Miracle-dz/UniFAR-FTUs huggingface dataset:
Model predictive control based deep neural network for dynamic manipulation

This paper proposes a trajectory planning method with neural networks that learn model predictive control for dynamic manipulation. The novelty of this method is that target positions and model parameters are added to the input of the neural network. The proposed method solves the dynamic trajectory planning issues with low calculation cost. This paper shows the effectiveness of the proposed method through demonstrations of a robot turning a pancake over under various parameters. In addition, we verify a performance change with respect to the number of training data.
A Probabilistic Palimpsest Model of Visual Short-term Memory

Working memory plays a key role in cognition, and yet its mechanisms remain much debated. Human performance on memory tasks is severely limited; however, the two major classes of theory explaining the limits leave open questions about key issues such as how multiple simultaneously-represented items can be distinguished. We propose a palimpsest model, with the occurrent activity of a single population of neurons coding for several multi-featured items. Using a probabilistic approach to storage and recall, we show how this model can account for many qualitative aspects of existing experimental data. In our account, the underlying nature of a memory item depends entirely on the characteristics of the population representation, and we provide analytical and numerical insights into critical issues such as multiplicity and binding. We consider representations in which information about individual feature values is partially separate from the information about binding that creates single items out of multiple features. An appropriate balance between these two types of information is required to capture fully the different types of error seen in human experimental data. Our model provides the first principled account of misbinding errors. We also suggest a specific set of stimuli designed to elucidate the representations that subjects actually employ.
Prosomatostatin Processing in Permeabilized Cells

Our laboratory has been using a permeabilized cell system derived from rat anterior pituitary GH cells expressing prosomatostatin (pro-SRIF) to study prohormone processing and nascent secretory vesicle formation in vitro. Because calcium is necessary for prohormone processing enzyme activity, secretory granule fusion with the plasma membrane, and possibly sorting to the regulated pathway, we treated permeabilized cells with the calcium ionophore A23187 to determine the role of calcium in pro-SRIF cleavage and nascent vesicle formation from the trans-Golgi network (TGN). Here we demonstrate that pro-SRIF cleavage was markedly inhibited when lumenal free calcium was chelated with EGTA in the presence of A23187. Surprisingly, submillimolar free calcium (15 μM) was sufficient to maintain prohormone cleavage efficiency, a value far lower than that estimated for total calcium levels in the TGN and secretory granules. Experiments using both A23187 and the protonophore CCCP revealed that free calcium is absolutely required for efficient pro-SRIF cleavage, even at the optimal pH of 6.1. Secretory vesicle formation by contrast was not inhibited by calcium chelation but rather by millimolar extralumenal free calcium. Together, these observations demonstrate that pro-SRIF processing and budding of nascent secretory vesicles from the TGN can be uncoupled and therefore have distinct biochemical requirements. Interestingly, our data using intact GH cells demonstrate that basal secretion of SRIF-related material is largely calcium-dependent and therefore cannot be equated with constitutive pathway secretion. These results underscore the importance of determining calcium requirements before assigning a secretion event to either the constitutive or regulated secretory pathway.
Differential inhibition of radiation‐induced apoptosis

The most common mechanism by which radiation kills cells is the induction of DNA double‐strand breaks that results in the loss of cell proliferation. Even though apoptosis is increasingly identified in experimental systems in vitro and in vivo, it is still generally regarded as a rare mode of radiation‐induced cell kill with minor relevance for the clinical effects of radiation. This review will focus on pro‐ and antiapoptotic signaling that affects the apoptotic outcome in irradiated mammalian cells. In particular, we will concentrate on the sphingomyelin/ceramide signal transduction pathway which is involved in initiation of stress‐induced apoptosis in a variety of normal and neoplastic cells. We will also discuss the crosstalk between the sphingomyelin/ceramide pathway and the protein kinase C pathway which constitutes an antiapoptotic pathway, and the potential for pharmacological modulation to increase the fraction of apoptotic cells undergoing apoptosis after radiation exposure. Stem Cells 1997; 15 (suppl 2): 43–47
Risk Factors Associated With Injury Attributable to Falling Among Elderly Population With History of Stroke

Background and Purpose— Stroke survivors are at high risk for falling. Identifying physical, clinical, and social factors that predispose stroke patients to falls may reduce further disability and life-threatening complications, and improve overall quality of life. Methods— We used 5 biennial waves (1998–2006) from the Health and Retirement Study to assess risk factors associated with falling accidents and fall-related injuries among stroke survivors. We abstracted demographic data, living status, self-evaluated general health, and comorbid conditions. We analyzed the rate ratio (RR) of falling and the OR of injury within 2 follow-up years using a multivariate random effects model. Results— We identified 1174 stroke survivors (mean age±SD, 74.4±7.2 years; 53% female). The 2-year risks of falling, subsequent injury, and broken hip attributable to fall were 46%, 15%, and 2.1% among the subjects, respectively. Factors associated with an increased frequency of falling were living with spouse as compared to living alone (RR, 1.4), poor general health (RR, 1.1), time from first stroke (RR, 1.2), psychiatric problems (RR, 1.7), urinary incontinence (RR, 1.4), pain (RR, 1.4), motor impairment (RR, 1.2), and past frequency of ≥3 falls (RR, 1.3). Risk factors associated with fall-related injury were female gender (OR, 1.5), poor general health (OR, 1.2), past injury from fall (OR, 3.2), past frequency of ≥3 falls (OR, 3.1), psychiatric problems (OR, 1.4), urinary incontinence (OR, 1.4), impaired hearing (OR, 1.6), pain (OR, 1.8), motor impairment (OR, 1.3), and presence of multiple strokes (OR, 3.2). Conclusions— This study demonstrates the high prevalence of falls and fall-related injuries in stroke survivors, and identifies factors that increase the risk. Modifying these factors may prevent falls, which could lead to improved quality of life and less caregiver burden and cost in this population.
Eastern margin of the Ross Sea Rift in western Marie Byrd Land, Antarctica: Crustal structure and tectonic development

The basement rock and structures of the Ross Sea rift are exposed in coastal western Marie Byrd Land (wMBL), West Antarctica. Thinned, extended continental crust forms wMBL and the eastern Ross Sea continental shelf, where faults control the regional basin‐and range‐type topography at ∼20 km spacing. Onshore in the Ford Ranges and Rockefeller Mountains of wMBL, basement rocks consist of Early Paleozoic metagreywacke and migmatized equivalents, intruded by Devonian‐Carboniferous and Cretaceous granitoids. Marine geophysical profiles suggest that these geological formations continue offshore to the west beneath the eastern Ross Sea, and are covered by glacial and glacial marine sediments. Airborne gravity and radar soundings over wMBL indicate a thicker crust and smoother basement inland to the north and east of the northern Ford Ranges. A migmatite complex near this transition, exhumed from mid crustal depths between 100–94 Ma, suggests a profound crustal discontinuity near the inboard limit of extended crust, ∼300 km northeast of the eastern Ross Sea margin. Near this limit, aeromagnetic mapping reveals an extensive region of high amplitude anomalies east of the Ford ranges that can be interpreted as a sub ice volcanic province. Modeling of gravity data suggests that extended crust in the eastern Ross Sea and wMBL is 8–9 km thinner than interior MBL (β = 1.35). Gravity modeling also outlines extensive regions of low‐density (2300–2500 kg m−3) buried basement rock that is lighter than rock exposed at the surface. These regions are interpreted as bounded by throughgoing east‐west faults with vertical separation. These buried low‐density rocks are possibly a low‐density facies of Early Paleozoic metagreywacke, or the low‐density epizonal facies of Cretaceous granites, or felsic volcanic rocks known from moraines. These geophysical features and structures on land in the wMBL region preserve the record of middle and Late Cretaceous development of the Ross Sea rift. Thermochronology data from basement rocks and offshore stratigraphy suggest that the wMBL rift margin formed and most extension occurred in mid‐ and Late Cretaceous time, before seafloor spreading initiated between wMBL and the Campbell Plateau. The Cretaceous tectonic record in wMBL contrasts with the Transantarctic Mountains that form the western rift margin, where significant rift‐flank relief developed in middle Tertiary time.
Classification of mouse fRNA genes using evolved neural networks

Functional RNAs (fRNAs) play a key role in gene regulation, at both the transcriptional and translational levels. Identification of fRNA genes can be difficult, given that some classes of fRNAs (especially microRNAs) have short coding regions and do not use classical signals common to protein coding genes. Following on previous experiments to generate pattern recognition models for the identification of fRNA genes using evolved neural networks, here we apply these approaches to the classification of fRNA genes in M. musculus.
Predict Functionally Important Residues Responsible for Estrogen Receptor Subtype Divergence

The estrogen receptor (ER) is a ligand-activated transcription factor that mediates the physiologicale ects of the female sex steroid hormone 17 beta estradiol (E2), and regulates the expression of genesinvolved in the growth, development and function of a diverge range of tissues. The ER is a memberof nuclear receptor (NR) superfamily, which shares a common structural organization including sixindependent but interacting functional domains. Two ER subtypes, although related, are separategenes and code for proteins of di ering lengths. We are interested in the selection constraint actingon the functional domains of ER subtypes after gene duplication. Because the sequence di erences ofER subtype in ligand binding domain (LBD) provide the molecular basis for the subtype physiologicalfunction, it is necessary to identify those functional related sites in order to investigate the functionaldivergence between two subtypes. In this study, we utilize the evolutionary rate analysis approach,combined with structural mapping, to predict the functionally important residues responsible for ERsubtype divergence.
Visual and Anatomical Outcomes Following Idiopathic Macular Epiretinal Membrane Surgery.

OBJECTIVE To assess the visual and anatomical outcomes following idiopathic macular epiretinal membrane (IERM) surgery. STUDY DESIGN Case series. PLACE AND DURATION OF STUDY Layton Rehmatulla Benevolent Trust (L.R.B.T), Free Base Eye Hospital, Karachi, from January 2015 to June 2016. METHODOLOGY Thirty eyes of thirty patients affected with idiopathic macular epiretinal membrane stage 2 were enrolled in this study. They subsequently underwent 23-gauge pars plana vitrectomy (PPV) with epiretinal membrane removal without internal limiting membrane peeling. The visual outcome was measured as improvement in best corrected visual acuity (BCVA) of at least two or more lines on ETDRS chart as compared to preoperative BCVA. The anatomical outcome was measured as decrease in foveal thickness on Spectral Domain-Optical Coherence Tomography (SD-OCT). Patients were followed for a period of 06 months. RESULTS At the end of follow-ups, 23 (76%) eyes out of 30 gained 2 or more lines of vision. In 05 (16%) eyes, BCVA remained same and only 02 (6.6%) eyes showed worsening of vision. Mean preoperative foveal thickness was 392 ±20 µm, whereas mean postoperative thickness was 305 ±16 µm with an average decrease of 87 µm, in foveal thickness. Recurrence of ERM was found to be the most frequent complication. CONCLUSION IERM surgery is a safe procedure and beneficial in achieving significant visual acuity improvement and anatomical recovery in the majority of cases.
Analysis of correlated mutations in HIV-1 protease using spectral clustering

Motivation: The ability of human immunodeficiency virus-1 (HIV-1) protease to develop mutations that confer multi-drug resistance (MDR) has been a major obstacle in designing rational therapies against HIV. Resistance is usually imparted by a cooperative mechanism that can be elucidated by a covariance analysis of sequence data. Identification of such correlated substitutions of amino acids may be obscured by evolutionary noise. Results: HIV-1 protease sequences from patients subjected to different specific treatments (set 1), and from untreated patients (set 2) were subjected to sequence covariance analysis by evaluating the mutual information (MI) between all residue pairs. Spectral clustering of the resulting covariance matrices disclosed two distinctive clusters of correlated residues: the first, observed in set 1 but absent in set 2, contained residues involved in MDR acquisition; and the second, included those residues differentiated in the various HIV-1 protease subtypes, shortly referred to as the phylogenetic cluster. The MDR cluster occupies sites close to the central symmetry axis of the enzyme, which overlap with the global hinge region identified from coarse-grained normal-mode analysis of the enzyme structure. The phylogenetic cluster, on the other hand, occupies solvent-exposed and highly mobile regions. This study demonstrates (i) the possibility of distinguishing between the correlated substitutions resulting from neutral mutations and those induced by MDR upon appropriate clustering analysis of sequence covariance data and (ii) a connection between global dynamics and functional substitution of amino acids. Contact: bahar@ccbb.pitt. edu Supplementary information: Supplementary data are available at Bioinformatics online.
Kinetic Model for Signal Binding to the Quorum Sensing Regulator LasR

We propose a kinetic model for the activation of the las regulon in the opportunistic pathogen Pseudomonas aeruginosa. The model is based on in vitro data and accounts for the LasR dimerization and consecutive activation by binding of two OdDHL signal molecules. Experimentally, the production of the active LasR quorum-sensing regulator was studied in an Escherichia coli background as a function of signal molecule concentration. The functional activity of the regulator was monitored via a GFP reporter fusion to lasB expressed from the native lasB promoter. The new data shows that the active form of the LasR dimer binds two signal molecules cooperatively and that the timescale for reaching saturation is independent of the signal molecule concentration. This favors a picture where the dimerized regulator is protected against proteases and remains protected as it is activated through binding of two successive signal molecules. In absence of signal molecules, the dimerized regulator can dissociate and degrade through proteolytic turnover of the monomer. This resolves the apparent contradiction between our data and recent reports that the fully protected dimer is able to “degrade” when the induction of LasR ceases.
Serotype Distribution and Susceptibility of Streptococcus pneumoniae Isolates from Pleural Fluid in Spain from 1997 to 2008

ABSTRACT Trends in serotype incidence and susceptibility (1997 to 2008) of Spanish Streptococcus pneumoniae pleural isolates (n = 831) were explored. Penicillin (oral) nonsusceptibility rates and the incidence of 7-valent pneumococcal conjugate vaccine (PCV-7) serotypes showed decreasing trends (R2 ≥ 0.600; P ≤ 0.002). The incidence of serotypes 1 and 19A showed increasing trends (R2 ≥ 0.759; P < 0.001), with no trends for serotype 3. Serotypes 19A, 1, and 3 represented 85% of pediatric isolates in 2008. In serotype 19A, the penicillin nonsusceptibility rate was 82.4% in 2008, associated with amoxicillin and cefotaxime nonsusceptibility in 21.4% of isolates. Inclusion of these serotypes in new vaccines offers the broadest coverage.
Nutritional status and dietary adequacy in rural communities of a protected area in Gabon

Abstract Objective As part of a larger study designed to understand how to protect the food and nutrition security of individuals living in a protected area of Gabon, we assessed their nutritional status and its relationship to dietary adequacy and health status. Design A 7 d food consumption survey was conducted during each of the two major seasons using a weighing method. Data were also collected on weight, height and health of individuals as well as on sociodemographic characteristics and potential determinants of the nutrition situation. Setting Four rural communities were intentionally selected to represent both inland and coastal settings and access to food markets. Subjects Approximately 500 individuals representing over 90 % of the population of these communities participated in the survey during each season. Results Undernutrition was present in the area, particularly among children <5 years of age and the elderly. Health was generally good and under-fives were most frequently ill. Energy, Fe and vitamin A requirements of individuals were generally not satisfied; the opposite was true for protein. The estimated prevalence of inadequate intakes of energy and vitamin A was very high in most age groups. Global nutrient adequacy was associated with nutritional outcome. Conclusions Individuals do not eat enough and breast-feeding practices are poor. Many suffer from undernutrition, particularly young children and the elderly. The results confirm the need to investigate the determinants of this poor nutrition situation to ensure that protection of natural resources will not be associated with harm to the well-being of the population.
Subclinical Hyperthyroidism and Cardiovascular Risk: Recommendations for Treatment

Subclinical hyperthyroidism (SHy), the mildest form of hyperthyroidism, is diagnosed in patients having a persistently low or undetectable serum concentration of thyroid-stimulating hormone (TSH) with normal free T4 and T3 concentrations. Although overt hyperthyroidism is associated with an increased risk of adverse cardiovascular outcomes, the cardiovascular risk of SHy is controversial. Multiple studies have demonstrated an increased risk of atrial fibrillation, especially in older individuals with TSH levels <0.1 mU/L. The effects of SHy on all-cause and cardiovascular mortality are not clear, but recent meta-analyses suggest a modest increase in mortality, with the risk increasing with age and associated with the lowest TSH levels. The long-term consequences of SHy in young- and middle-aged adults, and in those with TSH levels are mildly low, are uncertain. For these reasons, guidelines for treatment are based on patient age, the degree of TSH suppression, symptoms consistent with hyperthyroidism, and overall cardiovascular and osteoporotic fracture risks.
Speedy q-learning: a computationally efficient reinforcement learning algorithm with a near optimal rate of convergence

We consider the problem of model-free reinforcement learning (RL) in the Markovian decision processes (MDP) under the probably approximately correct (PAC) model. We introduce a new variant of Q-learning, called speedy Q-learning (SQL), to address the problem of the slow convergence in the standard Q-learning algorithm, and prove PAC bounds on the performance of this algorithm. The bounds indicate that for any MDP with n state-action pairs and discount factor γ ∈ [0, 1), a total number of O ( n log(n)/((1 − γ)ǫ) ) steps suffices for SQL to converge to an ǫ-optimal action-value function with high probability. We also derive a lower-bound of Ω ( n/((1−γ)2ǫ2) ) for all RL algorithms, which matches the upper bound in terms of n (up to a logarithmic factor) and ǫ. Moreover, our results have better dependencies on ǫ and 1−γ (the same dependency on n), and thus, are tighter than the best available results for Q-learning. The SQL algorithm also improves on existing results for the batch Q-value iteration, in terms of the computational budget required to achieve a near optimal solution.
Current MUAC Cut-Offs to Screen for Acute Malnutrition Need to Be Adapted to Gender and Age: The Example of Cambodia

Background Early identification of children <5 yrs with acute malnutrition is a priority. Acute malnutrition is defined by the World Health Organization as a mid-upper-arm circumference (MUAC) <12.5 cm or a weight-for-height Z-score (WHZ) <-2. MUAC is a simple and low-cost indicator to screen for acute malnutrition in communities, but MUAC cut-offs currently recommended by WHO do not identify the majority of children with weight-for-height Z-score (<-2 (moderate malnourished) or r<-3 (severe malnourished). Also, no cut-offs for MUAC are established for children >5 yrs. Therefore, this study aimed at defining gender and age-specific cut-offs to improve sensitivity of MUAC as an indicator of acute malnutrition. Methods To establish new age and gender-specific MUAC cut-offs, pooled data was obtained for 14,173 children from 5 surveys in Cambodia (2011–2013). Sensitivity, false positive rates, and areas under receiver-operator characteristic curves (AUC) were calculated using wasting for children <5yrs and thinness for children ≥5yrs as gold standards. Among the highest values of AUC, the cut-off with the highest sensitivity and a false positive rate ≤33% was selected as the optimal cut-off. Results Optimal cut-off values increased with age. Boys had higher cut-offs than girls, except in the 8–10.9 yrs age range. In children <2yrs, the cut-off was lower for stunted children compared to non stunted children. Sensitivity of MUAC to identify WHZ<-2 and <-3 z-scores increased from 24.3% and 8.1% to >80% with the new cut-offs in comparison with the current WHO cut-offs. Conclusion Gender and age specific MUAC cut-offs drastically increased sensitivity to identify children with WHZ-score <-2 z-scores. International reference of MUAC cut-offs by age group and gender should be established to screen for acute malnutrition at the community level.
Age, Body Mass Index, and Daytime and Nocturnal Hypoxia as Predictors of Hypertension in Patients With Obstructive Sleep Apnea

A growing body of evidence links obstructive sleep apnea (OSA) with hypertension. The authors performed a retrospective cohort study using the University Hospital of Larissa Sleep Apnea Database (1501 patients) to determine predictors of in‐laboratory diagnosed OSA for development of hypertension. Differences in continuous variables were assessed via independent samples t test, whereas discrete variables were compared by Pearson's chi‐square test. Multivariate analysis was performed via discriminant function analysis. There were several significant differences between hypertensive and normotensive patients. Age, body mass index, comorbidity, daytime oxygen saturation, and indices of hypoxia during sleep were deemed the most accurate predictors of hypertension, whereas apnea‐hypopnea index and desaturation index were not. The single derived discriminant function was statistically significant (Wilk's lambda=0.771, χ2=289.070, P<.0001). Daytime and nocturnal hypoxia as consequences of chronic intermittent hypoxia play a central role in OSA‐related hypertension and should be further evaluated as possible severity markers in OSA.