Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploiting Laguerre functions to improve the feasibility/performance compromise in MPC

This paper develops a novel mechanism for managing the performance and feasibility trade off within predictive control. Specifically, it demonstrates that the potential of Laguerre functions needs more investigation by the community as this offers a simple and effective alternative to the more usual parameterisations using pulse operator in the predictions. The paper develops a simple and efficient dual-mode algorithm using Laguerre functions and demonstrates, by example, the improvements with respect to a conventional approach, in terms of performance and feasibility benefits.
Marine Protected Area

in the south of Italy in the Puglia Region. It is one of the biggest MPA in Italy (16.654 hectares, 32 km of coast) where 27 MPAs have been instituted till now. The objectives of the MPA are to protect marine habitats of outstanding ecological values such as Posidonia oceanica prairies, marine caves and coralligenous habitats, to regulate recreational and commercial activities within its boundaries, to promote environmental education and to perform scientifi c research.
Mutation-analysis driven functional verification of a soft microprocessor

This paper proposes a quality driven, simulation based approach to functional design verification, which applies mainly to IP-level HDL designs with well specified test instruction format and is evaluated on a soft microprocessor core MB-LITE [5]. The approach utilizes mutation analysis as the quality metric to steer an automated simulation data generation process. It leads to a simulation flow with two phases towards an enhanced mutation analysis result. First in a random simulation phase, an in-loop heuristics is deployed and adjusts dynamically the test probability distribution so as to improve the coverage efficiency. Next, for each remaining hard-to-kill mutant, a search heuristics on test input space is developed to iteratively locate a target test, using a specific objective cost function for the goal of killing HDL mutant. The effectiveness of this integrated two-phase simulation flow is demonstrated by the results with the MB-LITE microprocessor IP.
From microbiology to cancer biology: the Rid protein family prevents cellular damage caused by endogenously generated reactive nitrogen species

The Rid family of proteins is highly conserved and broadly distributed throughout the domains of life. Genetic and biochemical studies, primarily in Salmonella enterica, have defined a role for RidA in responding to endogenously generated reactive metabolites. The data show that 2‐aminoacrylate (2AA), a reactive enamine intermediate generated by some pyridoxal 5′‐phosphate‐dependent enzymes, accumulates in the absence of RidA. The accumulation of 2AA leads to covalent modification and inactivation of several enzymes involved in essential metabolic processes. This review describes the 2AA hydrolyzing activity of RidA and the effect of this biochemical activity on the metabolic network, which impacts organism fitness. The reported activity of RidA and the consequences encountered in vivo when RidA is absent have challenged fundamental assumptions in enzymology, biochemistry and cell metabolism regarding the fate of transiently generated reactive enamine intermediates. The current understanding of RidA in Salmonella and the broad distribution of Rid family proteins provide exciting opportunities for future studies to define metabolic roles of Rid family members from microbes to man.
On source transmission over deterministic relay networks

Lossless transmission of a set of correlated sources over a deterministic relay network is considered for two traffic requirements. In distributed multicast, the set of sources are to be delivered to a set of destinations. The source exchange requires all the nodes with access to sources to be able to reconstruct all other sources observed at other nodes. We develop achievable regions and outer bounds for both these situations. For linear deterministic networks, these bounds coincide, yielding a characterization.
Commentaries on Viewpoint: Why do some patients stop breathing after taking narcotics? Ventilatory chemosensitivity as a predictor of opioid-induced respiratory depression VIEWPOINT COMMENT ON VENTILATOR CHEMOSENSITIVITY AS A PREDICTOR OF OPIOID-INDUCED RESPIRATORY DEPRESSION

TO THE EDITOR: Patients who are to undergo opioid-induced ventilatory chemoreceptor depression respond variably to narcotics. This is illustrated in Potter and Moon’s (2) Fig. 1 in which great variability is shown of the hypercapnic ventilatory response (HCVR) test. In patients not undergoing pharmacological alterations (3, 4), there is great uniformity in hydrogen ion (H ) regulation. This might be explained by chemical stimulus being H and not carbon dioxide (CO2). Having tested their patients under partial anesthesia, increasing CO2, Potter and Moon (2) have a mix of stimuli but only an insensitive CO2 stimulus. Above the anaerobic threshold, H only drives ventilation. Patients may seriously underventilate and it does serious harm to patients when putting them under anesthesia. The reason for the variability is that the HCVR and the hypoxic ventilatory response (HVR) test of chemosensitivity may be insensitive and atypical when tested in nonphysiological ranges. This would be especially problematic if the patient has a background of heart or lung disease (4). Normal patients are extremely sensitive to H ventilatory regulation. However, they are insensitive to CO2 regulation over the entire range of chemical receptor control (3, 4). When arterial CO2 competes with hypoxemia or as the stimulus provided by CO2 gas, the CO2 loses its power and arterial [H ] wins. We conclude that the arterial [H ] is the chemical controller rather than CO2. See Fig. 4 in Ref. 3. This concept was in agreement with findings from other groups (1).
Relevance of evolutionary history for food web structure

Explaining the structure of ecosystems is one of the great challenges of ecology. Simple models for food web structure aim at disentangling the complexity of ecological interaction networks and detect the main forces that are responsible for their shape. Trophic interactions are influenced by species traits, which in turn are largely determined by evolutionary history. Closely related species are more likely to share similar traits, such as body size, feeding mode and habitat preference than distant ones. Here, we present a theoretical framework for analysing whether evolutionary history—represented by taxonomic classification—provides valuable information on food web structure. In doing so, we measure which taxonomic ranks better explain species interactions. Our analysis is based on partitioning of the species into taxonomic units. For each partition, we compute the likelihood that a probabilistic model for food web structure reproduces the data using this information. We find that taxonomic partitions produce significantly higher likelihoods than expected at random. Marginal likelihoods (Bayes factors) are used to perform model selection among taxonomic ranks. We show that food webs are best explained by the coarser taxonomic ranks (kingdom to class). Our methods provide a way to explicitly include evolutionary history in models for food web structure.
14C in Urban Secondary Carbonate Deposits: a New Tool for Environmental Study

Abstract Secondary carbonate deposits (similar to speleothems) in urban undergrounds, have been recently highlighted as powerful archives for reconstruction of the historical anthropogenic imprint on the environment. The precise chronology of these secondary carbonate deposits is a key issue for the accurate time reconstruction of environmental conditions. We present three 14C data sets for urban speleothem-like deposits that developed in contrasted man made environments. The first one was sampled in an underground technical gallery of the Palace of Versailles (France), and the other two in a manhole (Saint-Martin spring) of a historical underground aqueduct in Paris (France). The comparison of these records with the bomb peak and relative chronology (laminae counting) allowed us to identify: i) fast carbon transfer from the atmosphere to the urban underground; ii) a high proportion of dead carbon and a high damping effect in relation to possible old carbon stored within urban soils and/or the influence of local fossil carbon burning. This study also shows that the lamination of these deposits is bi-annual in these highly urbanized sites.
Successive convex optimization for point set registration

We propose a new robust point set registration technique utilizing the global information of the two sets, rather than looking locally, for constructing the point-wise correspondence and estimating the transformation in between. Then, a multi-scale scheme further extends the algorithm to handling nonlinear diffeomorphic transformations. The algorithm is tested on 3D geometric and protein structure data sets to demonstrate its robustness to severe distortions.
Hot air drying characteristics and nutrients of apricot armeniaca vulgaris lam pretreated with Radio Frequency(RF)

Apricot pretreated with RF and then dried with convective hot air at 65℃, 3.0m/s in this research. RF pretreatment time of 20, 30, 40 and 50min were chosen. Results showed that, there is only falling rate period during apricot hot air drying, and the drying rate of apricot is improved significantly; Herdenson and Pabis model is suitable for apricot hot air drying; retentions of flavonoids, polyphenols and Vc in dried apricot were higher than those of fresh apricot; when RF treating time was chosen 30mins, nutrients retentions of Vc, flavonoid and polyphenols were 0.9543mg/100g, 5.4089mg/100g and 7.3382mg/100g, separately. Keywords: apricot fruit, hot air drying, drying rate, nutrients, radio frequency
Contributions of Mamu-A*01 Status and TRIM5 Allele Expression, But Not CCL3L Copy Number Variation, to the Control of SIVmac251 Replication in Indian-Origin Rhesus Monkeys

CCL3 is a ligand for the HIV-1 co-receptor CCR5. There have recently been conflicting reports in the literature concerning whether CCL3-like gene (CCL3L) copy number variation (CNV) is associated with resistance to HIV-1 acquisition and with both viral load and disease progression following infection with HIV-1. An association has also been reported between CCL3L CNV and clinical sequelae of the simian immunodeficiency virus (SIV) infection in vivo in rhesus monkeys. The present study was initiated to explore the possibility of an association of CCL3L CNV with the control of virus replication and AIDS progression in a carefully defined cohort of SIVmac251-infected, Indian-origin rhesus monkeys. Although we demonstrated extensive variation in copy number of CCL3L in this cohort of monkeys, CCL3L CNV was not significantly associated with either peak or set-point plasma SIV RNA levels in these monkeys when MHC class I allele Mamu-A*01 was included in the models or progression to AIDS in these monkeys. With 66 monkeys in the study, there was adequate power for these tests if the correlation of CCL3L and either peak or set-point plasma SIV RNA levels was 0.34 or 0.36, respectively. These findings call into question the premise that CCL3L CNV is important in HIV/SIV pathogenesis.
IA-64: A Parallel Instruction Set: 5/31/99

Finally allowing a full evaluation of their new instruction set, Intel and Hewlett-Packard have released a full description of IA-64’s application-level architecture and instruction set. The disclosures address some previous criticisms of the architecture and provide more details concerning how IA-64 processors will execute both x86 and PA-RISC binaries. The disclosures show a thoroughly modern instruction set with a range of multimedia instructions and prefetch capabilities. Although IA-64 includes many RISC concepts, the architects added some rather complicated and specialized instructions. Concerns remain, however, about code density and just how much of an advantage these new features will provide over a standard RISC architecture. One criticism had been that the large register file, while effective for compute-intensive routines, would cause excessive overhead on subroutine calls, due to saving and restoring the contents of the registers. The vendors disclosed that IA-64 supports register frames that alleviate much of call/ save overhead.
Effect of procalcitonin-based guidelines vs standard guidelines on antibiotic use in lower respiratory tract infections: the ProHOSP randomized controlled trial.

CONTEXT In previous smaller trials, a procalcitonin (PCT) algorithm reduced antibiotic use in patients with lower respiratory tract infections (LRTIs). OBJECTIVE To examine whether a PCT algorithm can reduce antibiotic exposure without increasing the risk for serious adverse outcomes. DESIGN, SETTING, AND PATIENTS A multicenter, noninferiority, randomized controlled trial in emergency departments of 6 tertiary care hospitals in Switzerland with an open intervention of 1359 patients with mostly severe LRTIs randomized between October 2006 and March 2008. INTERVENTION Patients were randomized to administration of antibiotics based on a PCT algorithm with predefined cutoff ranges for initiating or stopping antibiotics (PCT group) or according to standard guidelines (control group). Serum PCT was measured locally in each hospital and instructions were Web-based. MAIN OUTCOME MEASURES Noninferiority of the composite adverse outcomes of death, intensive care unit admission, disease-specific complications, or recurrent infection requiring antibiotic treatment within 30 days, with a predefined noninferiority boundary of 7.5%; and antibiotic exposure and adverse effects from antibiotics. RESULTS The rate of overall adverse outcomes was similar in the PCT and control groups (15.4% [n = 103] vs 18.9% [n = 130]; difference, -3.5%; 95% CI, -7.6% to 0.4%). The mean duration of antibiotics exposure in the PCT vs control groups was lower in all patients (5.7 vs 8.7 days; relative change, -34.8%; 95% CI, -40.3% to -28.7%) and in the subgroups of patients with community-acquired pneumonia (n = 925, 7.2 vs 10.7 days; -32.4%; 95% CI, -37.6% to -26.9%), exacerbation of chronic obstructive pulmonary disease (n = 228, 2.5 vs 5.1 days; -50.4%; 95% CI, -64.0% to -34.0%), and acute bronchitis (n = 151, 1.0 vs 2.8 days; -65.0%; 95% CI, -84.7% to -37.5%). Antibiotic-associated adverse effects were less frequent in the PCT group (19.8% [n = 133] vs 28.1% [n = 193]; difference, -8.2%; 95% CI, -12.7% to -3.7%). CONCLUSION In patients with LRTIs, a strategy of PCT guidance compared with standard guidelines resulted in similar rates of adverse outcomes, as well as lower rates of antibiotic exposure and antibiotic-associated adverse effects. TRIAL REGISTRATION isrctn.org Identifier: ISRCTN95122877.
A Comparison of Tools Used for Tuberculosis Diagnosis in Resource-Limited Settings: A Case Study at Mubende Referral Hospital, Uganda

Background This study compared TB diagnostic tools and estimated levels of misdiagnosis in a resource-limited setting. Furthermore, we estimated the diagnostic utility of three-TB-associated predictors in an algorithm with and without Direct Ziehl-Neelsen (DZM). Materials and Methods Data was obtained from a cross-sectional study in 2011 conducted at Mubende regional referral hospital in Uganda. An individual was included if they presented with a two weeks persistent cough and or lymphadenitis/abscess. 344 samples were analyzed on DZM in Mubende and compared to duplicates analyzed on direct fluorescent microscopy (DFM), growth on solid and liquid media at Makerere University. Clinical variables from a questionnaire and DZM were used to predict TB status in multivariable logistic and Cox proportional hazard models, while optimization and visualization was done with receiver operating characteristics curve and algorithm-charts in Stata, R and Lucid-Charts respectively. Results DZM had a sensitivity and specificity of 36.4% (95% CI = 24.9–49.1) and 97.1%(95% CI = 94.4–98.7) compared to DFM which had a sensitivity and specificity of 80.3%(95% CI = 68.7–89.1) and 97.1%(95% CI = 94.4–98.7) respectively. DZM false negative results were associated with patient’s HIV status, tobacco smoking and extra-pulmonary tuberculosis. One of the false negative cases was infected with multi drug resistant TB (MDR). The three-predictor screening algorithm with and without DZM classified 50% and 33% of the true cases respectively, while the adjusted algorithm with DZM classified 78% of the true cases. Conclusion The study supports the concern that using DZM alone risks missing majority of TB cases, in this case we found nearly 60%, of who one was an MDR case. Although adopting DFM would reduce this proportion to 19%, the use of a three-predictor screening algorithm together with DZM was almost as good as DFM alone. It’s utility is whoever subject to HIV screening all TB suspects.
Special Focus: Research Challenges and Animal Models in Biological Defense REVIEW PAPER: Pathology of Animal Models of Alphavirus Encephalitis

The encephalitides caused by Venezuelan (VEEV), eastern (EEEV), and western (WEEV) equine encephalitis viruses are important natural diseases of horses and humans and potential agents of biowarfare or bioterrorism. No licensed vaccines or specific therapies exist to prevent or treat human infections with VEEV, EEEV, or WEEV. Well-characterized animal models are needed to support the development of such medical countermeasures under the United States Food and Drug Administration’s ‘‘Animal Rule. ’’ This review focuses on the pathological features and pathogenetic mechanisms of these alphaviral encephalitides in animal models, with an emphasis on aerosol infections. Infection of mice, nonhuman primates, and other species with VEEV, EEEV, and WEEV causes encephalitis and often death. There is great variability in the specific manifestations of disease in the different models, however. Many aspects of the disease in animal models and in humans remain to be characterized using modern methods. Especially needed is a better understanding of the fundamental mechanisms involved in 3 key phases of the pathogenesis of alphavirus encephalitis. These are the early extraneural phase, the process of neuroinvasion itself, and virus and host factors related to neurovirulence. A greater understanding of these aspects could provide avenues for the development of medical countermeasures and better establish suitable animal models of alphavirus encephalitis for testing them under the Animal Rule.
Improving prescribing patterns for the elderly through an online drug utilization review intervention: a system linking the physician, pharmacist, and computer.

CONTEXT Pharmacotherapy is among the most powerful interventions to improve health outcomes in the elderly. However, since some medications are less appropriate for older patients, systems approaches to improving pharmacy care may be an effective way to reduce inappropriate medication use. OBJECTIVE To determine whether a computerized drug utilization review (DUR) database linked to a telepharmacy intervention can improve suboptimal medication use in the elderly. DESIGN Population-based cohort design, April 1, 1996, through March 31, 1997. SETTING Ambulatory care. PATIENTS A total of 23269 patients aged 65 years and older throughout the United States receiving prescription drug benefits from a large pharmaceutical benefits manager during a 12-month period. INTERVENTION Evaluation of provider prescribing through a computerized online DUR database using explicit criteria to identify potentially inappropriate drug use in the elderly. Computer alerts triggered telephone calls to physicians by pharmacists with training in geriatrics, whereby principles of geriatric pharmacology were discussed along with therapeutic substitution options. MAIN OUTCOME MEASURES Contact rate with physicians and change rate to suggested drug regimen. RESULTS A total of 43007 alerts were triggered. From a total of 43007 telepharmacy calls generated by the alerts, we were able to reach 19368 physicians regarding 24 266 alerts (56%). Rate of change to a more appropriate therapeutic agent was 24% (5860), but ranged from 40% for long half-life benzodiazepines to 2% to 7% for drugs that theoretically were contraindicated by patients' self-reported history. Except for rate of change of beta-blockers in patients with chronic obstructive pulmonary disease, all rates of change were significantly greater than the expected baseline 2% rate of change. CONCLUSIONS Using a system integrating computers, pharmacists, and physicians, our large-scale intervention improved prescribing patterns and quality of care and thus provides a population-based approach to advance geriatric clinical pharmacology. Future research should focus on the demonstration of improved health outcomes resulting from improved prescribing choices for the elderly.
Parser lexicalisation through self-learning

We describe a new self-learning framework for parser lexicalisation that requires only a plain-text corpus of in-domain text. The method first creates augmented versions of dependency graphs by applying a series of modifications designed to directly capture higherorder lexical path dependencies. Scores are assigned to each edge in the graph using statistics from an automatically parsed background corpus. As bilexical dependencies are sparse, a novel directed distributional word similarity measure is used to smooth edge score estimates. Edge scores are then combined into graph scores and used for reranking the topn analyses found by the unlexicalised parser. The approach achieves significant improvements on WSJ and biomedical text over the unlexicalised baseline parser, which is originally trained on a subset of the Brown corpus.
An active feedback system for isotonic studies of smooth muscle

A feedback system used to perform isotonic studies of smooth muscle is presented. This system is capable of applying a constant force to muscle samples regardless of their contractile activities. The force applied to the tissue is controlled using a proportional integral control system that drives a linear motor. The device is integrated into a sucrose gap tissue bath apparatus where measurements of displacement and electrical activity are also possible. The frequency of canine colonic smooth-muscle electrical oscillations was found to be positively related to applied force. <<ETX>>
Direct reconstruction of displaced subdivision surface from unorganized points

We propose a new mesh reconstruction algorithm that produces a displaced subdivision mesh directly from unorganized points. The displaced subdivision surface is a new mesh representation that defines a detailed mesh with a displacement map over a smooth domain surface. This mesh representation has several benefits-compact mesh size, piecewise regular connectivity-to overcome limitations of an irregular mesh produced by an ordinary mesh reconstruction scheme, but the original displaced subdivision surface generation algorithm needs an explicit polygonal mesh to be converted. Our approach is producing displaced subdivision surface directly from input points during the mesh reconstruction process. The main ideas of our algorithm are building initial coarse control mesh by the shrink-wrapping like projection and sampling fine surface detail from unorganized points along the each limit vertex normal without any connectivity information of given points. We employ an existing subdivision surface fitting scheme to generate a parametric domain surface, and suggest a surface detail sampling scheme that determines a valid sampling triangle which can be made with combinations of input points. We show several reconstruction examples and applications to show the validity of suggested sampling technique and benefits of the result like multiresolution modeling.