Miracle-dz/UniFAR-FTUs huggingface dataset:
Quality Measures for Gene Expression Biclusters

An noticeable number of biclustering approaches have been proposed proposed for the study of gene expression data, especially for discovering functionally related gene sets under different subsets of experimental conditions. In this context, recognizing groups of co-expressed or co-regulated genes, that is, genes which follow a similar expression pattern, is one of the main objectives. Due to the problem complexity, heuristic searches are usually used instead of exhaustive algorithms. Furthermore, most of biclustering approaches use a measure or cost function that determines the quality of biclusters. Having a suitable quality metric for bicluster is a critical aspect, not only for guiding the search, but also for establishing a comparison criteria among the results obtained by different biclustering techniques. In this paper, we analyse a large number of existing approaches to quality measures for gene expression biclusters, as well as we present a comparative study of them based on their capability to recognize different expression patterns in biclusters.
Reversible jump MCMC for Bayesian NMF

Figure 1: Illustration of birth-death and splitmerge proposals: Components are removed, and new components are generated and refined through restricted Gibbs sampling. The final proposed components are generated through one last restricted Gibbs sweep. The proposal density is computed by keeping track of all transition probabilities in the final Gibbs sweep. In non-negtive matrix factorization (NMF), a data matrix X is modelled as the product of two matrices A and B with nonnegative entries. Taking a Bayesian approach to NMF entails specifying an appropriate likelihood and priors for the factorizing matrices and the number of components K (colums of A and rows of B.) Related to Bayesian NMF is also models based on the Indian buffet process [5, 4, 2]. For a given value of K, inference can be performed using standard methods such as Gibbs sampling [7] or variational approximation [1]; however, infering K is more challenging. Computationally expensive approaches including Chib’s method [7], thermodynamic integration, and reversible jump independence MCMC [8] have been proposed.
Autoinduction and signal transduction in the regulation of staphylococcal virulence

The accessory genes of Staphylococcus aureus, in‐cluding those involved in pathogenesis, are controlled by a complex regulatory network that includes at least four two‐component systems, one of which, agr, is a quorum sensor, an alternative sigma factor and a large set of transcription factors, including at least two of the superantigen genes, tst and seb. These regulatory genes are hypothesized to act in a time‐ and population density‐dependent manner to integrate signals received from the external environment with the internal metabolic machinery of the cell, in order to achieve the production of particular subsets of accessory/virulence factors at the time and in quantities that are appropriate to the needs of the organism at any given location. From the standpoint of pathogenesis, the regulatory agenda is presumably tuned to particular sites in the host organism. To address this hypothesis, it will be necessary to understand in considerable detail the regulatory interactions among the organism's numerous controlling systems. This review is an attempt to integrate a large body of data into the beginnings of a model that will hopefully help to guide research towards a full‐scale test.
Cerebral blood flow measurements and electroencephalograms during carotid endarterectomy.

✓ Ninety-three endarterectomies for carotid stenosis were monitored with cerebral blood flow (CBF) measurements, and 113 with both CBF measurements and a continuous electroencephalogram (EEG). Significant CBF increase occurred only when carotid endarterectomy was for a stenosis greater than 90%. A high correlation between CBF and EEG indicated when a shunt was required. To sustain a normal EEG, the CBF ascertained by the initial slope technique must be 18 ml/100 gm/min at an arterial carbon dioxide tension (PaCO2) of 40 torr. The degree of EEG change below this level during occlusion reflected the severity of reduced blood flow and was reversible with replacement of a shunt. The value and limitations of these monitoring techniques and a concept of ischemic tolerance and critical CBF are discussed.
External fixation or arteriogram in bleeding pelvic fracture: initial therapy guided by markers of arterial hemorrhage.

BACKGROUND Bleeding pelvic fractures (BPF) carry mortality as high as 60%, yet controversy remains over optimal initial management. Some base initial intervention on fracture pattern, with immediate external fixation (EX FIX) in amenable fractures aimed at controlling venous bleeding. Others feel ongoing hemodynamic instability indicates arterial bleeding, and prefer early angiography (ANGIO) before EX-FIX. Our aim was to evaluate markers of arterial bleeding in patients with BPF, thus identifying patients requiring early ANGIO regardless of fracture pattern. METHODS Patients with pelvis fracture were identified from a Level I trauma center registry over a 7-year period and records reviewed. From this group, two subsets were analyzed: those with initial hypotension related to pelvic fracture, and those without hypotension who underwent pelvic ANGIO. Data included hemodynamics, response to resuscitation, presence of contrast blush on CT, fracture treatment and outcome. Adequate response to initial resuscitation (R) was defined as a sustained (>2 hours) improvement of systolic blood pressure to >90 mm Hg systolic after the administration of < or = 2 units packed red blood cells. Those with repeated episodes of hypotension despite resuscitation were classified as non-responders (NR) RESULTS: From 1/94-1/01, 1171 patients were admitted with pelvic ring fracture. Thirty-five (0.3%) had hypotension attributable to pelvis fracture. 28 fell into the NR group, and 26 of these underwent ANGIO. Nineteen (73%) showed arterial bleeding while 3 resuscitation response patients underwent ANGIO with none demonstrating bleeding (p = 0.03). Sensitivity and specificity of inadequate response to initial resuscitation for predicting the presence of arterial bleeding on ANGIO were 100% and 30% respectively while negative and positive predictive value were 100% and 73%. In patients with fractures amenable to external fixation (n = 16), 44% had arterial bleeding on ANGIO, and all were in the NR group. An additional 17 patients without hypotension also underwent ANGIO. Contrast blush on admission CT was seen in 4, 3 of which had arterial bleeding seen on ANGIO (75%). Sensitivity and specificity for contrast blush in predicting bleeding on ANGIO were 60% and 92% with positive and negative predictive value being 75% and 85%. CONCLUSIONS In patients with hypotension and pelvic fracture, therapy selection based on initial response to resuscitation in BPF yields a 73% positive ANGIO rate in NR patients. Delay in ANGIO for EX FIX in patients with amenable fractures would have delayed embolization in the face of ongoing arterial bleeding in 44% of patients. In stable patients with pelvic fracture, contrast blush also indicates a high likelihood of arterial injury and ANGIO is indicated. Optimal therapy in the face of BPF requires early determination of the presence of arterial bleeding so that ANGIO can be rapidly obtained, and response to initial resuscitation as well as the presence of contrast blush aid in this decision.
Clinical, Pathological and Immunohistochemical Effects of Arsenical-Ferruginous SPA Waters on Mild-To-Moderate Psoriatic Lesions: A Randomized Placebo-Controlled Study

Thermalism and spa treatments are traditionally considered effective in a number of dermatologic inflammatory conditions, yet there is scarce evidence about spring water effectiveness on psoriasis in a daily setting. We enrolled 34 patients with mild-to-moderate psoriasis in a double-blind, randomized, placebo-contralaterally-controlled trial, to evaluate Levico and Vetriolo arsenical-ferruginous water effectiveness on psoriatic lesions by daily 20-minute wet packing for 12 consecutive days. Clinical, histopathologic and immunohistochemical parameters were considered. A statistically significant difference between spa water-treated lesions and placebo-treated lesions in the same patients was demonstrated for histopathologic and immunohistochemical parameters. Since iron ions have an antiproliferative effect on epithelia, and magnesium ions have an anti-inflammatory effect, Levico and Vetriolo water effectiveness on psoriasis could be addressed to their content of these ions.
A new mechanism to deal with process variability in NoC links

Associated with the ever growing integration scale of VLSI technologies is the increase in process variability, which makes silicon devices to become less predictable. In the context of network-on-chip (NoC), this variability affects the maximum frequency that could be sustained by each wire of the link that interconnects two cores in a CMP system.
Generalised blind sampling of images

Blind sampling is a sampling scheme which uses no knowledge about the image except for the measurements it obtains. An adaptive blind sampling scheme makes use of that knowledge to wisely choose the next sample. In this work we consider generalised sampling, where each measurement is obtained by computing an inner product between the image and some mask. The context of this paper is second order statistical models for images. We discuss the reconstruction of images from arbitrary generalised sampling and present criteria for selecting an optimal mask from a dictionary (family) of masks, or from the set of all possible masks. The latter case leads to PCA. We further propose adaptive sampling schemes that produce different sets of sampling masks for different images, and experimentally verify the advantage of the adaptive schemes over nonadaptive ones.
NONCODE v2.0: decoding the non-coding

The NONCODE database is an integrated knowledge database designed for the analysis of non-coding RNAs (ncRNAs). Since NONCODE was first released 3 years ago, the number of known ncRNAs has grown rapidly, and there is growing recognition that ncRNAs play important regulatory roles in most organisms. In the updated version of NONCODE (NONCODE v2.0), the number of collected ncRNAs has reached 206 226, including a wide range of microRNAs, Piwi-interacting RNAs and mRNA-like ncRNAs. The improvements brought to the database include not only new and updated ncRNA data sets, but also an incorporation of BLAST alignment search service and access through our custom UCSC Genome Browser. NONCODE can be found under http://www.noncode. org or http://noncode.bioinfo. org.cn.
Coexpression of multiple acetylcholine receptor genes in neurons: quantification of transcripts during development

A large family of genes encoding subunits of nicotinic ACh receptors (AChRs) has been identified in vertebrates and shown to be expressed in the nervous system. The multiplicity of genes raises questions about which gene products coassemble to produce native receptor subtypes and how the expression of receptor genes is regulated in neurons. We report here that five neuronal AChR genes are expressed in the chick ciliary ganglion at both early and late times in development. Quantitative RNase protection experiments demonstrated that at embryonic day 18 (E18) the ganglion contains about 1800 copies of alpha 7 transcript per neuron, 900 copies of alpha 3 transcript per neuron, and 200–300 copies each of alpha 5, beta 2, and beta 4 transcripts per neuron. The same five genes are expressed at significantly lower levels at E8 but show the same rank order of abundance in transcripts per neuron. Few, if any, transcripts were found for the alpha 2, alpha 4, alpha 8, and beta 3 AChR genes in ciliary ganglion RNA at either E8 or E18. The 6- and 13- fold increases previously reported for two classes of AChRs on the neurons between E8 and E18 approximate the 4–14-fold increases observed here in AChR gene mRNA levels per neuron over the same time period. The alpha 3, alpha 5, alpha 7, and beta 4 genes have previously been correlated with subunits of ciliary ganglion AChRs, but the beta 2 gene has not. The abundance of beta 2 transcripts raises the possibility either that the known AChRs in the ganglion have a more complex subunit composition than previously described or that additional receptor subtypes remain to be discovered. Northern blot analysis revealed no changes in transcript pattern for the alpha 3, alpha 5, and beta 4 genes between E8 and E18; a small change may occur in the transcript pattern for the alpha 7 gene. In situ hybridizations demonstrated that alpha 5 and beta 4 transcripts are expressed in essentially all ciliary ganglion neurons as has been shown previously for the more abundant alpha 3 transcript and inferred for the alpha 7 transcript. The results indicate that neurons can stably coexpress multiple AChR genes, including three of the alpha type, and that transcript levels may be rate limiting for accumulation of AChRs during development.
Airway smooth muscle hypertrophy and hyperplasia in asthma.

RATIONALE Increased thickness of the airway smooth muscle (ASM) layer in asthma may result from hyperplasia or hypertrophy of muscle cells or increased extracellular matrix (ECM). OBJECTIVES To relate ASM hypertrophy, ASM hyperplasia, and deposition of ECM to the severity and duration of asthma. METHODS Airways from control subjects (n = 51) and from cases of nonfatal (n = 49) and fatal (n = 55) asthma were examined postmortem. Mean ASM cell volume (V(C)), the number of ASM cells per length of airway (N(L)), and the volume fraction of extracellular matrix (f(ECM)) within the ASM layer were estimated. Comparisons between subject groups were made on the basis of general linear regression models. MEASUREMENTS AND MAIN RESULTS Mean V(C) was increased in the large airways of cases of nonfatal asthma (P = 0.015) and fatal asthma (P < 0.001) compared with control subjects. N(L) was similar in nonfatal cases and control subjects but increased in large (P < 0.001), medium (P < 0.001), and small (P = 0.034) airways of cases of fatal asthma compared with control subjects and with nonfatal cases (large and medium airways, P ≤ 0.003). The f(ECM) was similar in cases of asthma and control subjects. Duration of asthma was associated with a small increase in N(L). CONCLUSIONS Hypertrophy of ASM cells occurs in the large airways in both nonfatal and fatal cases of asthma, but hyperplasia of ASM cells is present in the large and small airways in fatal asthma cases only. Both are associated with an absolute increase in ECM. Duration of asthma has little or no effect on ASM hypertrophy or hyperplasia or f(ECM).
Sevoflurane mimics ischemic preconditioning effects on coronary flow and nitric oxide release in isolated hearts.

BACKGROUND Like ischemic preconditioning, certain volatile anesthetics have been shown to reduce the magnitude of ischemia/ reperfusion injury via activation of K+ adenosine triphosphate (ATP)-sensitive (K(ATP)) channels. The purpose of this study was (1) to determine if ischemic preconditioning (IPC) and sevoflurane preconditioning (SPC) increase nitric oxide release and improve coronary vascular function, as well as mechanical and electrical function, if given for only brief intervals before global ischemia of isolated hearts; and (2) to determine if K(ATP) channel antagonism by glibenclamide (GLB) blunts the cardioprotective effects of IPC and SPC. METHODS Guinea pig hearts were isolated and perfused with Krebs-Ringer's solution at 55 mm Hg and randomly assigned to one of seven groups: (1) two 2-min total coronary occlusions (preconditioning, IPC) interspersed with 5 min of normal perfusion; (2) two 2-min occlusions interspersed with 5 min of perfusion while perfusing with GLB (IPC+GLB); (3) SPC (3.5%) for two 2-min periods; (4) SPC+GLB for two 2-min periods; (5) no treatment before ischemia (control [CON]); (6) CON+GLB; and (7) no ischemia (time control). Six minutes after ending IPC or SPC, hearts of ischemic groups were subjected to 30 min of global ischemia and 75 min of reperfusion. Left-ventricular pressure, coronary flow, and effluent NO concentration ([NO]) were measured. Flow and NO responses to bradykinin, and nitroprusside were tested 20-30 min before ischemia or drug treatment and 30-40 min after reperfusion. RESULTS After ischemia, compared with before (percentage change), left-ventricular pressure and coronary flow, respectively, recovered to a greater extent (P<0.05) after IPC (42%, 77%), and treatment with SPC (45%, 76%) than after CON (30%, 65%), IPC+GLB (24%, 64%), SPC+GLB (20%, 65%), and CON+GLB (28%, 64%). Bradykinin and nitroprusside increased [NO] by 30+/-5 (means +/- SEM) and 29+/-4 nM, respectively, averaged for all groups before ischemia. [NO] increased by 26+/-6 and 27+/-7 nM, respectively, in SPC and IPC groups after ischemia, compared with an average [NO] increase of 8+/-5 nM (P<0.01) after ischemia in CON and each of the three GLB groups. Flow increases to bradykinin and nitroprusside were also greater after SPC and IPC. CONCLUSIONS Preconditioning with sevoflurane, like IPC, improves not only postischemic contractility, but also basal flow, bradykinin and nitroprusside-induced increases in flow, and effluent [NO] in isolated hearts. The protective effects of both SPC and IPC are reversed by K(ATP) channel antagonism.
A Robust Multi-camera 3D Ellipse Fitting for Contactless Measurements

Ellipses are a widely used cue in many 2D and 3D object recognition pipelines. In fact, they exhibit a number of useful properties. First, they are naturally occurring in many man-made objects. Second, the projective invariance of the class of ellipses makes them detectable even without any knowledge of the acquisition parameters. Finally, they can be represented by a compact set of parameters that can be easily adopted within optimization tasks. While a large body of work exists in the literature about the localization of ellipses as 2D entities in images, less effort has been put in the direct localization of ellipses in 3D, exploiting images coming from a known camera network. In this paper we propose a novel technique for fitting elliptical shapes in 3D space, by performing an initial 2D guess on each image followed by a multi-camera optimization refining a 3D ellipse simultaneously on all the calibrated views. The proposed method is validated both with synthetic data and by measuring real objects captured by a specially crafted imaging head. Finally, to evaluate the feasibility of the approach within real-time industrial scenarios, we tested the performance of a GPU-based implementation of the algorithm.
Non-invasive detection of bladder cancer by identification of abnormal CD44 proteins in exfoliated cancer cells in urine

Aims—To investigate the expression of CD44 proteins in exfoliated urothelial cells and in tumour tissues from bladder cancer patients. A further objective was to evaluate the diagnostic potential of the changes observed in the expression of these proteins as a marker for non-invasive detection of bladder cancer. Methods—Naturally voided urine specimens were collected from 47 patients with bladder cancer or severe urothelial dysplasia (n=3) and from a control group of 43 people with no evidence of neoplastic disease. Exfoliated urothelial cells floating in the urine were pelleted by centrifugation and lysed, and their constituent proteins extracted. The pattern of expression of CD44 proteins in each sample was examined by western blot analysis using a monoclonal antibody, Hermes 3, which recognises an epitope on the polypeptide backbone of the CD44 protein. Immunohistochemical studies were performed on neoplastic (n=10) and normal (n=4) bladder tissue specimens which were snap frozen in liquid nitrogen before examination with antibodies to CD44 gene products (CD44s and CD44v6). Results—Western blot analysis revealed several high molecular weight CD44 isoforms > 160 kDa in urine cell lysates from 75% of patients with histologically confirmed bladder cancer and in two of the three patients with severe dysplasia. Such patterns were not detected in the urine cell pellets from any persons in the control group. Immunohistochemical studies of the tissue distribution of CD44s and CD44v6 showed that the differentiation and maturation of the epithelial cells in the normal bladder mucosa is accompanied by a decrease in CD44 protein expression. However, carcinoma cells overexpress standard and variant CD44 isoforms and continue to do so as they proceed through the thickened epithelial layer to the luminal surface and after they are shed into the urine. Conclusions—The abnormal expression of CD44 proteins in exfoliated cancer cells may be a useful marker for the noninvasive diagnosis of bladder cancer.
Performance in Adaptive Manipulator Control

Effective adaptive controller designs potentially combine high speed and high precision in robot manipulation and further more can considerably simplify high-level programming by providing consistent performance in the face of large varia tions in loads or tasks. A simple, globally tracking-conver gent, direct adaptive manipulator controller has previously been developed and experimentally demonstrated. In this article, we further explore the performance issues linked to a computationally effective implementation. Specifically, we develop a recursive implementation applicable to both open and closed kinematic chains, as well as rules for obtaining minimal parametrizations. We also discuss implementations of the algorithm directly in Cartesian space, the exploitation of kinematic redundancies, and applications to adaptive compliant motion control. These developments are illustrated experimentally on a four-degrees-of-freedom articulated robot arm and suggest a wide range of application well beyond adaptation to grasped loads.
Towards Pay-As-You-Consume Cloud Computing

Cloud computing enables users to perform their computation tasks in the public virtualized cloud using a pay-as-you-go style. Current pay-as-you-go pricing schemes typically charge on the incurred virtual machine hours. Our case studies demonstrate significant variations in the user costs, indicating significant unfairness among different users from the micro-economic perspective. Further studies reveal the reason for such variations is interference among concurrent virtual machines. The amount of interference cost depends on various factors, including workload characteristics, the number of concurrent VMs, and scheduling in the cloud. In this paper, we adopt the concept of pricing fairness from micro economics, and quantitatively analyze the impact of interference on the pricing fairness. To solve the unfairness caused by interference, we propose a pay-as-you-consume pricing scheme, which charges users according to their effective resource consumption excluding interference. The key idea behind the pay-as-you-consume pricing scheme is a machine learning based prediction model of the relative cost of interference. Our preliminary results with Xen demonstrate the accuracy of the prediction model, and the fairness of the pay-as-you-consume pricing scheme.