Miracle-dz/UniFAR-FTUs huggingface dataset:
On the limits of clustering in high dimensions via cost functions

This paper establishes a negative result for clustering: above a certain ratio of random noise to nonrandom information, it is impossible for a large class of cost functions to distinguish between two partitions of a data set. In particular, it is shown that as the dimension increases, the ability to distinguish an accurate partitioning from an inaccurate one is lost unless the informative components are both sufficiently numerous and sufficiently informative. We examine squared error cost functions in detail. More generally, it is seen that the VC‐dimension is an essential hypothesis for the class of cost functions to satisfy for an impossibility proof to be feasible. Separately, we provide bounds on the probabilistic behavior of cost functions that show how rapidly the ability to distinguish two clusterings decays. In two examples, one simulated and one with genomic data, bounds on the ability of squared‐error and other cost functions to distinguish between two partitions are computed. Thus, one should not rely on clustering results alone for high dimensional low sample size data and one should do feature selection. Copyright © 2010 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 4: 30–53 2011
Bacterial species exhibit diversity in their mechanisms and capacity for protein disulfide bond formation

Protein disulfide bond formation contributes to the folding and activity of many exported proteins in bacteria. However, information about disulfide bond formation is limited to only a few bacterial species. We used a multifaceted bioinformatic approach to assess the capacity for disulfide bond formation across this biologically diverse group of organisms. We combined data from a cysteine counting method, in which a significant bias for even numbers of cysteine in proteins is taken as an indicator of disulfide bond formation, with data on the presence of homologs of known disulfide bond formation enzymes. These combined data enabled us to make predictions about disulfide bond formation in the cell envelope across bacterial species. Our bioinformatic and experimental results suggest that many bacteria may not generally oxidatively fold proteins, and implicate the bacterial homolog of the enzyme vitamin K epoxide reductase, a protein required for blood clotting in humans, as part of a disulfide bond formation pathway present in several major bacterial phyla.
Comparison of methods to detect neoplasia in patients undergoing endoscopic ultrasound-guided fine-needle aspiration.

BACKGROUND & AIMS Digital image analysis (DIA) and fluorescence in situ hybridization (FISH) can be used to evaluate biliary strictures with greater accuracy than conventional cytology (CC). We performed a prospective evaluation of the accuracy of CC, compared with that of DIA and FISH, in detection of malignancy in patients undergoing endoscopic ultrasonography (EUS) fine-needle aspiration (FNA). METHODS We collected a minimum of 6 FNA samples from each of 250 patients during EUS. CC or DIA and FISH analyses were performed on every other specimen (from every other FNA pass); patients were randomly assigned to the first test performed. CC slides were reviewed by gastrointestinal cytopathologists who were blinded to all data. Findings from cytohistologic analysis, after a minimum 24-month follow-up period, were used as the standard (n = 202; median age, 65 years). RESULTS Aspirates were collected from lymph nodes (n = 111), pancreas (n = 61), gastrointestinal lumen wall (n = 9), periluminal mass (n = 4), liver (n = 8), and miscellaneous sites (n = 9). Matched samples provided a mean of 3.2 passes for CC and 1.6 passes for DIA and FISH. The data indicate a potential lack of utility for DIA. The combination of CC and FISH detected malignancy with 11% greater sensitivity than CC alone (P = .0002), but specificity was reduced from 100% to 96%. CONCLUSIONS FISH analysis identifies neoplastic lesions with significantly greater sensitivity than CC in patients with diverse pathologies who underwent EUS with FNA, despite limited tissue sampling for FISH analysis.
Is the upgrade rate of atypical ductal hyperplasia diagnosed by core needle biopsy of calcifications different for digital and film-screen mammography?

OBJECTIVE The purpose of this study was to establish the upgrade rate of atypical ductal hyperplasia (ADH) diagnosed by stereotactic vacuum-assisted core needle biopsy for calcifications detected by digital mammography as compared with film-screen mammography. MATERIALS AND METHODS A retrospective record search identified 101 cases of ADH. Criteria included women with calcifications biopsied using stereotactic vacuum-assisted core needle biopsy at our institution between January 2001 and December 2011. The center transitioned from film-screen mammography in 2001 to all digital mammography by 2010. Stereotactic vacuum-assisted core needle biopsies were performed using 11-gauge (59/101 [58%]) or 8-gauge (42/101 [42%]) needles. All pathology was interpreted by breast pathologists using standard criteria. RESULTS Of 101 cases of ADH, 57 (56.4%) were detected using digital and 44 (43.6%) were detected using film-screen mammography. Seven of 57 (12.3%) cases of ADH detected by digital mammography were upgraded to ductal carcinoma in situ (DCIS) (n = 6) or invasive cancer (n = 1). Six of 44 (13.6%) cases of ADH detected by film-screen mammography were upgraded to DCIS (n = 5) or invasive cancer (n = 1) (p = 0.84). There was a trend toward low-grade DCIS in cases detected by digital mammography (3/7 [42.9%]) as compared with film-screen mammography (1/6 [16.7%]) (p = 0.68). A nonsignificant overall higher percentage of upgrades occurred when calcifications were not completely removed (10/52 [19.2%]) as compared with completely removed (3/47 [6.4%]). There was no difference in upgrade rate of stereotactic vacuum-assisted core needle biopsy performed using 11-gauge (7/59 [11.9%]) versus 8-gauge (6/42 [14.3%]) needles. CONCLUSION The upgrade rate of ADH diagnosed by stereotactic vacuum-assisted core needle biopsy was not significantly different between digital and film-screen mammography. The current recommendation for excision of ADH diagnosed by stereotactic vacuum-assisted core needle biopsy should be applied to ADH detected by digital mammography.
A prospective survey of the characteristics, treatments and outcomes of patients with acute coronary syndromes in Europe and the Mediterranean basin; the Euro Heart Survey of Acute Coronary Syndromes (Euro Heart Survey ACS).

AIMS To better delineate the characteristics, treatments, and outcomes of patients with acute coronary syndromes (ACS) in representative countries across Europe and the Mediterranean basin, and to examine adherence to current guidelines. METHODS AND RESULTS We performed a prospective survey (103 hospitals, 25 countries) of 10484 patients with a discharge diagnosis of acute coronary syndromes. The initial diagnosis was ST elevation ACS in 42.3%, non-ST elevation ACS in 51.2%, and undetermined electrocardiogram ACS in 6.5%. The discharge diagnosis was Q wave myocardial infarction in 32.8%, non-Q wave myocardial infarction in 25.3%, and unstable angina in 41.9%. The use of aspirin, beta-blockers, angiotensin converting enzyme inhibitors, and heparins for patients with ST elevation ACS were 93.0%, 77.8%, 62.1%, and 86.8%, respectively, with corresponding rates of 88.5%, 76.6%, 55.8%, and 83.9% for non-ST elevation ACS patients. Coronary angiography, percutaneous coronary interventions, and coronary bypass surgery were performed in 56.3%, 40.4%, and 3.4% of ST elevation ACS patients, respectively, with corresponding rates of 52.0%, 25.4%, and 5.4% for non-ST elevation ACS patients. Among patients with ST elevation ACS, 55.8% received reperfusion treatment; 35.1% fibrinolytic therapy and 20.7% primary percutaneous coronary interventions. The in-hospital mortality of patients with ST elevation ACS was 7.0%, for non-ST elevation ACS 2.4%, and for undetermined electrocardiogram ACS 11.8%. At 30 days, mortality was 8.4%, 3.5%, and 13.3%, respectively. CONCLUSIONS This survey demonstrates the discordance between existing guidelines for ACS and current practice across a broad region in Europe and the Mediterranean basin and more extensively reflects the outcomes of ACS in real practice in this region.
Sporadic pairwise synchronization for decentralized decision-making in mobile agent teams

This paper focuses on the problem of cooperative search and task response in a heterogeneous team of autonomous mobile agents with limited communication. The agents are engaged in a mission to search for targets, to verify their existence, and to take appropriate action for each verified target in an uncertain environment. Each agent makes its decisions based on a subjective information base (SIB), constructed through observation and communication with other agents. Communication between agents is of two types: type I) Each agent periodically broadcasts recently obtained or generated information over a limited radius; and type II) When two agents come sufficiently close, they exchange and merge their entire SIBs. Type I communication results in the diffusion of information among all the agents, and is, in principle, sufficient for decision-making. However, for a fixed population of agents with specified dynamics, this places a lower limit on the range and frequency of broadcast. We hypothesize that including a small amount of type II communication allows for significant decrease in these limits, and leads to a more efficient system. This hybrid approach represents a general communication strategy for multi-agent systems
A Joint Design of Opportunistic Forwarding and Energy-Efficient MAC Protocol in Wireless Sensor Networks

Motivated by the highly dynamic topology in wireless sensor networks with asynchronous duty cycle, and its impact on reliable data delivery, we propose a light-weight opportunistic forwarding (LWOF) scheme. Differing from other recently proposed schemes, LWOF neither employs historical network information nor a contention process to select a forwarder prior to data transmission. It takes advantage of the preamble in low power listening (LPL) media access control (MAC) protocols and dual-channel communication to remove the overhead of making a forwarding decision. Along with LWOF, we propose an energyefficient MAC protocol (LWMAC) with a shortened preamble, to exploit the non-deterministic characteristics of opportunistic forwarding. The preamble length in LWMAC is a function of the node density and sleep duration. Simulation results show that LWOF, along with LWMAC, can provide reliable service of data delivery with less energy consumption.
Characterization and Feasibility Assessment of Recycled Paper Mill Sludges for Land Application in Relation to the Environment

The disposal of industrial paper mill sludge waste is a big issue and has a great importance all over the world. A study was conducted to determine the chemical properties of recycled paper mill sludge (RPMS) and assess its possibilities for land application. RPMS samples were collected from six different paper mills in Malaysia and analyzed for physical and chemical properties, heavy metals, polycyclic aromatic hydrocarbons, 13C-NMR spectra and for the presence of dioxins/furans. The RPMS was dewatered, sticky with a strong odour, an average moisture of 65.08%, pH 7.09, cation exchange capacity (CEC) 14.43 cmol (+) kg–1, N 1.45, P 0.18, K 0.12, Ca 0.82, Mg 0.73, Na 0.76 and Al, 1.38%. The polycyclic aromatic hydrocarbons (PAHs) and heavy metals levels were below the standard Class 2 limits. The dioxin and furan were in below the standard concentration of Class 1. The most prominent peak in the 13C-NMR spectra of RPMS was centered at 31 ppm, proving the presence of methylene (-CH2) groups in long aliphatic chains, with lipids and proteins. The signal at 89 ppm and highly shielded shoulder at 83 ppm were due to presence of cellulose carbon C-4, and the peak at 63 and 65 ppm was due to the cellulose carbon spectrum. The RPMS therefore contains significant amount of nutrients with safe levels of heavy metals and PAHs for environment and can be used as a fertilizer and soil amendment for land application.
Poly(ethylene oxide) facilitates the characterization of an affinity between strongly basic proteins with DNA by affinity capillary electrophoresis

In order to study kin17 protein‐DNA affinity, we have developed a fast and reproducible capillary electrophoresis (CE) analysis of a strongly basic protein: kin17 protein, using a nonpermanent coating based on poly(ethylene oxide) (PEO) to avoid adsorption of kin17. The coating procedure was optimized to provide a residual and stable electroosmotic flow (EOF = 5 × 10−5 cm2/V × s), exhibiting RSD of 0.3% and excellent long‐term stability. Good intraday and interday reproducibility of kin17 migration times (0.8 and 0.3% relative standard deviation (RSD), respectively) enabled us to consider that the recovery percentage obtained for kin17 protein was satisfactory (79%). The potential of this PEO‐based coating procedure was evaluated for affinity CE method in order to study the affinity of kin17 protein for two single‐stranded DNA (ssDNA) models: polydeoxyadenylic acid and polydeoxycytidilic acid (pdA and pdC). Binding constants (1.5×107 ± 17% and 1.7×107 + 25%M−1) were evaluated assuming a 1:1 affinity between kin17 and pdA or pdC, respectively.
Comparison of Gentamicin and Kanamycin Alone and in Combination with Ampicillin in Experimental Escherichia coli Bacteremia and Meningitis

ABSTRACT: The conventional antimicrobial therapy of gram-negative infection in the newborn is the combination of ampicillin and an aminoglycoside, usually gentamicin or kanamycin. Although gentamicin and kanamycin have been used interchangeably, efficacies of the two drugs have not been carefully compared. In addition, the contribution of ampicillin to the outcome of neonatal gram-negative meningitis is controversial. We evaluated the activity of gentamicin and kanamycin alone and in combinations with ampicillin in vitro and in vivo against a K1 Escherichia coli strain. In vitro, the E. coli strain was relatively sensitive to ampicillin, gentamicin, and kanamycin, with the minimal inhibitory and minimal bactericidal concentrations of 2 and 4, 2 and 2, and 4 and 8 μg/ml, respectively. Checkerboard determinations of minimal inhibitory and minimal bactericidal concentrations of drug combinations exhibited an indifferent response for both ampicillin + gentamicin and ampicillin + kanamycin. However, in vivo studies using an experimental E. coli bacteremia and meningitis model in newbown rats suggested that gentamicin was more effective than kanamycin. This was shown by more rapid bacterial clearance from the blood, a decreased incidence of meningitis in bacteremic animals, and improved survival. Furthermore, the addition of ampicillin improved the outcome of kanamycin, but not gentamicin, suggesting that the contribution of ampicillin may vary depending on the type of aminoglycoside used. These findings suggest that kanamycin is less effective than gentamicin in vivo against E. coli and should be used in combination with ampicillin to achieve an outcome comparable to that of gentamicin in this model of E. coli infection.
Robotically assisted vs laparoscopic hysterectomy among women with benign gynecologic disease.

IMPORTANCE Although robotically assisted hysterectomy for benign gynecologic conditions has been reported, little is known about the incorporation of the procedure into practice, its complication profile, or its costs compared with other routes of hysterectomy. OBJECTIVES To analyze the uptake of robotically assisted hysterectomy, to determine the association between use of robotic surgery and rates of abdominal and laparoscopic hysterectomy, and to compare the in-house complications of robotically assisted hysterectomy vs abdominal and laparoscopic procedures. DESIGN, SETTING, AND PATIENTS Cohort study of 264,758 women who underwent hysterectomy for benign gynecologic disorders at 441 hospitals across the United States from 2007 to 2010. MAIN OUTCOME MEASURES Uptake of and factors associated with utilization of robotically assisted hysterectomy. Complications, transfusion, reoperation, length of stay, death, and cost for women who underwent robotic hysterectomy compared with both abdominal and laparoscopic procedures were analyzed. RESULTS Use of robotically assisted hysterectomy increased from 0.5% in 2007 to 9.5% of all hysterectomies in 2010. During the same time period, laparoscopic hysterectomy rates increased from 24.3% to 30.5%. Three years after the first robotic procedure at hospitals where robotically assisted hysterectomy was performed, robotically assisted hysterectomy accounted for 22.4% of all hysterectomies. The rates of abdominal hysterectomy decreased both in hospitals where robotic-assisted hysterectomy was performed as well as in those where it was not performed. In a propensity score-matched analysis, the overall complication rates were similar for robotic-assisted and laparoscopic hysterectomy (5.5% vs 5.3%; relative risk [RR], 1.03; 95% CI, 0.86-1.24). Although patients who underwent a robotic-assisted hysterectomy were less likely to have a length of stay longer than 2 days (19.6% vs 24.9%; RR, 0.78, 95% CI, 0.67-0.92), transfusion requirements (1.4% vs 1.8%; RR, 0.80; 95% CI, 0.55-1.16) and the rate of discharge to a nursing facility (0.2% vs 0.3%; RR, 0.79; 95% CI, 0.35-1.76) were similar. Total costs associated with robotically assisted hysterectomy were $2189 (95% CI, $2030-$2349) more per case than for laparoscopic hysterectomy. CONCLUSIONS AND RELEVANCE Between 2007 and 2010, the use of robotically assisted hysterectomy for benign gynecologic disorders increased substantially. Robotically assisted and laparoscopic hysterectomy had similar morbidity profiles, but the use of robotic technology resulted in substantially more costs.
Smart Polymers and their Applications: A Review

Smart polymers are materials that respond to small external stimuli. These are also referred as stimuli responsive materials or intelligent materials. Smart polymers that can exhibit stimuli-sensitive properties are becoming important in many commercial applications. These polymers can change shape, strength and pore size based on external factors such as temperature, pH and stress. The stimuli include salt, UV irradiation, temperature, pH, magnetic or electric field, ionic factors etc. Smart polymers are very promising applicants in drug delivery, tissue engineering, cell culture, gene carriers, textile engineering, oil recovery, radioactive wastage and protein purification. The study is focused on the entire features of smart polymers and their most recent and relevant applications. Water soluble polymers with tunable lower critical solution temperature (LCST) are of increasing interest for biological applications such as cell patterning, smart drug release, DNA sequencing etc.
AMFIBIA: A Meta-Model for the Integration of Business Process Modelling Aspects

AMFIBIA is a meta-model that formalizes the essential as- pects and concepts of business process modelling. Though AMFIBIA is not the first approach to formalizing the aspects and concepts of busi- ness process modelling, it is more ambitious in the following respects: First, it is independent from particular modelling formalisms of busi- ness processes and it is designed in such a way that any formalisms for modelling some aspect of a business process can be plugged into AM- FIBIA. Therefore, AMFIBIA is formalism-independent. Second it is not biased toward any aspect of business process and the dierent aspects can be, basically, considered and modelled independently of each other. Moreover, it is not restricted to a fixed set of aspects; further aspects of business processes can be easily integrated. Third, AMFIBIA does not only name and relate the concepts of business process modelling, as it is typically done in ontologies or architectures for business process modelling. Rather, AMFIBIA also captures the interaction among the dierent aspects and concepts, and therefore fully defines the dynamic behaviour of a business process model, with its dierent aspects modelled in dierent notations. To prove this claim, we implemented a prototype of a formalism-independent workflow engine based on AMFIBIA: This workflow engine, also called AMFIBIA, is open for new aspects of busi- ness process modelling and new modelling formalisms can be added to it. In this paper, we will present AMFIBIA and the prototype workflow engine based on this meta-model and discuss the principles and concepts of its design.
Spatial multiplexing for outdoor MIMO-OFDM systems with limited feedback costraint

In this paper we propose a spatial multiplexing technique for the downlink of a multiple-input-multiple-output (MIMO) orthogonal-frequency-division-multiplexing (OFDM) system. For outdoor environments with a limited angular spread at the base station, the proposed technique is able to separate the users' streams through a joint spatial processing at both the transmitter and the receiver requiring only a limited feedback from each user. Adaptive transmission is adopted on each stream to set a fixed probability of error. Numerical simulations show that the proposed technique is able to provide significant throughput gains compared to fixed-beams based approaches proposed in the literature.
Controlling a Motorized Marionette with Human Motion Capture Data

In this paper, we present a method for controlling a motorized, string-driven marionette using motion capture data from human actors and from a traditional marionette operated by a professional puppeteer. We are interested in using motion capture data of a human actor to control the motorized marionette as a way of easily creating new performances. We use data from the hand-operated marionette both as a way of assessing the performance of the motorized marionette and to explore whether this technology could be used to preserve marionette performances. The human motion data must be extensively adapted for the marionette because its kinematic and dynamic properties differ from those of the human actor in degrees of freedom, limb length, workspace, mass distribution, sensors, and actuators. The motion from the hand-operated marionette requires less adaptation because the controls and dynamics are a closer match. Both data sets are adapted using an inverse kinematics algorithm that takes into account marker positions, joint motion ranges, string constraints, and potential energy. We also apply a feedforward controller to prevent extraneous swings of the hands. Experimental results show that our approach enables the marionette to perform motions that are qualitatively similar to the original human motion capture data.
Exploiting Non-local Low Rank Structure in Image Reconstruction

Constrained image models based on linear dependence are commonly used in high dimensional imaging and computer vision to exploit or extract structure, which can be expressed with low rank matrix approximations. Natural images also have a self-similarity property, where features tend to repeat themselves all over the image, and linear dependence relationships may be non-local. To exploit non-local linear dependence structure for image reconstruction, we develop a novel and flexible framework using low rank matrix reconstruction and a union of subspaces model, which is learned using subspace clustering. Subspace clustering makes weaker assumptions about the image than similar methods and also scales to very large-sized problems. We extend this approach for tensors, which are natural representations for images. We demonstrate a benefit of non-local low rank modeling for image denoising and reconstruction of MRI and light field images.