Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of microsatellite instability in gastric cancer and dysplasia tissues.

OBJECTIVE We aimed to investigate the association between gastric cancer and microsatellite instability (MSI) in the present study. METHOD Phenol-chloroform method was employed for DNA extraction from the cancer tissues of 65gastric cancer patients and the dysplasia tissues and normal control tissues of 32 non-gastric cancer patients. The microsatellite loci Bat25, Bat26, D2S123, D5S346 and D17S250 were detected by using PCR-SSCP silver staining technique, and the MSI of the gastric cancer tissues and the precancerous tissues was analyzed. RESULTS Of 65 gastric cancer cases, MSI was detected in 43 cases, with the detection rate of 66.2%. There were 13 cases showing MSI-H and 30 cases showing MSI-L, accounting for 30.2% and 69.8%, respectively. Among 32 cases of dysplasia tissues, MSI was detected in 10 cases, with the detection rate of 31.3%. Two cases of dysplasia tissues showed MSI-H and 8 cases showed MSI-L, accounting for 20.0% and 80.0%, respectively. CONCLUSION Gastric cancer patients had a high detection rate of MSI. It is speculated that MSI is another molecular mechanism of carcinogenesis and may serve as a sensitive diagnostic indicator of gastric cancer.
New gastropod assemblages from the Early/Middle Miocene of Riedensheim and Adelschlag-Fasanerie, southern Germany

This work presents a taxonomic study and paleoecological reconstructions of the continental gastropod assemblages from two new Miocene localities in the German part of the North Alpine Foreland Basin, Bavaria. Riedensheim (next to the town of Rennertshofen) and Fasanerie (next to the town of Adelschlag). The fossil rich deposits belong to the Upper Freshwater Molasse (OSM), correlated to the regional biostratigraphic unit C+D (Burdigalian/Langhian;MN 5 in the European mammal Neogene zone). 17 gastropod species (almost exclusively pulmonates) were found in Adelschlag-Fasanerie and 35 species in Riedensheim. 13 species are shared by both assemblages. Of these, the following species have their distribution expanded in Germany: Azeca peneckei, Carychium (Carychium) galli, Vitrea ammoni and Urticicola perchtae;and possibly also Stagnicola cf. praebouiletti and Truncatellina cf. pantherae. Paleoecological reconstructions indicate a rich freshwater gastropod community in Riedensheim, with a well-vegetated area immediately surrounding the water body (which diminished in size with time), and a surrounding environment dominated by humid forest. The fauna from Adelschlag-Fasanerie, which was much impoverished in comparison, might represent flood plain and fluvial channel deposits. Finally, a comparison to the molluscan faunas of coeval and nearby localities (Adelschlag, Attenfeld, Sandelzhausen and Undorf) is provided.
Prevalence of Ideal Cardiovascular Health and Its Relationship With the 4-Year Cardiovascular Events in a Northern Chinese Industrial City

Background— The American Heart Association Committee recently developed definitions of “ideal,” “intermediate,” and “poor” cardiovascular health based on 7 cardiovascular disease (CVD) risk factors or health behaviors. This study evaluated the prevalence of “ideal” American Heart Association cardiovascular health metrics from June 2006 to October 2007 in the Kailuan cohort (n=101 510; age 18–98 years) in northern China and its relationship with the 4-year CVD incidence. Methods and Results— We used Cox proportional hazards regression to calculate hazard ratios and 95% confidence intervals for baseline health behaviors and risk factor categories. The majority of participants (63 676; 69.45%) presented with ⩽3 ideal cardiovascular health metrics, whereas 8342 participants (9.1%) had 5 to 7 ideal metrics. Only 93 of 91 698 participants (0.1%) had all 7 metrics in the ideal range. There was a strong relationship between the cumulative incidence of CVD events in the 4-year follow-up and the number of ideal health metrics at baseline; the 1111 participants with 6 and 7 ideal metrics had a significantly lower cumulative incidence of CVD than subjects with no or only 1 ideal health metric (0.8% versus 3.3%). Men had higher rates of CVD events than women (2.46% versus 1.18%). Conclusions— Few adults had ideal cardiovascular health according to the modified American Heart Association definition. We detected a strong inverse relationship between the cumulative CVD incidence and the number of ideal health metrics at baseline. Population-wide prevention, especially lifestyle improvement, is critical to increase the low-risk prevalence and thereafter decrease CVD events. Clinical Trial Registration— URL: http://www.chictr. org/cn/proj/show.aspx? proj=1441. Unique identifier: ChiCTR-TNC-11001489.
Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges

Precision medicine aims to predict a patient's disease risk and best therapeutic options by using that individual's genetic sequencing data. The Critical Assessment of Genome Interpretation (CAGI) is a community experiment consisting of genotype–phenotype prediction challenges; participants build models, undergo assessment, and share key findings. For CAGI 4, three challenges involved using exome‐sequencing data: Crohn's disease, bipolar disorder, and warfarin dosing. Previous CAGI challenges included prior versions of the Crohn's disease challenge. Here, we discuss the range of techniques used for phenotype prediction as well as the methods used for assessing predictive models. Additionally, we outline some of the difficulties associated with making predictions and evaluating them. The lessons learned from the exome challenges can be applied to both research and clinical efforts to improve phenotype prediction from genotype. In addition, these challenges serve as a vehicle for sharing clinical and research exome data in a secure manner with scientists who have a broad range of expertise, contributing to a collaborative effort to advance our understanding of genotype–phenotype relationships.
Data learning techniques and methodology for Fmax prediction

The question of whether or not structural test measurements can be used to predict functional or system Fmax, has been studied for many years. This paper presents a data learning approach to study the question. Given Fmax values and structural delay measurements on a set of sample chips, we propose a method called conformity check whose goal is to select a subset of conformal samples such that a more reliable predictor can be built on. Our predictor consists of two models, a conformal model that decides on a given chip if its Fmax is predictable or not, and a prediction model that outputs the predicted Fmax based on results obtained from structural test measurements. We explain the data learning methodology and study various data learning techniques using frequency data collected on a high-performance microprocessor design.
Amplify-and-Forward Cooperative Diversity Schemes for Multi-Carrier Systems

We propose generic relay and subcarrier allocation schemes for multicarrier (MC) system with amplify-and-forward (AF) relays. The outage probability bounds are derived analytically for each scheme. Simulation results show that these bounds are very tight and better than the bounds obtained straightforwardly from the analysis in the Single-Carrier (SC) case. This is because in our analysis we reckon with the increased degree of freedom brought by the parallel channels. One of the proposed schemes, the Average Best Relay Selection scheme, is best suited for practical implementation since it approaches the best performance while minimizing the required amount of signaling.
Unity in Diversity: Phylogenetic-inspired Techniques for Reverse Engineering and Detection of Malware Families

We developed a framework for abstracting, aligning and analysing malware execution traces and performed a preliminary exploration of state of the art phylogenetic methods, whose strengths lie in pattern recognition and visualisation, to derive the statistical relationships within two contemporary malware families. We made use of phylogenetic trees and networks, motifs, logos, composition biases, and tree topology comparison methods with the objective of identifying common functionality and studying sources of variation in related samples. Networks were more useful for visualising short nop-equivalent code metamorphism than trees, tree topology comparison was suited for studying variations in multiple sets of homologous procedures. We found logos could be used for code normalisation, which resulted in 33% to 62% reduction in the number of instructions. A motif search showed that API sequences related to the management of memory, I/O, libraries and threading do not change significantly amongst malware variants, composition bias provided an efficient way to distinguish between families. Using context-sensitive procedure analysis, we found that 100% of a set of memory management procedures used by the FakeAV-DO and "Skyhoo" malware families were uniquely identifiable. We discuss how phylogenetic techniques can aid the reverse engineering and detection of malware families and describe some related challenges.
Invited editorial on "Effects of chest wall vibration on breathlessness during hypercapnic ventilatory response".

over the past 20-30 years, substantial progress has been made in our understanding of dyspnea. We have come to the realization that dyspnea encompasses a number of distinct sensations ([16][1]) and that a diverse array of receptors in the chest wall, lungs, airways, and central nervous system may
Structural and Functional Consequences of Altering a Peptide MHC Anchor Residue1

To better understand TCR discrimination of multiple ligands, we have analyzed the crystal structures of two Hb peptide/I-Ek complexes that differ by only a single amino acid substitution at the P6 anchor position within the peptide (E73D). Detailed comparison of multiple independently determined structures at 1.9 Å resolution reveals that removal of a single buried methylene group can alter a critical portion of the TCR recognition surface. Significant variance was observed in the peptide P5-P8 main chain as well as a rotamer difference at LeuP8, ∼10 Å distal from the substitution. No significant variations were observed in the conformation of the two MHC class II molecules. The ligand alteration results in two peptide/MHC complexes that generate bulk T cell responses that are distinct and essentially nonoverlapping. For the Hb-specific T cell 3.L2, substitution reduces the potency of the ligand 1000-fold. Soluble 3.L2 TCR binds the two peptide/MHC complexes with similar affinity, although with faster kinetics. These results highlight the role of subtle variations in MHC Ag presentation on T cell activation and signaling.
Determinants of Employment and GDP Resilience in the Context of an Economic Crisis: Evidence from EU countries and regions

Existuje mnoho studii, ktere analyzovaly dopady ukazatelů na ekonomickou odolnost zemi a regionů, ale studie zaměřene na rozdily mezi ucinky faktorů ovlivňujicich odolnost zaměstnanosti a odolnost HDP chybi. Tento dokument je předběžný pokus o zaplněni teto mezery tim, že poskytuje nove důkazy o odlisnem působeni faktorů ovlivňujicich odolnost měřenou podle HDP a zaměstnanosti napřic zeměmi a regiony EU. Analyticka cast přispěvku je založena na analýze odolnosti zaměstnanosti a odolnosti HDP zemi a regionů NUTS 2 EU v kontextu hospodařske krize z roku 2008. Hlavni metoda použita v teto studii je korelacni analýza. Výsledky ukazuji na existenci specifických determinant pro daný typ odolnosti na narodni urovni (jedna se napřiklad o ukazatele ekonomicke struktury). Faktory spojene s kvalitou lidskeho kapitalu ukazuji silný pozitivni vztah s oběma typy odolnosti na narodni i regionalni urovni (zejmena pokud jde o růst zaměstnanosti a produkt).
Human Umbilical Mesenchymal Stem Cells Promote Recovery After Ischemic Stroke

Background and Purpose— Stroke is a cerebrovascular defect that leads to many adverse neurological complications. Current pharmacological treatments for stroke remain unclear in their effectiveness, whereas stem cell transplantation shows considerable promise. Previously, we have shown that human umbilical mesenchymal stem cells (HUMSCs) can differentiate into neurons in neuronal-conditioned medium. Here we evaluate the therapeutic potential of HUMSC transplantation for ischemic stroke in rats. Methods— Focal cerebral ischemia was produced by middle cerebral artery occlusion and reperfusion. The HUMSCs treated with neuronal-conditioned medium or not treated were transplanted into the ischemic cortex 24 hours after surgery. Results— Histology and MRI revealed that rats implanted with HUMSCs treated with neuronal-conditioned medium or not treated exhibited a trend toward less infarct volume and significantly less atrophy compared with the control group, which received no HUMSCs. Moreover, rats receiving HUMSCs showed significant improvements in motor function, greater metabolic activity of cortical neurons, and better revascularization in the infarct cortex. Implanted HUMSCs, treated or not treated, survived in the infarct cortex for at least 36 days and released neuroprotective and growth-associated cytokines, including brain-derived neurotrophic factor, platelet-derived growth factor-AA, basic fibroblast growth factor, angiopoietin-2, CXCL-16, neutrophil-activating protein-2, and vascular endothelial growth factor receptor-3. Conclusions— Our results demonstrate the therapeutic benefits of HUMSC transplantation for ischemic stroke, likely due to the ability of the cells to produce growth-promoting factors. Thus, HUMSC transplantation may be an effective therapy in the future.
Physician Workload and Hospital Reimbursement: Overworked Physicians Generate Less Revenue per Patient

We study the impact of physician workload on hospital reimbursement utilizing a detailed data set from the trauma department of a major urban hospital. We find that the proportion of patients assigned a “high-severity” status for reimbursement purposes, which maps, on average, to a 47.8% higher payment for the hospital, is substantially reduced as the workload of the discharging physician increases. This effect persists after we control for a number of systematic differences in patient characteristics, condition, and time of discharge. Furthermore, we show that it is unlikely to be caused by selection bias or endogeneity in either discharge timing or allocation of discharges to physicians. We attribute this phenomenon to a workload-induced reduction in diligence of paperwork execution. We estimate the associated monetary loss to be approximately 1.1% (95% confidence interval, 0.4%--1.9%) of the department's annual revenue.
Local and Large-Scale Environment of Seyfert Galaxies

We present a three-dimensional study of the local (≤100 h-1 kpc) and the large-scale (≤1 h-1 Mpc) environment of the two main types of Seyfert AGN galaxies. For this purpose we use 48 Seyfert 1 galaxies (with redshifts in the range 0.007 ≤ z ≤ 0.036) and 56 Seyfert 2 galaxies (with 0.004 ≤ z ≤ 0.020), located at high galactic latitudes, as well as two control samples of nonactive galaxies having the same morphological, redshift, and diameter size distributions as the corresponding Seyfert samples. Using the Center for Astrophysics (CfA2) and Southern Sky Redshift Survey (SSRS) galaxy catalogs (mB ~ 15.5) and our own spectroscopic observations (mB ~ 18.5), we find that within a projected distance of 100 h-1 kpc and a radial velocity separation of δv ≲ 600 km s-1 around each of our AGNs, the fraction of Seyfert 2 galaxies with a close neighbor is significantly higher than that of their control (especially within 75 h-1 kpc) and Seyfert 1 galaxy samples, confirming a previous two-dimensional analysis of Dultzin-Hacyan et al. We also find that the large-scale environment around the two types of Seyfert galaxies does not vary with respect to their control sample galaxies. However, the Seyfert 2 and control galaxy samples do differ significantly when compared to the corresponding Seyfert 1 samples. Since the main difference between these samples is their morphological type distribution, we argue that the large-scale environmental difference cannot be attributed to differences in nuclear activity but rather to their different type of host galaxies.
BRVO: Predicting pedestrian trajectories using velocity-space reasoning

We introduce a novel, online method to predict pedestrian trajectories using agent-based velocity-space reasoning for improved human–robot interaction and collision-free navigation. Our formulation uses velocity obstacles to model the trajectory of each moving pedestrian in a robot’s environment and improves the motion model by adaptively learning relevant parameters based on sensor data. The resulting motion model for each agent is computed using statistical inferencing techniques, including a combination of ensemble Kalman filters and a maximum-likelihood estimation algorithm. This allows a robot to learn individual motion parameters for every agent in the scene at interactive rates. We highlight the performance of our motion prediction method in real-world crowded scenarios, compare its performance with prior techniques, and demonstrate the improved accuracy of the predicted trajectories. We also adapt our approach for collision-free robot navigation among pedestrians based on noisy data and highlight the results in our simulator.
[Effect of medicines for activating blood and reinforcing Qi on angiogenesis in infarcted myocardium edge area of acute myocardial infarction model in rats].

OBJECTIVE To study the effect of medicines for activating blood and reinforcing Qi on the number of new micro-vessels and the protein expressions of VEGF and bFGF in the infarcted myocardium edge area of acute myocardial infarction (AMI) model in rats. METHOD The AMI model of rats was established. After the successful model establishment, rats were randomly divided into the sham-operated group, the model group, the Danshen-Huangqi (1 : 2) group, the Danshen-Huangqi (1 : 1) group, the Chuanxiong-Huangqi (1 : 2) group, the Danshen group, the Chuanxiong group, the Chishao group and the Shexiang Baoxin pill group, with five rats in each group. Rats in each medicated group were orally administered with drugs as per 13.5 g x kg(-1) x d(-1) once everyday for three weeks. The immunohistochemical SP method was adopted to detect the expression of vWF in myocardial tissues, and count the number of micro-vessels (MVC). The protein expression of VEGF and bFGF in myocardial tissues were determined by Western blot. RESULT The new micro-vessels stained by vWF factor could be found in the infarcted myocardium edge area of the sham-operated group, the model group and all of medicated groups. The sham-operated group show unobvious new micro-vessels in myocardial tissues. A small amount of new micro-vessels could be seen in the infarcted myocardium edge area of the model group. Whereas a larger number of micro-vessels could be seen in the infarcted myocardium edge area of all of medicated groups. The differences between the sham-operated group and the model group had statistical significance (P < 0.05). The differences between each medicated group and the model group had statistical significance as well (P < 0.05 or P < 0.01). The lowest protein expression of VEGF and bFGF was found in myocardium of the sham-operated group, with the statistical significance compared with the model group (P < 0.05). Compared with the model group, each medicated group showed significant increase in the protein expression of VEGF and bFGF, with the statistical significance between them (P < 0.05 or P < 0.01). CONCLUSION The Danshen group, the Chuanxiong group, the Chishao group, the Danshen-Huangqi (1 : 2) group, the Danshen-Huangqi (1 : 1) group and the Chuanxiong-Huangqi (1 : 2) group show the effect in promoting angiogenesis. Their mechanism for promoting angiogenesis may be related to the improvement of the protein expressions of VEGF and bFGF, so as to increase the contents of VEGF and bFGF and promote the angiogenesis of new vessels.
Delay fault diagnosis using timing information

In modern technologies, process variations can be quite substantial, often causing design timing failures. It is essential that those errors be correctly and quickly diagnosed. Unfortunately, the resolution of the existing delay-fault diagnostic methodologies is still unsatisfactory. In this paper, we investigate the feasibility of using the circuit timing-information to guide the delay-fault diagnosis. We propose a novel and efficient diagnostic approach based on the timing window propagation (TWP) to achieve significantly better diagnostic results than those of an existing delay-fault diagnostic commercial tool. Besides locating the source of the timing errors, for each identified candidate our method determines the most probable delay defect size. The experimental results indicate that the new method diagnoses timing faults with very good resolution.
Long noncoding RNA associated with microvascular invasion in hepatocellular carcinoma promotes angiogenesis and serves as a predictor for hepatocellular carcinoma patients' poor recurrence‐free survival after hepatectomy

Survival of patients with hepatocellular carcinoma (HCC) remains poor, which is largely attributed to active angiogenesis. However, the mechanisms underlying angiogenesis in HCC remain to be discovered. In this study, we found that long noncoding RNA associated with microvascular invasion in HCC (lncRNA MVIH) (lncRNA associated with microvascular invasion in HCC) was generally overexpressed in HCC. In a cohort of 215 HCC patients, the overexpression of MVIH was associated with frequent microvascular invasion (P = 0.016) and a higher tumor node metastasis stage (P = 0.009) as well as decreased recurrence‐free survival (RFS) (P < 0.001) and overall survival (P = 0.007). Moreover, the up‐regulation of MVIH served as an independent risk factor to predict poor RFS. We also found that MVIH could promote tumor growth and intrahepatic metastasis by activating angiogenesis in mouse models. Subsequent investigations indicated that MVIH could activate tumor‐inducing angiogenesis by inhibiting the secretion of phosphoglycerate kinase 1 (PGK1). Additionally, in 65 HCC samples, MVIH expression was inversely correlated with the serum level of PGK1 and positively correlated with the microvessel density. Conclusion: Deregulation of lncRNA MVIH is a predictor for poor RFS of HCC patients after hepatectomy and could be utilized as a potential target for new adjuvant therapies against active angiogenesis. (HEPATOLOGY 2012;56:2142–2153)
High-throughput monodisperse alginate gel bead formation using microfluidic pseudo-check valve

This paper reports a microfluidic-based, high throughput method for preparing sub-100 micron monodisperse alginate microbeads at rates of up to 1 kHz. The robustness of the bead-generation system allows further scaling up. Various imaging contrast agents have been incorporated into these microbeads, which can be coated with a range of polycations to limit contrast agent leaching. The synthesized beads have been shown to remain stable for up to two months without aggregation. Cells can be co-encapsulated with the contrast agents, allowing imaging-assisted delivery of therapeutic cells.