatosis oncogene (c-Myc) signaling status revealed that methylselenol inhibited the phosphorylation of extracellular-regulated kinase1/2 and p38 mitogen-activated protein kinase and the expression of c-Myc in HCT116 cells, but also to a lesser extent in NCM460 cells. The other finding is that methylselenol inhibits sarcoma kinase phosphorylation in HCT116 cells. In contrast, methylselenol upregulated the phosphorylation of sarcoma and focal adhesion kinase survival signals in the noncancerous NCM460 cells. Collectively, methylselenol's stronger potential of inhibiting cell proliferation/survival signals in the cancerous HCT116 cells when compared with that in noncancerous NCM460 cells may partly explain the potential of methylselenol's anticancer action.