Miracle-dz/UniFAR-FTUs huggingface dataset:
The use of in‐line intravenous filters in sick newborn infants

Aim: This study assesses the improvement in outcome for newborn infants by decreasing major complications associated with intravenous fluid therapy by using an in‐line filter, and evaluates the economical impact this might have in relation to daily changing of i.v. lines. Methods: In a prospective controlled study, 88 infants were randomly assigned to receive either filtered (except for lipids, blood and blood products) or non‐filtered infusions via a central catheter. Main outcome measures such as bacteraemia, phlebitis, extravasation, thrombosis, septicaemia and necrosis were all scored. The costs attributable to patients during a standard 8‐day stay were also recorded. Results: Significant reductions were found in major complications such as thrombi and clinical sepsis (control group (21), filter group (8); p < 0.05). Bacterial cultures of the filters showed a contamination rate on the upstream surface of 15/109 filters (14%). The mean costs of disposables were less in the filter group, showing a reduction from ±31.17 to ±23.79.
Lyapunov Spectral Intervals: Theory and Computation

Different definitions of spectra have been proposed over the years to characterize the asymptotic behavior of nonautonomous linear systems. Here, we consider the spectrum based on exponential dichotomy of Sacker and Sell [J. Differential Equations, 7 (1978), pp. 320--358] and the spectrum defined in terms of upper and lower Lyapunov exponents. A main goal of ours is to understand to what extent these spectra are computable. By using an orthogonal change of variables transforming the system to upper triangular form, and the assumption of integral separation for the diagonal of the new triangular system, we justify how popular numerical methods, the so-called continuous QR and SVD approaches, can be used to approximate these spectra. We further discuss how to verify the property of integral separation, and hence how to a posteriori infer stability of the attained spectral information. Finally, we discuss the algorithms we have used to approximate the Lyapunov and Sacker--Sell spectra and present some numerical results.
Research Statement for

Security Much of the blame for the mushrooming information security crisis is attributable to defects at the language-design level, e.g., buffer overflows and injection attacks. Many of these defects could have been prevented outright (or at least ameliorated) when the programming language in use was designed. Viewing security as the combined responsibility of the compiler and the language lends itself to a two-pronged approach in my research: designing expressive, efficient, secure linguistic constructs for new languages; and building security-minded static analyses for languages with entrenched code bases.
The Early Growth Response Gene EGR-1 Behaves as a Suppressor Gene That Is Down-Regulated Independent of ARF / Mdm 2 but not p 53 Alterations in Fresh Human Gliomas 1

Purpose: EGR-1 is an immediate early gene with diverse functions that include the suppression of growth. EGR-1 is down-regulated many cancer cell types, suggesting a tumor suppressor role, and may critically involve the p53 pathway. The aim of this work was to measure the expression of EGR-1 and the p16/INK4a/ARF-Mdm2-p53 pathway status in fresh human gliomas. Experimental Design: Thirty-one human gliomas with different grades of malignancy were investigated for Egr-1 mRNA and the protein expression, frequency, and spectrum of p53 gene mutations, mdm2 gene amplification, and p16/ INK4a/ARF allele loss. Results: The amplification of Mdm2 and the deletion of the p16/INK4a gene was found in 3 and 5 cases, respectively, whereas mutations of p53, including two novel mutations, were observed in 10 other cases. The three types of changes occurred strictly mutually exclusively, emphasizing that these genes operate in a common pathway critical to glioma progression. EGR-1 mRNA was significantly down-regulated in astrocytomas (14.7 5.1%) and in glioblastomas (33.6 10.0%) versus normal brain. Overall, EGR-1 mRNA was strongly suppressed (average, 15.2 13.9%) in 27 of 31 cases (87%), independent of changes in p16/INK4a/ARF and Mdm2; whereas 4 of 31 cases with residual EGR-1 expression as well as the highest EGR-1 variance segregated with p53 mutations. Immunohistochemical analyses confirmed the suppression of EGR-1 protein. Conclusions: These results indicate that EGR-1 is commonly suppressed in gliomas independent of p16/INK4a/ ARF and Mdm2 and that suppression is less crucial in tumors bearing p53 mutations, and these results implicate an EGR-1 growth regulatory mechanism as a target of inactivation during tumor progression.
Genome-Wide Binding Site Analysis of FAR-RED ELONGATED HYPOCOTYL3 Reveals Its Novel Function in Arabidopsis Development[W]

This work analyzed genome-wide binding sites of a transposase-derived transcription factor, FHY3, using a chromatin immunoprecipitation–based sequencing approach and identified a role for FHY3 in controlling chloroplast development by directly activating the expression of ARC5, a key gene involved in chloroplast division. FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and its homolog FAR-RED IMPAIRED RESPONSE1 (FAR1), two transposase-derived transcription factors, are key components in phytochrome A signaling and the circadian clock. Here, we use chromatin immunoprecipitation–based sequencing (ChIP-seq) to identify 1559 and 1009 FHY3 direct target genes in darkness (D) and far-red (FR) light conditions, respectively, in the Arabidopsis thaliana genome. FHY3 preferentially binds to promoters through the FHY3/FAR1 binding motif (CACGCGC). Interestingly, FHY3 also binds to two motifs in the 178-bp Arabidopsis centromeric repeats. Comparison between the ChIP-seq and microarray data indicates that FHY3 quickly regulates the expression of 197 and 86 genes in D and FR, respectively. FHY3 also coregulates a number of common target genes with PHYTOCHROME INTERACTING FACTOR 3-LIKE5 and ELONGATED HYPOCOTYL5. Moreover, we uncover a role for FHY3 in controlling chloroplast development by directly activating the expression of ACCUMULATION AND REPLICATION OF CHLOROPLASTS5, whose product is a structural component of the latter stages of chloroplast division in Arabidopsis. Taken together, our data suggest that FHY3 regulates multiple facets of plant development, thus providing insights into its functions beyond light and circadian pathways.
Spatial Distributions of Young Stars

We analyze the spatial distribution of young stars in Taurus-Auriga and Upper Sco, as determined from the two-point correlation function (i.e., the mean surface density of neighbors). The corresponding power-law fits allow us to determine the fractal dimensions of each association’s spatial distribution, measure the stellar velocity dispersions, and distinguish between the bound binary population and chance alignments of members. We find that the fractal dimension of Taurus is D ∼ 1.05, consistent with its filamentary structure. The fractal dimension of Upper Sco may be even shallower (D ∼ 0.7), but this fit is uncertain due to the limited area and possible spatially variable incompleteness. We also find that random stellar motions have erased all primordial structure on scales of ≲0.07° in Taurus and ≲1.7° in Upper Sco; given ages of ~1 and ~5 Myr, the corresponding internal velocity dispersions are ~0.2 and ~1.0 km s−1, respectively. Finally, we find that binaries can be distinguished from chance alignments at separations of ≲120'' (17,000 AU) in Taurus and ≲75'' (11,000 AU) in Upper Sco. The binary populations in these associations that we previously studied, spanning separations of 3''-30'', is dominated by binary systems. However, the few lowest mass pairs (Mprim ≲ 0.3 M☉) might be chance alignments.
The Performance of Betting Lines for Predicting the Outcome of NFL Games

We investigated the performance of the collective intelligence of NFL fans predicting the outcome of games as realized through the Vegas betting lines. Using data from 2560 games (all post-expansion, regular- and post-season games from 2002-2011), we investigated the opening and closing lines, and the margin of victory. We found that the line difference (the difference between the opening and closing line) could be used to retroactively predict divisional winners with no less accuracy than 75% accuracy (i.e., "straight up" predictions). We also found that although home teams only beat the spread 47% of the time, a strategy of betting the home team underdogs (from 2002-2011) would have produced a cumulative winning strategy of 53.5%, above the threshold of 52.38% needed to break even.
Serum gastrin concentrations in dogs with liver disorders

Dogs with liver disorders often display gastrointestinal signs that may be triggered by ulceration. The liver is important for inactivation of some forms of gastrin. Therefore, hypergastrinaemia has been implicated in the pathogenesis of gastrointestinal ulcerations related to liver dysfunction. The aim of this study was to determine serum gastrin concentrations in dogs with liver disease. Fasted blood samples were collected from 15 dogs with newly diagnosed liver disease and 18 healthy dogs. Gastrin concentrations were significantly lower in dogs with congenital portosystemic shunt compared with healthy dogs (P=0.003). No significant difference (P=0.6) in gastrin concentration was revealed between dogs with hepatocellular disease and healthy dogs. Serum gastrin concentrations were not significantly associated with the occurrence of vomiting, anorexia, diarrhoea, or melaena in dogs with liver disorders. These findings did not provide support for the role of hypergastrinaemia in the development of gastrointestinal signs associated with liver disease in dogs. Decreased serum concentrations of gastrin in a dog with liver disease may suggest the presence of portosystemic shunt. Further investigation is warranted to determine the importance of hyopogastrinaemia in congenital postosystemic shunts in dogs and to evaluate potential alterations in serum gastrin concentrations in specific hepatocellular diseases.
Prevalence of hepatitis E virus infection in pediatric solid organ transplant recipients – A single‐center experience

Hoerning A, Hegen B, Wingen A‐M, Cetiner M, Lainka E, Kathemann S, Fiedler M, Timm J, Wenzel JJ, Hoyer PF, Gerner P. Prevalence of hepatitis E virus infection in pediatric solid organ transplant recipients – A single‐center experience.
PRADA: a high-performance reconfigurable parallel architecture based on the dataflow model

This work proposes and implements a reconfigurable parallel architecture based on dataflow for numerical computation, named PRADA. This architecture uses concepts of parallel processing to obtain a scalable performance and the dataflow concept for controlling the parallel execution of instructions. PRADA is composed by a control unit and several processing elements (PEs). In the control unit, there are several functional blocks, including data and instruction memories. Each PE is composed by an ALU and buffers. PRADA is organised as a cluster, in which several independent dataflow modules are interconnected together. PRADA was developed in VHDL and implemented in reconfigurable hardware using a FPGA device. Therefore, it can offer high performance, scalability and customised solutions for engineering problems. Results of the application of PRADA to the computation of a digital filter and a cryptography algorithm are presented. Results are also compared with other different architectures, such as microprocessors, ASICs, DSPs, reconfigurable architectures and dataflow architectures. In most cases, PRADA achieved either competitive or higher performance than the other architectures, regarding the measures used. Overall results suggest that this architecture can be applied to several classes of problems that may require a high throughput, such as cryptography, optimisation and scientific computing.
Modeling Immiscible Two‐Phase Flow in Rough Fractures From Capillary to Viscous Fingering

We develop an efficient computational model for simulating fluid invasion patterns emerging in variable aperture fractures. This two‐dimensional model takes into account the effect of capillary force on the fluid‐fluid interfaces and viscous pressure drop in both fluid phases. The pressure distribution is solved at each time step based on mass balance and local cubic law, considering an imposed pressure jump condition at the fluid‐fluid interface. This pressure jump corresponds to the Laplace pressure which includes both terms related to the out‐of‐plane (aperture‐spanning) curvature and to the in‐plane curvature. Simulating a configuration that emulates viscous fingering in two‐dimensional random porous media confirms that the model accounts properly for the role of viscous forces. Furthermore, direct comparison with previously obtained experimental results shows that the model reproduces the observed drainage patterns in a rough fracture reasonably well. The evolutions of tip location, the inlet pressures, and the invading phase fractal dimensions are analyzed to characterize the transition from capillary fingering to viscous fingering regimes. A radial injection scenario of immiscible invasion is also studied with varying modified capillary number and viscosity ratio, showing displacement patterns ranging from capillary fingering to viscous fingering to stable displacement. Such simulations using two contact angles show that the invading phase becomes more compact when the wetting condition changes from strong to weak drainage, as already observed in 2‐D porous media. The model can be used to bridge the gap in spatial scales of two‐phase flow between pore‐scale modeling approaches and the continuum Darcy‐scale models.
Speech Perception in Tones and Noise via Cochlear Implants Reveals Influence of Spectral Resolution on Temporal Processing

Under normal conditions, human speech is remarkably robust to degradation by noise and other distortions. However, people with hearing loss, including those with cochlear implants, often experience great difficulty in understanding speech in noisy environments. Recent work with normal-hearing listeners has shown that the amplitude fluctuations inherent in noise contribute strongly to the masking of speech. In contrast, this study shows that speech perception via a cochlear implant is unaffected by the inherent temporal fluctuations of noise. This qualitative difference between acoustic and electric auditory perception does not seem to be due to differences in underlying temporal acuity but can instead be explained by the poorer spectral resolution of cochlear implants, relative to the normally functioning ear, which leads to an effective smoothing of the inherent temporal-envelope fluctuations of noise. The outcome suggests an unexpected trade-off between the detrimental effects of poorer spectral resolution and the beneficial effects of a smoother noise temporal envelope. This trade-off provides an explanation for the long-standing puzzle of why strong correlations between speech understanding and spectral resolution have remained elusive. The results also provide a potential explanation for why cochlear-implant users and hearing-impaired listeners exhibit reduced or absent masking release when large and relatively slow temporal fluctuations are introduced in noise maskers. The multitone maskers used here may provide an effective new diagnostic tool for assessing functional hearing loss and reduced spectral resolution.
Contextual Word Similarity and Estimation From Sparse Data

In recent years there is much interest in word cooccurrence relations, such as n-grams, verb-object combinations, or cooccurrence within a limited context. This paper discusses how to estimate the probability of cooccurrences that do not occur in the training data. We present a method that makes local analogies between each specific unobserved cooccurrence and other cooccurrences that contain similar words, as determined by an appropriate word similarity metric. Our evaluation suggests that this method performs better than existing smoothing methods, and may provide an alternative to class based models.
Abdominal color of the Asian citrus psyllid, Diaphorina citri, is associated with susceptibility to various insecticides.

BACKGROUND Color morphs of an insect species are known to vary in activities of detoxifying enzymes and associated susceptibility to insecticides. In Diaphorina citri, three color morphs are known to occur. In the present study, susceptibility to four insecticides was compared among gray/brown, blue/green and orange/yellow color morphs of field-collected D. citri. RESULTS The orange/yellow morph was significantly more susceptible to fenpropathrin than the blue/green morph, and imidacloprid and chlorpyrifos caused higher mortality in the orange/yellow morph than in the blue/green and gray/brown morphs. To confirm the genetic basis of variable levels of susceptibility, the relative expression of five CYP4 genes was compared among the color morphs. CYP4C67 was expressed at significantly higher levels in the blue/green than in the orange/yellow and gray/brown morphs. CYP4DA1, CYP4C68, CYP4G70 and CYP4DB1 were expressed at significantly higher levels in the blue/green and gray/brown morphs than in the orange/yellow morph. Lower expression of CYP4 genes in the orange/yellow morph as compared with the others was correlated with reduced signal of 45 kD cytochrome P450 proteins, as determined by the western blot. CONCLUSIONS The results indicate differential susceptibility of D. citri color morphs to insecticides, which will need to be accounted for in future insecticide monitoring programs and may affect management programs.
Recommender Systems from an Industrial and Ethical Perspective

Over the recent years, a plethora of recommender systems (RS) have been proposed by academics. The degree of adoptability of these algorithms by industrial e-commerce platforms remains unclear. To get an insight into real-world recommendation engines, we survey more than 30 existing shopping cart solutions and compare the performance of popular recommendation algorithms on proprietary e-commerce datasets. Our results show that deployed systems rarely go beyond trivial "best seller" lists or very basic personalized recommendation algorithms, which nevertheless exhibit superior performance to more elaborate techniques both in our experiments and other related studies. We also perform chronological dataset splits to demonstrate the importance of preserving the sequence of events during evaluation, and the recency of events during training. The second part of our research is still ongoing and focuses on various ethical challenges that complicate the design of recommender systems. We believe that this direction of research remains mostly neglected despite its increasing impact on RS' quality and safety.
Scanning electron microscopy and immunohistochemical observations of the vascular nerve plexuses in the dental pulp of rat incisor

The innervation of rat incisors, which are continuously erupting teeth, is quite unique. Although many reports have documented the neural control of the pulpal blood flow, only a few studies have examined the structure and distribution of vascular nerves in the rat incisors. This study examined the nerve plexuses and the spatial relationship of nerve terminals to smooth muscle cells of the pulp vessels of rat incisors.
TLR9-Targeted STAT3 Silencing Abrogates Immunosuppressive Activity of Myeloid-Derived Suppressor Cells from Prostate Cancer Patients

Purpose: Recent advances in immunotherapy of advanced human cancers underscored the need to address and eliminate tumor immune evasion. The myeloid-derived suppressor cells (MDSC) are important inhibitors of T-cell responses in solid tumors, such as prostate cancers. However, targeting MDSCs proved challenging due to their phenotypic heterogeneity. Experimental Design: Myeloid cell populations were evaluated using flow cytometry on blood samples, functional assays, and immunohistochemical/immunofluorescent stainings on specimens from healthy subjects, localized and metastatic castration-resistant prostate cancer patients. Results: Here, we identify a population of Lin−CD15HICD33LO granulocytic MDSCs that accumulate in patients' circulation during prostate cancer progression from localized to metastatic disease. The prostate cancer–associated MDSCs potently inhibit autologous CD8+ T cells' proliferation and production of IFNγ and granzyme-B. The circulating MDSCs have high levels of activated STAT3, which is a central immune checkpoint regulator. The granulocytic pSTAT3+ cells are also detectable in patients' prostate tissues. We previously generated an original strategy to silence genes specifically in Toll-like Receptor-9 (TLR9) positive myeloid cells using CpG-siRNA conjugates. We demonstrate that human granulocytic MDSCs express TLR9 and rapidly internalize naked CpG-STAT3siRNA, thereby silencing STAT3 expression. STAT3 blocking abrogates immunosuppressive effects of patients-derived MDSCs on effector CD8+ T cells. These effects depended on reduced expression and enzymatic activity of Arginase-1, a downstream STAT3 target gene and a potent T-cell inhibitor. Conclusions: Overall, we demonstrate the accumulation of granulocytic MDSCs with prostate cancer progression and the feasibility of using TLR9-targeted STAT3siRNA delivery strategy to alleviate MDSC-mediated immunosuppression. Clin Cancer Res; 21(16); 3771–82. ©2015 AACR.
Transforming growth factor {beta}1 induces epithelial-mesenchymal transition by activating the JNK-Smad3 pathway in rat peritoneal mesothelial cells.

BACKGROUND Peritoneal fibrosis is a serious complication in long-term peritoneal dialysis (PD) patients. Epithelial-mesenchymal transition (EMT) plays an important role in peritoneal fibrosis, and TGFbeta1 is the crucial inducer of EMT. Phosphorylation of Smad proteins is required for TGFbeta1-induced EMT. It was reported that C-Jun N-terminal kinase (JNK) was involved in the TGFbeta1/Smad signaling pathway and might regulate the activation of Smad proteins. However, whether JNK is activated by TGFbeta1 in rat peritoneal mesothelial cells (RPMCs) and the role taken by JNK signaling in EMT induced by TGFbeta1 remains undetermined. In the present study, we investigated the role of JNK-Smad pathway in EMT induced by TGFbeta1 in RPMCs. METHODS We harvested RPMCs from the peritoneum of male Sprague-Dawley rats and then cultured the cells in Dulbecco modified Eagle medium/F12 medium with 15% (volume:volume) fetal bovine serum. The cells were pretreated with SP600125, a specific inhibitor of JNK, for 4 hours before incubation with TGFbeta1. The protein expression levels of phosphorylated JNK, Smad2, and Smad3 were detected by Western blotting. The messenger RNA levels and protein expression of alpha-smooth muscle actin (alpha-SMA), E-cadherin, and collagen I were determined with reverse transcriptase polymerase chain reaction and Western blotting respectively. RESULTS Expression of alpha-SMA and collagen I were significantly increased and expression of E-cadherin decreased with TGFbeta1 in RPMCs. Transforming growth factor beta1 can stimulate phosphorylated JNK expression from 5 minutes, with the peak at 10 minutes, and phosphorylated Smad2 and Smad3 expression from 10 minutes, with the peak at 30 minutes. The addition of SP600125, which blocked activation of JNK, effectively inhibited TGFbeta1-induced phosphorylation of Smad3, but not Smad2. Also, our results showed that SP600125 effectively suppressed TGFbeta1-induced high expression of alpha-SMA and collagen I, and prevented TGFbeta1-induced downregulation of E-cadherin expression in RPMCs. CONCLUSIONS This study demonstrated that JNK signaling may play an important role in EMT induced by TGFbeta1 in RPMCs through activation of Smad3, suggesting that JNK inhibitor may prove to be a novel therapeutic agent for peritoneal fibrosis.