Miracle-dz/UniFAR-FTUs huggingface dataset:
A fast, robust solution to the Stewart platform forward kinematics

The Stewart platform is a six degree-of-freedom fully-in-parallel linkage well-suited to robotic tasks where structural rigidity and high small motion bandwidth are required. In this article we describe an approach for computing the forward kinematics of this device that is both fast and robust. Our solution is based on the simultaneous solution of three constraint equations using a Newton-Raphson scheme. A well-known property of Newton-Raphson is its tendency to fail when the constraint equations become poorly conditioned, and the main contribution of this article is the development of two algorithms for overcoming this limitation and hence for providing robustness. Certain other matters, such as the singular configurations of the Stewart platform and its assembly modes, are touched upon.
Bcl-3 is an interleukin-1-responsive gene in chondrocytes and synovial fibroblasts that activates transcription of the matrix metalloproteinase 1 gene.

OBJECTIVE To define the role of Bcl-3, a member of the inhibitor of nuclear factor kappaB (NF-kappaB) family and a known regulator of NF-kappaB, in interleukin-1 (IL-1)-induced matrix metalloproteinase 1 (MMP-1) transcription in chondrocytes and synovial fibroblasts. METHODS SW-1353 cells, a human chondrosarcoma cell line, were stimulated with IL-1beta, and the harvested RNA was subjected to microarray analysis and quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR). The SW-1353 cells were stimulated with IL-1 or transfected with a plasmid that constitutively expressed Bcl-3, and then MMP-1 messenger RNA (mRNA) expression was assayed by quantitative real-time RT-PCR. SW-1353 cells were transfected with antisense oligonucleotides to Bcl-3, and IL-1-induced MMP-1 mRNA expression was assayed by quantitative RT-PCR. SW-1353 cells and rabbit synovial fibroblasts were transfected with a 4.3-kb human MMP-1 promoter construct along with Bcl-3 and NF-kappaB1 expression constructs, and MMP-1 transcription was assayed. RESULTS Microarray analysis and real-time RT-PCR showed Bcl-3 to be an IL-1beta-responsive gene in SW-1353 cells. Exogenous expression of Bcl-3 in SW-1353 cells activated MMP-1 transcription. Endogenous Bcl-3 expression was required for IL-1beta induction of MMP-1 gene expression. Bcl-3 also activated MMP-1 transcription in primary synovial fibroblasts. We showed previously that NF-kappaB1 contributes to IL-1beta induction of MMP-1 transcription in stromal cells. We showed here that Bcl-3 can cooperate with NF-kappaB1 to activate MMP-1 transcription in SW-1353 cells. CONCLUSION These data define a new role for Bcl-3 in joint cells as an IL-1beta-responsive early gene involved in cell-mediated cartilage remodeling. Our findings implicate Bcl-3 as an important contributor to chronic inflammatory disease states, such as osteoarthritis and rheumatoid arthritis.
Mandibular advancement appliances for the treatment of paediatric obstructive sleep apnea: a systematic review.

OBJECTIVE To evaluate the effectiveness of mandibular advancement appliances (MAAs) for treatment of pediatric obstructive sleep apnea (OSA). METHODS Several electronic databases (The Cochrane Database, EMBASE, Healthstar, MEDLINE, PubMed) were systematically searched, as well as a limited grey literature (Google Scholar) and manual searches. A health sciences librarian helped with the selection of Medical Subject Headings (MeSH), key words, and combinations of key words with truncations to account for any differences in controlled terminology in the different databases. Only studies that evaluated the effects of MAAs in children with OSA were pursued. RESULTS Only 4 articles satisfied all inclusion criteria. Selected studies were retrospective except one study that was a quasi-randomized clinical trial. High risk of bias (Cochrane Risk of Bias assessment) was judged in all included studies. Based on the limited available evidence use of MAAs in a POSA population may result in improvements in Apnea Hypopnea Index (AHI) scores. However complete normalization of AHI scores was not demonstrated. Heterogeneity in study designs and collected information precluded meta-analysis. LIMITATIONS There are significant weaknesses in the existing evidence due primarily to absence of control groups, small sample sizes, lack of randomization and short-term results. Determination of AHI scores with MAAs still in the mouth should be avoided. CONCLUSIONS The current limited evidence may be suggestive that MAAs result in short-term improvements in AHI scores, but it is not possible to conclude that MMAs are effective to treat pediatric OSA. Medium- and long-term assessments are still required.
Segmentation of speech: child's play?

The difficulty of the task of segmenting a speech signal into its words is immediately clear when listening to a foreign language; it is much harder to segment the signal into its words, since the words of the language are unknown. Infants are faced with the same task when learning their first language. This study provides a better understanding of the task that infants face while learning their native language. We employed an automatic algorithm on the task of speech segmentation without prior knowledge of the labels of the phonemes. An analysis of the boundaries erroneously placed inside a phoneme showed that the algorithm consistently placed additional boundaries in phonemes in which acoustic changes occur. These acoustic changes may be as great as the transition from the closure to the burst of a plosive or as subtle as the formant transitions in low or back vowels. Moreover, we found that glottal vibration may attenuate the relevance of acoustic changes within obstruents. An interesting question for further research is how infants learn to overcome the natural tendency to segment these ‘dynamic’ phonemes.
Mucus clearance as a primary innate defense mechanism for mammalian airways.

The conducting airways branch 20–25 times between the trachea and the alveoli as inhaled air passes from the relatively constricted nasal/tracheal passages to the large surface area of alveoli (70 m2), where gas exchange occurs. This branching anatomy leads to a surface area that expands greatly from proximal airways (e.g., third generation; ∼50 cm2) to distal airways (20th to 25th generation; ∼2 m2). The regional differences in airway surface area (or airway perimeters; ref. 1), which is often depicted by showing the airways as an inverted funnel (Figure ​(Figure1),1), pose interesting challenges for lung defense. Because many of the particles that settle on airway surfaces are infectious, airways have evolved innate defense mechanisms that constantly protect airways against bacterial and other types of infection. Figure 1 Pulmonary defense mechanisms preventing chronic bacterial infection. The lung is depicted as an inverted funnel, reflecting the relative surface area of distal versus proximal airways. The mechanical-clearance-of-mucus hypothesis is shown on the left. There is still little agreement on the nature of these innate airway defense mechanisms (2, 3) (Figure ​(Figure1). 1). In the more traditional view, mechanical clearance of mucus is considered the primary innate airway defense mechanism (4–6). In this view, the role of the epithelia lining airway surfaces is to provide the integrated activities required for mucus transport, including ciliary activity and regulation of the proper quantity of salt and water on airway surfaces via transepithelial ion transport. More recently, a second view of innate airway defense has emerged as a result of studies of the pathogenesis of cystic fibrosis (CF) (7). This view emphasizes a role for a “chemical shield” in protecting the lung against inhaled bacteria (8). In this hypothesis, the two important functions for epithelia are the production of salt-sensitive defensins that are secreted into airway lumens, and the production of a low-salt (<50 mM NaCl) liquid on airway surfaces that renders defensins active (9). The predictions of each of these models and the relevant data have been extensively reviewed (2, 3, 10, 11). Here, we will focus on the role of mucus clearance in the lung as the more important innate defense mechanism in health and disease, including CF. We will attempt to fill in the gaps in our knowledge regarding important aspects of the mucus clearance system, and, where relevant, point out differences between the two views of innate airway defense.
Reduction of the excess sludge production by biological alternating process: real application results and metabolic uncoupling mechanism

The biological solution proposed to reduce the wasted sludge production is based on a process of alternating phases realized in a specific reactor (alternate cycles in sludge line (ACSL)) where a quote of the recycle sludge is treated and sent back to the main activated sludge process. The ACSL process was applied in two urban wastewater treatment plants (WWTPs). The reduction was tested by changing the hydraulic retention time and the conditions of oxidation reduction potential. The main mechanism of the process is recognized in the metabolic uncoupling. In fact, an increase in the specific oxygen uptake rate in the biological reactors was recorded (up to 20 mg/g VSS/h), which was stimulated by the fasting condition in the ACSL. The process is able to reduce the observed sludge yield on average of 25–30% with final average values reaching 0.179 kg VSS/kg chemical oxygen demand (COD) for WWTP1 and 0.117 kg VSS/kg COD for WWTP2.
Optimizing Photo Composition

Aesthetic images evoke an emotional response that transcends mere visual appreciation. In this work we develop a novel computational means for evaluating the composition aesthetics of a given image based on measuring several well‐grounded composition guidelines. A compound operator of crop‐and‐retarget is employed to change the relative position of salient regions in the image and thus to modify the composition aesthetics of the image. We propose an optimization method for automatically producing a maximally‐aesthetic version of the input image. We validate the performance of the method and show its effectiveness in a variety of experiments.
Minimally invasive video-assisted versus conventional open thyroidectomy on immune response: a meta analysis.

OBJECTIVES The aim of this study was to compare the immune response between the minimally invasive video-assisted thyroidectomy (MIVAT) and conventional thyroidectomy (CT). METHODS An exhaustive literature search was performed in the Medline, Embase, and Cochrane Library to identify the randomized controlled trials comparing the immune response between MIVAT and CT. Relevant data were extracted and statistical analysis was done using RevMan 5.0. RESULTS Twelve trials including 389 patients were identified. Immune-competent cells demonstrated no significant differences between MIVAT and CT. The including trails were assessed various perioperative plasma cytokine concentrations with no significant differences in interleukin-6 (IL-6), T lymphocytes (CD4(+), CD8(+), CD4/CD8) and NK cells between the MIVAT and CT. However, meta-analysis showed lower counts on postoperative days at 72 h was showed lower C-reactive protein (CRP) level compared to the preoperation levels but showed no significant difference within 24 h in MIVAT S group compared with CT group. Tumor necrosis factor alpha (TNF-α) level after surgery within 24 h and 72 h showed lower TNF-α level after MIVAT surgery within 24 h and 72 h. CONCLUSIONS This meta-analysis demonstrates that, MIVAT has less immune response outcomes and that it is a more ideal choice for the patients relative to the conventional surgery.
Stagewise Weak Gradient Pursuits

Finding sparse solutions to underdetermined inverse problems is a fundamental challenge encountered in a wide range of signal processing applications, from signal acquisition to source separation. This paper looks at greedy algorithms that are applicable to very large problems. The main contribution is the development of a new selection strategy (called stagewise weak selection) that effectively selects several elements in each iteration. The new selection strategy is based on the realization that many classical proofs for recovery of sparse signals can be trivially extended to the new setting. What is more, simulation studies show the computational benefits and good performance of the approach. This strategy can be used in several greedy algorithms, and we argue for the use within the gradient pursuit framework in which selected coefficients are updated using a conjugate update direction. For this update, we present a fast implementation and novel convergence result.
Using Senses in HMM Word Alignment

Some of the most used models for statistical word alignment are the IBM models. Although these models generate acceptable alignments, they do not exploit the rich information found in lexical resources, and as such have no reasonable means to choose better translations for specific senses. We try to address this issue by extending the IBM HMM model with an extra hidden layer which represents the senses a word can take, allowing similar words to share similar output distributions. We test a preliminary version of this model on English-French data. We compare different ways of generating senses and assess the quality of the alignments relative to the IBM HMM model, as well as the generated sense probabilities, in order to gauge the usefulness in Word Sense Disambiguation.
A cryo-EM–based model of phosphorylation- and FKBP12.6-mediated allosterism of the cardiac ryanodine receptor

Conformational rigidity of the cardiac intracellular Ca2+ channel RyR2 may be enhanced by FKBP12.6 binding and reduced by phosphorylation. More flexible with phosphorylation? The type 2 ryanodine receptor (RyR2) mediates Ca2+ release from the sarcoplasmic reticulum of cardiomyocytes to initiate cardiac muscle contraction. Mutations in this intracellular Ca2+ channel are associated with cardiac diseases that may lead to heart failure. Dhindwal et al. used cryo-EM to determine the structure of rabbit RyR2 in complex with the regulatory protein FKBP12.6 in the closed state at 11.8 Å resolution. They found two conformations of RyR2, which may correspond to the extent of phosphorylation of a domain that harbors several disease-associated mutations. Because the more flexible conformation may correspond to phosphorylated RyR2, the authors suggest that phosphorylation may reduce the energy required for the Ca2+ channel to transition to an open state. These results provide a structural basis for understanding how phosphorylation may affect the activation of RyR2. Type 2 ryanodine receptors (RyR2s) are calcium channels that play a vital role in triggering cardiac muscle contraction by releasing calcium from the sarcoplasmic reticulum into the cytoplasm. Several cardiomyopathies are associated with the abnormal functioning of RyR2. We determined the three-dimensional structure of rabbit RyR2 in complex with the regulatory protein FKBP12.6 in the closed state at 11.8 Å resolution using cryo-electron microscopy and built an atomic model of RyR2. The heterogeneity in the data set revealed two RyR2 conformations that we proposed to be related to the extent of phosphorylation of the P2 domain. Because the more flexible conformation may correspond to RyR2 with a phosphorylated P2 domain, we suggest that phosphorylation may set RyR2 in a conformation that needs less energy to transition to the open state. Comparison of RyR2 from cardiac muscle and RyR1 from skeletal muscle showed substantial structural differences between the two, especially in the helical domain 2 (HD2) structure forming the Clamp domain, which participates in quaternary interactions with the dihydropyridine receptor and neighboring RyRs in RyR1 but not in RyR2. Rigidity of the HD2 domain of RyR2 was enhanced by binding of FKBP12.6, a ligand that stabilizes RyR2 in the closed state. These results help to decipher the molecular basis of the different mechanisms of activation and oligomerization of the RyR isoforms and could be extended to RyR complexes in other tissues.
Nutritional supply of proteins and absorption of their hydrolysis products: consequences on metabolism

Except in nibblers such as the rat the food intake of single-stomached animals, particularly omnivores, is discontinuous and varies in amount and composition. These quantitative and qualitative variations in food intake pose a number of questions. Do they affect the digestive processes which are related to food transit and enzyme hydrolysis, especially the extent of nutrient absorption and its kinetics? What effect do they have on the storage of nutrients in the liver and the temporal distribution in the tissues? Do they lead to a modification of the nutritive value? These questions cannot be answered merely by measuring digestibility. Digestibility is used to evaluate the disappearance of ingested nutrients either in the whole digestive tract (rectal digestibility) or in its proximal part (ileal digestibility), where the nutrients are not metabolized by the flora and are, thus, absorbed in their initial form of diet components. Whichever technique is used, these digestibility measures are global and static and do not account for the different absorption rates which vary for different nutrients. Since body reserves of free amino acids are small, the relative timing of the input of amino acids and of carbohydrates can markedly affect protein synthesis and the efficiency of feed utilization (Geiger, 1950). For example, if a pig is supplied with a limiting amino acid (AA) at a time other than when the rest of the diet, deficient in that one AA, is given the growth rate and feed efficiency will be lower than when the diet and supplement are given simultaneously (RCrat & Bourdon, 1975). Study of kinetics associated with differences in the relative absorption rate of the various nutrients is necessary for a fuller understanding of variations in the nutritive value of feeds. Also, the chemical substances which appear in the body during digestion must be identified so that we may evaluate the changes in feeds which result mainly from microbial metabolism, as they pass through the digestive tract and during their transport by the enterocyte. The importance of these transformations is that they can lie at the origin of changes in their nutritive value. The use of a technique which allows direct measurement of intestinal absorption and hepatic metabolism of nutrients has helped to resolve some of these problems. The technique has allowed assessment of the amounts of nutrients appearing in blood, their composition and changes with time, as well as the kinetics of their uptake and release by the liver. Furthermore, it has provided us with an appreciation of the endocrine reactions of the enterohepatic axis involved in the regulation of absorption and metabolism. This paper reports some findings relating to proteins and gives experimental results obtained in our laboratory on the kinetics of intestinal absorption of nitrogenous nutrients and their consequences for hepatic and peripheral metabolism.
Optimal control for a polynomial system with a quadratic criterion over infinite horizon

This paper proposes an optimal control algorithm for a polynomial system with a quadratic criterion over infinite horizon. The designed regulator gives a closed form solution to the infinite horizon optimal control problem for a polynomial system with a quadratic criterion. The obtained solution consists in a feedback control law obtained by solving a Riccati algebraic equation dependent on the state. Numerical simulations in the example show advantages of the developed algorithm.
Reducing the risk of severe complications among patients with Clostridium difficile infection.

BACKGROUND The incidence and severity of Clostridium difficile infections are increasing, and there is a need to optimize the prevention of complicated disease. OBJECTIVE To identify modifiable processes of care associated with an altered risk of C difficile complications. METHODS A retrospective cohort study (with prospective case ascertainment) of all C difficile infections during 2007⁄2008 at a tertiary care hospital was conducted. RESULTS Severe complications were frequent (occurring in 97 of 365 [27%] C difficile episodes), with rapid onset (median three days postdiagnosis). On multivariable analysis, nonmodifiable predictors of complications included repeat infection (OR 2.67), confusion (OR 2.01), hypotension (OR 0.97 per increased mmHg) and elevated white blood cell count (OR 1.04 per 109 cells⁄L). Protection from complications was associated with initial use of vancomycin (OR 0.24); harm was associated with ongoing use of exacerbating antibiotics (OR 3.02). CONCLUSION C difficile infections often occur early in the disease course and are associated with high complication rates. Clinical factors that predicted a higher risk of complications included confusion, hypotension and leukocytosis. The most effective ways to improve outcomes for patients with C difficile colitis are consideration of vancomycin as first-line treatment for moderate to severe cases, and the avoidance of unnecessary antibiotics.
Demonstration of an online tool to assist managed care formulary evidence-based decision making: meta-analysis of topical prostaglandin analog efficacy

Background The purpose of this paper was to demonstrate the use of an online service for conducting a systematic review and meta-analysis of the efficacy of topical prostaglandin analogs in reducing intraocular pressure (IOP) in glaucoma and ocular hypertension. Methods An online service provider (Doctor Evidence) reviewed and extracted data from the peer-reviewed literature through September 2009. Randomized controlled studies of at least three months’ duration assessing at least two prostaglandin analogs in patients with primary open-angle glaucoma, ocular hypertension, or normal-tension glaucoma were included. The primary endpoint was mean IOP. Summary estimates were created using random-effects models. The Q Chi-square test was used to assess statistical heterogeneity. Results Sixteen studies satisfied the inclusion criteria and were analyzed. On average, greater IOP-lowering was seen with bimatoprost relative to latanoprost (1 mmHg, P = 0.025) and travoprost (0.8 mmHg, P = 0.033) based on mean IOP after 12–26 weeks of treatment. No statistical difference was observed in IOP-lowering between latanoprost and travoprost (P = 0.841). Findings were similar to previously published meta-analyses of topical prostaglandin analogs. Conclusion Systematic reviews relying on meta-analytic techniques to create summary statistics are considered to be the “gold standard” for synthesizing evidence to support clinical decision-making. However, the process is time-consuming, labor-intensive, and outside the capability of most formulary managers. We have demonstrated the effectiveness of a commercial service that facilitates the process of conducting such reviews.