Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Histone Deacetylase 3 as a Biomarker for Tumor Recurrence Following Liver Transplantation in HBV-Associated Hepatocellular Carcinoma

Background Recent studies have shown that high expression levels of class I histone deacetylases (HDACs) correlate with malignant phenotype and poor prognosis in some human tumors. However, the expression patterns and prognostic role of class I HDAC isoforms in hepatocellular carcinoma (HCC) remain unclear. Methodology/Principal Findings The expression patterns and clinical significance of class I HDAC isoforms were assessed by immunohistochemistry in a cohort of 43 hepatitis B virus-associated HCC patients treated with liver transplantation. In addition, the effects of HDAC inhibition on HCC cell behavior were investigated by knockdown of the HDAC isoform with short interfering RNA. Class I HDACs were highly expressed in a subset of HCCs with positivity for HDAC1 in 51.2%, HDAC2 in 48.8%, and HDAC3 in 32.6% of cases. The expression levels of HDAC isoforms were significantly associated with the proliferation index of HCC. Kaplan-Meier curves showed that a high expression level of HDAC2 or HDAC3 implicated significantly reduced recurrence-free survival. Cox proportional hazards model analysis revealed HDAC3 overexpression was an unfavorable independent prognostic factor (P = 0.002; HR 3.907). In vitro, inhibition of HDAC2 and HDAC3, but not HDAC1, suppressed proliferation and the invasiveness of liver cancer cells. Conclusions/Significance Our findings demonstrate that HDAC3 plays a significant role in regulating tumor cell proliferation and invasion, and it could be served as a candidate biomarker for predicting the recurrence of hepatitis B virus-associated HCC following liver transplantation and a potential therapeutic target.
Advanced Metal Gate/High-K Dielectric Stacks for High-Performance CMOS Transistors

1. Abstract We have successfully engineered n-type and p-type metal electrodes with the correct work functions on high-K gate dielectrics for high-performance CMOS applications. The resulting metal gate/high-K dielectric stacks have i) equivalent oxide thickness (EOT) of 1.0nm with negligible gate oxide leakage, ii) desirable transistor threshold voltages for n-and p-channel MOSFETs, and iii) transistor channel mobilities close to those of SiO2. The CMOS transistors fabricated with these advanced metal gate/high-K dielectric stacks achieve the expected high drive current performance. 2. Introduction For more than 15 years the physical thickness of SiO2 has been aggressively scaled for low-power, high-performance CMOS applications. Figure 1 shows the physical thickness trend of SiO2. Recently SiO2 with physical thickness of 1.2nm (see Fig. 2) has been successfully implemented in the 90nm logic node [1]. In addition, SiO2 with physical thickness of 0.8nm (see Fig. 3) has been demonstrated in the laboratory [2-3]. Continual gate oxide scaling, however, will require the use of dielectric materials with higher dielectric constant (K) since i) the gate oxide leakage is increasing with decreasing SiO2 thickness, and ii) SiO2 is running out of atoms for further scaling. So far t he most common high-K dielectric materials investigated by both academia and industry are Hf-based and Zr-based [4-5]. 3. Challenges in Replacing SiO2 with High-K Dielectrics 3a. PolySi/High-K Dielectric Stack There are two typical problems in replacing polySi/SiO2 with the polySi/high-K dielectric stack for high-performance CMOS applications. First, high-K dielectrics and polySi are incompatible due to the Fermi level pinning at the polySi/high-K interface [6], which causes high threshold voltages in MOSFET transistors. The Fermi level pinning is most likely caused by defect formation at the polySi/high-K dielectric interface, as illustrated in Fig. 4. Second, polySi/high-K transistors exhibit severely degraded channel mobility due to the coupling of low energy surface optical (SO) phonon modes arising from the polarization of the high-K dielectric to the inversion channel charge carriers [7-8]. 3b. Metal-gate/High-K Dielectric Stack Metal gate electrodes may be more effective than polySi in screening the high-K SO phonons from coupling to the channel under inversion conditions, resulting in improved channel mobility [7-8]. However, the use of high-K/metal-gate require a n-type metal and a p-type metal with the right work functions on the high-K dielectric for high-performance CMOS logic applications on bulk Si [9]. So far, all the metal gate electrodes reported in literature have work functions that are mid-gap or …
Phylogeny and Patterns of Diversity of Goat mtDNA Haplogroup A Revealed by Resequencing Complete Mitogenomes

We sequenced to near completion the entire mtDNA of 28 Sardinian goats, selected to represent the widest possible diversity of the most widespread mitochondrial evolutionary lineage, haplogroup (Hg) A. These specimens were reporters of the diversity in the island but also elsewhere, as inferred from their affiliation to each of 11 clades defined by D-loop variation. Two reference sequences completed the dataset. Overall, 206 variations were found in the full set of 30 sequences, of which 23 were protein-coding non-synonymous single nucleotide substitutions. Many polymorphic sites within Hg A were informative for the reconstruction of its internal phylogeny. Bayesian and network clustering revealed a general similarity over the entire molecule of sequences previously assigned to the same D-loop clade, indicating evolutionarily meaningful lineages. Two major sister groupings emerged within Hg A, which parallel distinct geographical distributions of D-loop clades in extant stocks. The pattern of variation in protein-coding genes revealed an overwhelming role of purifying selection, with the quota of surviving variants approaching neutrality. However, a simple model of relaxation of selection for the bulk of variants here reported should be rejected. Non-synonymous diversity of Hg's A, B and C denoted that a proportion of variants not greater than that allowed in the wild was given the opportunity to spread into domesticated stocks. Our results also confirmed that a remarkable proportion of pre-existing Hg A diversity became incorporated into domestic stocks. Our results confirm clade A11 as a well differentiated and ancient lineage peculiar of Sardinia.
Time-Induced Progressive Alteration of Kir Current in Cerebral Smooth Muscle Cells of Stroke-Prone Spontaneously Hypertensive Rats

We investigated the involvement of potassium inward rectifier current (Kir) impairment in smooth muscle cells of cerebral arteries under the condition of increased susceptibility of stroke, in spontaneously hypertensive stroke-prone (SHRsp) rats compared to spontaneously hypertensive (SHR) ones as well as to controls (WKY). Kir current was studied with whole-cell patch-clamp techniques on freshly isolated single smooth muscle cells (SMC) of middle cerebral artery (MCA) from SHRsp, SHR, and WKY male rats (are range 12–32 weeks). A significant and progressive Kir current density reduction was observed on SMC of SHRsp rats from the 22nd week of age on, as opposed to the Kir current density stability observed over the same time in the SMC of WKY and SHR rats. The Kir density alteration was correlated to the age of the SHRsp animals. These results suggest that in the cerebral vascular smooth muscle cells of SHRsp rats, there is a progressive Kir channel impairment, leading to a reduction of Kir current density. This impairment may underpin a lack of vasodilation of the MCA and be implicated in the stroke-proneness observed on SHRsp animals.
Sampling-based depth recovery in dynamic environments with motion assistance

This paper extends one state-of-the-art filter-based depth recovery method in dynamic environments with motion assistance and sampling. Our method fuses a depth data stream and a visual image stream, well calibrated, to achieve a high quality depth representation of the dynamic environments. For motion assistance, we use the optical flow between visual images to calculate the position of each point in target frame, and use the coordinates of this position as our new features named as Projection Coordinates (PC). After using these new features together with classical features (such as color, image coordinates, and time) to build a whole feature space, we propose a sampling-based High Dimensional Gaussian Filter (HDGF) framework for depth recovery. For any target point, we first find its k nearest neighbors in the feature space, which have corresponding known depth values, and calculate its distance to each neighbor. Then, we use a HDGF to integrate these k distances and k known depth values, to estimate the depth of the target point. Our method shows significant advantages in both qualitative and quantitative comparisons with the state-of-the-art method.
Compliance with vessel speed restrictions to protect North Atlantic right whales

Environmental regulations can only be effective if they are adhered to, but the motivations for regulatory compliance are not always clear. We assessed vessel operator compliance with a December 2008 regulation aimed at reducing collisions with the endangered North Atlantic right whale that requires vessels 65 feet or greater in length to travel at speeds of 10 knots or less at prescribed times and locations along the U.S. eastern seaboard. Extensive outreach efforts were undertaken to notify affected entities both before and after the regulation went into effect. Vessel speeds of 201,862 trips made between November 2008 and August 2013 by 8,009 individual vessels were quantified remotely, constituting a nearly complete census of transits made by the regulated population. Of these, 437 vessels (or their parent companies), some of whom had been observed exceeding the speed limit, were contacted through one of four non-punitive information programs. A fraction (n = 26 vessels/companies) received citations and fines. Despite the efforts to inform mariners, initial compliance was low (<5% of the trips were completely <10 knots) but improved in the latter part of the study. Each notification/enforcement program improved compliance to some degree and some may have influenced compliance across the entire regulated community. Citations/fines appeared to have the greatest influence on improving compliance in notified vessels/companies, followed in order of effectiveness by enforcement-office information letters, monthly summaries of vessel operations, and direct at-sea radio contact. Trips by cargo vessels exhibited the greatest change in behavior followed by tanker and passenger vessels. These results have application to other regulatory systems, especially where remote monitoring is feasible, and any setting where regulatory compliance is sought.
Cell proliferation in the attainment of constant sizes and shapes: the Entelechia model.

The Entelechia model is a generative model of morphogenesis where individual cells exhibit surface labels that express scalar difference and planar polarity along two orthogonal axes X and Y. The amount of surface label depends on the level of Martial (M) gene product within each cell. The model assumes that the confrontation of cells on both sides of compartment borders causes an increase in their level of M gene expression. The resulting disparity between the M value of border cells and that of their neighbors induces the latter to divide. After each division the daughter cells increase their own M value, and allocate to the best matching value position. The increase in M value at the borders therefore extends through the anlage in a cascade of proliferation. The Entelechia condition is reached when the border cells attain the species-specific maximal M values, and the value differences between adjacent cells become indistinguishable. Computer simulations reveal that this model accounts for a variety of observations made on imaginal discs, e.g., 1) each disc attains a constant size in terms of number of cells, independently of the growing conditions; 2) clonal restrictions separate populations of cells which proliferate by intercalar growth; 3) dissociated cells are capable of reconstructing original patterns upon reaggregation, and 4) genetic mosaics of morphogenetic mutations show local effects that may differ depending on the position of the mutant cells in the growing anlage.
Complex preferences for the integration of neural codes

This paper presents a complex preference framework of integrating pulsed neural networks into neural/symbolic hybrid approaches. In particular, we introduce an interpretation of neural codes as multidimensional complex neural preferences and preference classes which allow the integration of knowledge from different neural and symbolic models. We define some basic operations on complex preferences and preference classes that allow them to be directly integrated into symbolic models. Furthermore, we show the interpretation of mean firing rate, time-to-first-spike, synchrony and phase codes as complex neural preferences and the interpretation of the operations on preference classes of these codes. The symbolic interpretation and simultaneous processing of mean firing rate and pulse coding schemes in a preferences framework are addressed.
The more you learn , the less you store : memory-controlled incremental support vector machines

The capability to learn from experience is a key property for a visual recognition algorithm working in realistic settings. This paper presents an SVM-based algorithm, capable of learning model representations incrementally while keeping under control memory requirements. We combine an incremental extension of SVMs [1] with a method reducing the number of support vectors needed to build the decision function without any loss in performance [2], introducing a parameter which permits a user-set trade-off between performance and memory. The resulting algorithm is guaranteed to achieve the same recognition results as the original incremental method while reducing the memory growth. Moreover, experiments in two domains of material and place recognition show the possibility of a consistent reduction of memory requirements with only a moderate loss in performance. For example, results show that when the user accepts a reduction in recognition rate of 5%, this yields a memory reduction of up to 50%.
Gun DNA Immunization T Cell Responses in Gene + for Inducing CD8 Cross-Priming as a Predominant Mechanism

DNA immunization induces CD8 (cid:1) CTL responses by bone marrow-derived APCs, which are directly transfected with a plasmid DNA and/or acquire Ags from DNA-transfected non-APCs. To investigate the relative contribution of DNA-transfected APCs vs non-APCs to the initiation of CD8 (cid:1) T cell responses, we used tissue-speciﬁc promoter-directed gene expression and adoptive transfer systems in gene gun DNA immunization. In this study, we demonstrated that non-APC-speciﬁc gene expressions induced signiﬁcant CD8 (cid:1) CTL and IFN- (cid:2) -producing cells and Ab responses, whereas APC-speciﬁc gene expressions led to moderate CTL and IFN- (cid:2) -producers, but no Ab responses. Interestingly, mice immunized with a non-APC-speciﬁc plasmid induced more rapid, vigorous, and prolonged proliferation of adoptively transferred Ag-speciﬁc CD8 (cid:1) T cells than APC-speciﬁc plasmid-immunized mice. In addition, the in vivo proliferative responses elicited by a non-APC-speciﬁc plasmid administration were dependent on TAP, but were independent of CD4 (cid:1) T cell help. Collectively, our results suggest that cross-priming, in which Ags expressed in non-APCs are taken up, processed, and presented by APCs, plays an important role in the initiation, magnitude, and maintenance of CD8 (cid:1) T cell responses in gene gun DNA immunization. The Journal of Immunology, 2001, 167: 5549–5557. t DNA immunization potent (cid:1) T cell responses are for viral clear-ance and host protection (1, 2). These responses have been an Ag-presenting ability of bone marrow-derived contrast, there was no luciferase activity in the nonspeciﬁc COS-7 cell line. We also could not detect any signiﬁcant luciferase activity in other cell lines including the muscle, kidney, melanoma, ovary, colon, cer-vix, liver, and ﬁbroblast cell lines (data not shown). Similar results were also obtained when the green ﬂuorescent protein (GFP) was used as the reporter gene (data not shown). It was notable that the relative luciferase activity driven by the K14 promoter in HaCaT cells was similar to that driven by the CD11b or the MHCII promoter in RAW264.7 cells, although their activities were approxi-mately two to three times lower than those driven by the CMV promoter. These results indicate that a plasmid DNA containing the CD11b, the MHCII, or the K14 promoter would allow us to separately investigate the in vivo function of DNA-transfected APCs and non-APCs after gene gun DNA immunization.
Organizational commitment among licensed practical nurses: Exploring associations with empowerment, conflict, and trust

Healthcare organizational stability rests on organizational commitment. This study adds to the literature that demonstrates the mediating effects of empowerment on organizational commitment in a long understudied population of Licensed Practical Nurses (LPNs) employed full time. Organizational commitment encourages extra role behaviors, paramount in times of decreasing resources such as that facing all sectors of national health care. A 45-item work environment survey was distributed to all registered LPNs employed full time in one state (N = 5486) and 1164 (21%) responded. Data revealed that empowerment is associated with LPN organizational commitment and mediates effects of organizational conflict and trust on commitment to the organization. Further empowerment and organizational climate, especially organizational conflict and trust, matter to full-time LPNs. Results contribute to initial knowledge about linkages to organizational commitment among lower educated and less skilled nurses and have implications for managers in healthcare settings who employ full-time LPNs. LPNs may be more highly valued by scholars in nursing if LPN-sensitive research shows their continued value and cost effectiveness for specific and important organizational outcomes, especially in light of the growing geriatric population that will require increasingly chronic and routine care. As bedside RNs become more highly educated, they may increasingly disdain employment that involves the repetitive, low-risk patient care that LPNs currently provide. There is a real need to better understand the current work environment of those employees responsible for delivering low-risk repetitive healthcare to chronically ill and elderly patients. LPNs are key among those.
Water Compression Visualisation

Molecular simulations generate large amounts of data, over many days. The ability to compress this data will be advantageous; both for storage, as well as data transmission. As molecular simulations use water as the solvent for the simulation, there are large amounts of water present in the volume. The water compression project thus aims to achieve high compression ratios by exploiting certain structural properties of water to effectively compress water dominant molecular simulations. The visualisation aspect of the water compression project is there to support the main compression goal of the system, the compression of molecular simulations. To facilitate compression, the molecular data is quantised: floating point values are mapped to integer values. The visualisation component of the system has thus been split up into two main parts: visualisation of the molecular data, and an experiment to measure the perceptual impact of quantisation. The quantisation experiment is used to recommend a quantisation level for data used for viewing. A number of different visualisation techniques have been developed in order to visualise the molecular data, two of which were used in the quantisation experiment. The quantisation experiment tested 4 different quantisation levels: 4, 6, 8 and 10 bit quantisation levels. The results indicate that 8 and 10 bit quantisation yields results that are perceived to be similar to the original data. Further quantisation to 6 and 4 bits, yields results that are rated significantly different from the original data. Thus, 8 bit quantisation is the recommended quantisation level to use for data used for visual inspection.
Arithmetic Coding- A Reliable Implementation

Arithmetic compression scheme is one of the commonly used techniques to represent more amount of information using the available units of resources. It has been known that arithmetic coding has a better coding efficiency than other compression schemes. However, when used in an error prone environment, the poor error resistance property of the method is a severe disadvantage. It is difficult to locate an error when arithmetic coding is used and a large portion of a data must be discarded when an error occurs. In this paper, a novel technique is proposed to improve the error resilience of arithmetic coding, in which the decoder is less affected by the errors caused in the transmission of data over the network. A comparative study with the basic algorithm demonstrates that the time performance of the error resilient arithmetic coder is somewhat comparable to the basic algorithm. General Terms Arithmetic Coding, Error Resilient Coder
Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved α+β core domain and an auxiliary C-terminal treble-clef zinc finger

The first structures from the FmdE Pfam family (PF02663) reveal that some members of this family form tightly intertwined dimers consisting of two domains (N-terminal α+β core and C-terminal zinc-finger domains), whereas others contain only the core domain. The presence of the zinc-finger domain suggests that some members of this family may perform functions associated with transcriptional regulation, protein–protein interaction, RNA binding or metal-ion sensing.
Based on PSoC Electric Angle Meter

This paper presents a new design scheme that an electronic protractor includes two swing arms and one variable resistor located on the top of swing arms for measuring angles. The variable resistor connects the liquid crystal display (LCD) screen through an angle-to-voltage (A/V) controlled circuit, an analog-to-digital (A/D) converter, a single chip processor, and a LCD driver. The protractor can change the resistance of the variable resistor simultaneously and display the measuring angle on the LCD screen through the processing of the A/V controlled circuit, the A/D converter, single chip processor, and the LCD driver when the swing arms are open or close to make the angular deviations. The present electronic protractor is claimed on those measuring devices through the above process.
Effect of Lactation on Physico-Chemical Properties of Local Goat Milk

The present investigation was undertaken in the Department of Animal Husbandry and Dairying, Dr.PDKV. , Akola. The main objective of present investigation was to study the effect of lactation on composition and physico-chemical properties of local goat milk. During the entire study the fresh goat milk samples were collected from local goats in I, II, III and IV lactations of which four goats were in each lactation. The lactation had significant increasing effect on fat, protein, ash, TS, SNF, titratable acidity and viscosity. All milk components are gradually increased from I to IV lactation with exception of lactose and pH.