Miracle-dz/UniFAR-FTUs huggingface dataset:
Parthenolide Is Neuroprotective in Rat Experimental Stroke Model: Downregulating NF-κB, Phospho-p38MAPK, and Caspase-1 and Ameliorating BBB Permeability

Inflammatory damage plays an important role in cerebral ischemic pathogenesis and may represent a target for treatment. Parthenolide (PN) has been proved to elicit a wide range of biological activities through its anti-inflammatory action in the treatment of migraine, arthritis, and atherosclerosis. To decide whether this effect applies to ischemic injury in brain, we therefore investigate the potential neuroprotective role of PN and the underlying mechanisms. Male Sprague-Dawley rats were randomly divided into Saline, Vehicle, and PN groups and a permanent middle cerebral artery occlusion (MCAO) model was used. PN administered intraperitoneally immediately after cerebral ischemia and once daily on the following days. At time points after MCAO, neurological deficit, infarct volume, and brain water content were measured. Immunohistochemistry, western blot and RT-PCR were used to analyze the expression of NF-κB and caspase-1 in ischemic brain tissue. Phospho-p38MAPK and claudin-5 were detected by western blot. The results indicated that PN dramatically ameliorated neurological deficit, brain water content, and infarct volume, downregulated NF-κB, phospho-p38MAPK, and caspase-1 expressions, and upregulated claudin-5 expression in ischemic brain tissue. Conclusions. PN protected the brain from damage caused by MCAO; this effect may be through downregulating NF-κB, phosho-p38MAPK, and caspase-1 expressions and ameliorating BBB permeability.
Hypergraph Based Clustering in High-Dimensional Data Sets: A Summary of Results

Clustering of data in a large dimension space is of a great interest in many data mining appli cations In this paper we propose a method for clustering of data in a high dimensional space based on a hypergraph model In this method the relationship present in the original data in high dimensional space are mapped into a hypergraph A hyperedge represents a relationship a n ity among subsets of data and the weight of the hyperedge re ects the strength of this a nity A hypergraph partitioning algorithm is used to nd a partitioning of the vertices such that the corresponding data items in each partition are highly related and the weight of the hyperedges cut by the partitioning is minimized We present results of experiments on two di erent data sets S P stock data for the period of and protein coding data These experiments demonstrate that our approach is applicable and e ective in high dimensional datasets
F1000 recommendations as a new data source for research evaluation: A comparison with citations

F1000 is a post-publication peer review service for biological and medical research. F1000 aims to recommend important publications in the biomedical literature, and from this perspective F1000 could be an interesting tool for research evaluation. By linking the complete database of F1000 recommendations to the Web of Science bibliographic database, we are able to make a comprehensive comparison between F1000 recommendations and citations. We find that about 2% of the publications in the biomedical literature receive at least one F1000 recommendation. Recommended publications on average receive 1.30 recommendations, and over 90% of the recommendations are given within half a year after a publication has appeared. There turns out to be a clear correlation between F1000 recommendations and citations. However, the correlation is relatively weak, at least weaker than the correlation between journal impact and citations. More research is needed to identify the main reasons for differences between recommendations and citations in assessing the impact of publications.
Simulation analysis of international-departure passenger flows in an airport terminal

An entire airport terminal building is simulated to examine passenger flows, especially international departures. First, times needed for passengers to be processed in the terminal building are examined. It is found that the waiting time for check-in accounts for more than 80 percent of the total waiting time of passengers spent in the airport. A special-purpose data-generator is designed and developed to create experimental data for executing a simulation. It is found that the possible number of passengers missing their flights could be drastically reduced by adding supporting staff to and by making use of first- and business-class check-in counters for processing economy- and group-class passengers.
Developing an activity-based costing approach for system development and implementation

This paper proposes the use of the Activity Based Costing (ABC) approach to software estimation. Like other more traditional approaches to software estimation, ABC provides man-day estimates. In addition, it also provides detailed costing information that is useful for management control and decision making. The paper shows how the ABC approach can be applied to software estimation by building an ABC model using data from twenty-two projects in a financial services firm. The model is then used for estimation, and comparisons between estimated and actual man-day are computed (variance analysis). The data generated by the model and from the variance analysis are useful for management control and decision making in areas such as resource allocation, outsourcing of specific development activities, and learning from adoption of new development tools and practices.
The antimicrobial triclocarban stimulates embryo production in the freshwater mudsnail Potamopyrgus antipodarum

Recent research has indicated that the antimicrobial chemical triclocarban (TCC) represents a new type of endocrine disruptor, amplifying the transcriptional activity of steroid hormones and their receptors while itself exhibiting little affinity for these receptors. The effects of TCC were studied in the freshwater mudsnail Potamopyrgus antipodarum. Specimens were exposed to concentrations ranging from 0.05 to 10.5 µg/L dissolved TCC and were removed and dissected, and embryos contained within the brood pouch were counted and classified as shelled or unshelled after two and four weeks of exposure. After four weeks, environmentally relevant TCC concentrations of 1.6 to 10.5 µg/L resulted in statistically significant increases in the number of unshelled embryos, whereas 0.2, 1.6, and 10.5 µg/L exposures significantly increased numbers of shelled embryos. The lowest observed effect concentration (LOEC) was 0.2 µg/L, the no observed effect concentration (NOEC) was 0.05 µg/L; the 10% effective concentration (EC10) and the median effective concentration (EC50) for unshelled effects were 0.5 µg/L and 2.5 µg/L, respectively. Given the widespread occurrence of TCC in the environment and the effects shown at environmentally relevant concentrations, these results indicate that TCC may be causing reproductive effects in the environment. Furthermore, the present study indicates that environmental risk from a new class of endocrine‐disrupting chemicals (EDCs) is both qualitatively and quantitatively similar to risk from existing classes of EDCs. Environ. Toxicol. Chem. 2010;29:966–970. © 2009 SETAC
The Absolute Abundance of Iron in the Solar Corona

We present a measurement of the abundance of Fe relative to H in the solar corona using a technique that differs from previous spectroscopic and solar wind measurements. Our method combines EUV line data from the Coronal Diagnostic Spectrometer (CDS) on the Solar and Heliospheric Observatory with thermal bremsstrahlung radio data from the VLA. The coronal Fe abundance is derived by equating the thermal bremsstrahlung radio emission calculated from the EUV Fe line data to that observed with the VLA, treating the Fe/H abundance as the sole unknown. We apply this technique to a compact cool active region and find Fe/H = 1.56 × 10-4, or about 4 times its value in the solar photosphere. Uncertainties in the CDS radiometric calibration, the VLA intensity measurements, the atomic parameters, and the assumptions made in the spectral analysis yield net uncertainties of ~20%. This result implies that low first ionization potential elements such as Fe are enhanced in the solar corona relative to photospheric values.
Dreaming More Data: Class-dependent Distributions over Diffeomorphisms for Learned Data Augmentation

Data augmentation is a key element in training high-dimensional models. In this approach, one synthesizes new observations by applying pre-specified transformations to the original training data; e.g.~new images are formed by rotating old ones. Current augmentation schemes, however, rely on manual specification of the applied transformations, making data augmentation an implicit form of feature engineering. With an eye towards true end-to-end learning, we suggest learning the applied transformations on a per-class basis. Particularly, we align image pairs within each class under the assumption that the spatial transformation between images belongs to a large class of diffeomorphisms. We then learn a class-specific probabilistic generative models of the transformations in a Riemannian submanifold of the Lie group of diffeomorphisms. We demonstrate significant performance improvements in training deep neural nets over manually-specified augmentation schemes. Our code and augmented datasets are available online.
Detection of human cytomegalovirus DNA in various blood components after liver transplantation

The quantification of human cytomegalovirus (HCMV DNA) by real-time PCR is currently a primary option for laboratory diagnosis of HCMV infection. However, the optimal sample material remains controversial due to the use of different PCR assays. To explore the best blood component for HCMV DNA surveillance after liver transplantation, whole blood (WB), serum (SE), and plasma (PL) specimens were collected simultaneously from targeted patients and examined for HCMV DNA using one commercially available assay. The HCMV DNA-positive rate with WB (16.67%) was higher than that with either SE or PL (8.33%, both P<0.01). Quantitative DNA levels in WB were of greater magnitude than those in SE (WB-SE mean log-transformed difference, 0.99; 95%CI=0.74-1.25; P<0.0001) and PL (WB-PL mean log-transformed difference, 1.37; 95%CI=1.07-1.66; P<0.0001). Dynamic monitoring revealed that HCMV DNA in WB was positive sooner and had higher values for a longer period of time during therapy. With earlier positive detection, higher sensitivity, and yield of greater viral loads, WB compared favorably to SE or PL and hence is recommended as the superior material for HCMV DNA surveillance after liver transplantation. In addition, infant recipients require more intensive monitoring and prophylactic care because of their higher susceptibility to primary HCMV infection.
A Genome-Wide Screen for Promoter Methylation in Lung Cancer Identifies Novel Methylation Markers for Multiple Malignancies

Background Promoter hypermethylation coupled with loss of heterozygosity at the same locus results in loss of gene function in many tumor cells. The “rules” governing which genes are methylated during the pathogenesis of individual cancers, how specific methylation profiles are initially established, or what determines tumor type-specific methylation are unknown. However, DNA methylation markers that are highly specific and sensitive for common tumors would be useful for the early detection of cancer, and those required for the malignant phenotype would identify pathways important as therapeutic targets. Methods and Findings In an effort to identify new cancer-specific methylation markers, we employed a high-throughput global expression profiling approach in lung cancer cells. We identified 132 genes that have 5′ CpG islands, are induced from undetectable levels by 5-aza-2′-deoxycytidine in multiple non-small cell lung cancer cell lines, and are expressed in immortalized human bronchial epithelial cells. As expected, these genes were also expressed in normal lung, but often not in companion primary lung cancers. Methylation analysis of a subset (45/132) of these promoter regions in primary lung cancer (n = 20) and adjacent nonmalignant tissue (n = 20) showed that 31 genes had acquired methylation in the tumors, but did not show methylation in normal lung or peripheral blood cells. We studied the eight most frequently and specifically methylated genes from our lung cancer dataset in breast cancer (n = 37), colon cancer (n = 24), and prostate cancer (n = 24) along with counterpart nonmalignant tissues. We found that seven loci were frequently methylated in both breast and lung cancers, with four showing extensive methylation in all four epithelial tumors. Conclusions By using a systematic biological screen we identified multiple genes that are methylated with high penetrance in primary lung, breast, colon, and prostate cancers. The cross-tumor methylation pattern we observed for these novel markers suggests that we have identified a partial promoter hypermethylation signature for these common malignancies. These data suggest that while tumors in different tissues vary substantially with respect to gene expression, there may be commonalities in their promoter methylation profiles that represent targets for early detection screening or therapeutic intervention.
Neural Response to Reward Anticipation under Risk Is Nonlinear in Probabilities

A widely observed phenomenon in decision making under risk is the apparent overweighting of unlikely events and the underweighting of nearly certain events. This violates standard assumptions in expected utility theory, which requires that expected utility be linear (objective) in probabilities. Models such as prospect theory have relaxed this assumption and introduced the notion of a “probability weighting function,” which captures the key properties found in experimental data. This study reports functional magnetic resonance imaging (fMRI) data that neural response to expected reward is nonlinear in probabilities. Specifically, we found that activity in the striatum during valuation of monetary gambles are nonlinear in probabilities in the pattern predicted by prospect theory, suggesting that probability distortion is reflected at the level of the reward encoding process. The degree of nonlinearity reflected in individual subjects' decisions is also correlated with striatal activity across subjects. Our results shed light on the neural mechanisms of reward processing, and have implications for future neuroscientific studies of decision making involving extreme tails of the distribution, where probability weighting provides an explanation for commonly observed behavioral anomalies.
Input-to-output transformation in a model of the rat hippocampal CA1 network

Here we use computational modeling to gain new insights into the transformation of inputs in hippocampal field CA1. We considered input-output transformation in CA1 principal cells of the rat hippocampus, with activity synchronized by population gamma oscillations. Prior experiments have shown that such synchronization is especially strong for cells within one millimeter of each other. We therefore simulated a one-millimeter patch of CA1 with 23,500 principal cells. We used morphologically and biophysically detailed neuronal models, each with more than 1000 compartments and thousands of synaptic inputs. Inputs came from binary patterns of spiking neurons from field CA3 and entorhinal cortex (EC). On average, each presynaptic pattern initiated action potentials in the same number of CA1 principal cells in the patch. We considered pairs of similar and pairs of distinct patterns. In all the cases CA1 strongly separated input patterns. However, CA1 cells were considerably more sensitive to small alterations in EC patterns compared to CA3 patterns. Our results can be used for comparison of input-to-output transformations in normal and pathological hippocampal networks.
Contribution of Beta-HPV Infection and UV Damage to Rapid-Onset Cutaneous Squamous Cell Carcinoma during BRAF-Inhibition Therapy

Purpose: BRAF-inhibition (BRAFi) therapy for advanced melanoma carries a high rate of secondary cutaneous squamous cell carcinoma (cSCC) and risk of other cancers. UV radiation and α-genus human papillomavirus (HPV) are highly associated with SCC, but a novel role for β-genus HPV is suspected in BRAFi-cSCC. Cutaneous β-HPV may act in concert with host and environmental factors in BRAFi-cSCC. Experimental Design: Primary BRAFi-cSCC tissue DNA isolated from patients receiving vemurafenib or dabrafenib from two cancer centers was analyzed for the presence of cutaneous oncogenic viruses and host genetic mutations. Diagnostic specimens underwent consensus dermatopathology review. Clinical parameters for UV exposure and disease course were statistically analyzed in conjunction with histopathology. Results: Twenty-nine patients contributed 69 BRAFi-cSCC lesions. BRAFi-cSCC had wart-like features (BRAFi-cSCC-WF) in 22% of specimens. During vemurafenib therapy, BRAFi-cSCC-WF arose 11.6 weeks more rapidly than conventional cSCC when controlled for gender and UV exposure (P value = 0.03). Among all BRAFi-cSCC, β-genus HPV-17, HPV-38, HPV-111 were most frequently isolated, and novel β-HPV genotypes were discovered (CTR, CRT-11, CRT-22). Sequencing revealed 63% of evaluated BRAFi-cSCCs harbored RAS mutations with PIK3CA, CKIT, ALK, and EGFR mutations also detected. Conclusions: We examined clinical, histopathologic, viral, and genetic parameters in BRAFi-cSCC demonstrating rapid onset; wart-like histomorphology; β-HPV-17, HPV-38, and HPV-111 infection; UV damage; and novel ALK and CKIT mutations. Discovered β-HPV genotypes expand the spectrum of tumor-associated viruses. These findings enhance our understanding of factors cooperating with BRAF inhibition that accelerate keratinocyte oncogenesis as well as broaden the knowledge base of multifactorial mediators of cancer in general. Clin Cancer Res; 21(11); 2624–34. ©2015 AACR.
Addressing Safety and Security Contradictions in Cyber-Physical Systems

Modern cyber-physical systems are found in important domains such as automobiles, medical devices, building automation, avionics, etc. Hence, they are increasingly prone to security violations. Often such vulnerabilities occur as a result of contradictory requirements between the safety/real-time properties and the security needs of the system. In this paper we propose a formal framework that assists designers in detecting such conflicts early, thus increasing both, the safety and the security of the overall system.
Progress Against Poverty: Sustaining Mexico's Progresa-Oportunidades Program

In 1997, Mexico launched a new incentive-based poverty reduction program to enhance the human capital of those living in extreme poverty. This book presents a case study of Progresa-Oportunidades, focusing on the main factors that have contributed to the program's sustainability, policies that have allowed it to operate at the national level, and future challenges.
Activated mast cells in proximity to colonic nerves correlate with abdominal pain in irritable bowel syndrome.

BACKGROUND & AIMS The mechanisms underlying abdominal pain perception in irritable bowel syndrome (IBS) are poorly understood. Intestinal mast cell infiltration may perturb nerve function leading to symptom perception. We assessed colonic mast cell infiltration, mediator release, and spatial interactions with mucosal innervation and their correlation with abdominal pain in IBS patients. METHODS IBS patients were diagnosed according to Rome II criteria and abdominal pain quantified according to a validated questionnaire. Colonic mucosal mast cells were identified immunohistochemically and quantified with a computer-assisted counting method. Mast cell tryptase and histamine release were analyzed immunoenzymatically. Intestinal nerve to mast cell distance was assessed with electron microscopy. RESULTS Thirty-four out of 44 IBS patients (77%) showed an increased area of mucosa occupied by mast cells as compared with controls (9.2% +/- 2.5% vs. 3.3 +/- 0.8%, respectively; P < 0.001). There was a 150% increase in the number of degranulating mast cells (4.76 +/- 3.18/field vs. 2.42 +/- 2.26/field, respectively; P = 0.026). Mucosal content of tryptase was increased in IBS and mast cells spontaneously released more tryptase (3.22 +/- 3.48 pmol/min/mg vs. 0.87 +/- 0.65 pmol/min/mg, respectively; P = 0.015) and histamine (339.7 +/- 59.0 ng/g vs. 169.3 +/- 130.6 ng/g, respectively; P = 0.015). Mast cells located within 5 microm of nerve fibers were 7.14 +/- 3.87/field vs. 2.27 +/- 1.63/field in IBS vs. controls (P < 0.001). Only mast cells in close proximity to nerves were significantly correlated with severity and frequency of abdominal pain/discomfort (P < 0.001 and P = 0.003, respectively). CONCLUSIONS Colonic mast cell infiltration and mediator release in proximity to mucosal innervation may contribute to abdominal pain perception in IBS patients.
A Low-Noise Transimpedance Amplifier for BLM-Based Ion Channel Recording

High-throughput screening (HTS) using ion channel recording is a powerful drug discovery technique in pharmacology. Ion channel recording with planar bilayer lipid membranes (BLM) is scalable and has very high sensitivity. A HTS system based on BLM ion channel recording faces three main challenges: (i) design of scalable microfluidic devices; (ii) design of compact ultra-low-noise transimpedance amplifiers able to detect currents in the pA range with bandwidth >10 kHz; (iii) design of compact, robust and scalable systems that integrate these two elements. This paper presents a low-noise transimpedance amplifier with integrated A/D conversion realized in CMOS 0.35 μm technology. The CMOS amplifier acquires currents in the range ±200 pA and ±20 nA, with 100 kHz bandwidth while dissipating 41 mW. An integrated digital offset compensation loop balances any voltage offsets from Ag/AgCl electrodes. The measured open-input input-referred noise current is as low as 4 fA/√Hz at ±200 pA range. The current amplifier is embedded in an integrated platform, together with a microfluidic device, for current recording from ion channels. Gramicidin-A, α-haemolysin and KcsA potassium channels have been used to prove both the platform and the current-to-digital converter.
A complete view of the genetic diversity of the Escherichia coli O-antigen biosynthesis gene cluster

The O antigen constitutes the outermost part of the lipopolysaccharide layer in Gram-negative bacteria. The chemical composition and structure of the O antigen show high levels of variation even within a single species revealing itself as serological diversity. Here, we present a complete sequence set for the O-antigen biosynthesis gene clusters (O-AGCs) from all 184 recognized Escherichia coli O serogroups. By comparing these sequences, we identified 161 well-defined O-AGCs. Based on the wzx/wzy or wzm/wzt gene sequences, in addition to 145 singletons, 37 serogroups were placed into 16 groups. Furthermore, phylogenetic analysis of all the E. coli O-serogroup reference strains revealed that the nearly one-quarter of the 184 serogroups were found in the ST10 lineage, which may have a unique genetic background allowing a more successful exchange of O-AGCs. Our data provide a complete view of the genetic diversity of O-AGCs in E. coli showing a stronger association between host phylogenetic lineage and O-serogroup diversification than previously recognized. These data will be a valuable basis for developing a systematic molecular O-typing scheme that will allow traditional typing approaches to be linked to genomic exploration of E. coli diversity.