Miracle-dz/UniFAR-FTUs huggingface dataset:
The kinetics of ligand binding to plant hemoglobins. Structural implications.

The rates of reaction of oxygen, carbon monoxide, and nitric oxide with 14 plant hemoglobins have been determined by relaxation and stopped-flow methods. The combination rates for oxygen lie between 0.12 and 0.26 x 10(9)/M.s, for carbon monoxide between 0.01 and 0.07 x 10(9)/M.s, and for nitric oxide between 0.12 and 0.25 x 10(9)/M.s. The dissociation velocities for oxygen range from 5 to 25/s, and for CO from 0.005 to 0.011 s. The oxygen dissociation constants range only from 36 to 78 nM. Nanosecond relaxation experiments show large differences between the proteins. Five have known primary structures which correlate closely with the nanosecond relaxations and less immediately with the millisecond reactions. The relevant amino acid substitutions are concentrated in the C-E interhelical region.
Textbook multigrid efficiency for fluid simulations

▪ Abstract Recent advances in achieving textbook multigrid efficiency for fluid simulations are presented. Textbook multigrid efficiency is defined as attaining the solution to the governing system of equations in a computational work that is a small multiple of the operation counts associated with discretizing the system. Strategies are reviewed to attain this efficiency by exploiting the factorizability properties inherent to a range of fluid simulations, including the compressible Navier-Stokes equations. Factorizability is used to separate the elliptic and hyperbolic factors contributing to the target system; each of the factors can then be treated individually and optimally. Boundary regions and discontinuities are addressed with separate (local) treatments. New formulations and recent calculations demonstrating the attainment of textbook efficiency for aerodynamic simulations are shown.
Changes of circadian blood pressure patterns are associated with the occurence of lucunar infarction.

BACKGROUND The occurrence of lacunar infarction is closely related to arterial hypertension. However, there is only limited and partly controversial knowledge regarding the possible pathogenetic role of circadian blood pressure changes. OBJECTIVE To evaluate the relationship between circadian blood pressure rhythm, occurrence, and extent of lacunar infarction. METHODS We analyzed circadian blood pressure patterns, other cardiovascular risk factors, and occurrence of lacunar infarction in 118 hospitalized patients older than 55 years. Noninvasive 24-hour blood pressure measurements and magnetic resonance or computed tomographic brain imaging were performed in 61 patients with lacunar infarction and in 57 control patients. Daytime blood pressure variability was defined as the within-subject SD of all systolic and diastolic blood pressure readings during the daytime measurement period. Circadian blood pressure variation was defined as the average percentage change of nighttime blood pressure values compared with the daytime blood pressure values. RESULTS Patients with lacunar infarction were significantly older and showed more often a history of arterial hypertension, elevated average daytime blood pressure values, an increased systolic daytime blood pressure variability, and a reduced circadian blood pressure variation due to an increased incidence of a pathologic nighttime blood pressure increase. No significant correlation was found between these parameters and the number of lacunae. A logistic regression analysis revealed that a reduced systolic circadian blood pressure variation, age, systolic average daytime blood pressure, and a history of arterial hypertension were best correlated with the occurrence of lacunar infarction. CONCLUSION Reduced nighttime decline in systolic blood pressure may be an important risk factor for the development of lacunar infarction in addition to the absolute level of blood pressure and age.
VISUAL ACUITY LOSS IN RECESSIVE RETINITIS PIGMENTOSA AND ITS CORRELATION WITH MACULAR LESIONS

Purpose: To determine the visual acuity loss in patients with autosomal recessive retinitis pigmentosa and its relation to the presence of macular lesions. Methods: A total of 145 patients were included in the visual acuity analysis, and 139 patients were included in the analysis of their macular status. Patients with a history of parental consanguinity or an affected sister and parents unaffected with retinitis pigmentosa were considered as having an autosomal recessive mode of inheritance. Results: Regardless of age, 68 patients (47%) had visual acuity of 20/40 or better, 109 (75%) had better than 20/200 in at least 1 eye, and 36 (25%) had an acuity of 20/200 or worse in both eyes. An evaluation of the macular status demonstrated that 55 patients (39.6%) had no macular lesion and 77 (55.4%) had an atrophic lesion (either bull's-eye or geographic). Seventy-five percent of patients with no macular lesion had a visual acuity of 20/40 or better and 34 patients (44%) with an atrophic lesion had a visual acuity better than 20/70. Conclusion: These data can be useful to counsel patients on the potential visual acuity impairment likely to be observed at different ages and identify the association of visual acuity loss with macular changes.
Delayed Trunk Muscle Reflex Responses Increase the Risk of Low Back Injuries

Study Design. Prospective observational study with a 2- to 3-year follow-up. Objectives. To determine whether delayed muscle reflex response to sudden trunk loading is a result of or a risk factor for sustaining a low back injury (LBI). Summary of Background Data. Differences in motor control have been identified in individuals with chronic low back pain and in athletes with a history of LBI when compared with controls. However, it is not known whether these changes are a risk for or a result of LBI. Methods. Muscle reflex latencies in response to a quick force release in trunk flexion, extension, and lateral bending were measured in 303 college athletes. Information was also obtained regarding their personal data, athletic experience, and history of LBI. The data were entered into a binary logistic regression model to identify the predictors of future LBI. Results. A total of 292 athletes were used for the final analysis (148 females and 144 males). During the follow-up period, 31 (11%) athletes sustained an LBI. The regression model, consisting of history of LBI, body weight, and the latency of muscles shutting off during flexion and lateral bending load releases, predicted correctly 74% of LBI outcomes. The odds of sustaining LBI increased 2.8-fold when a history of LBI was present and increased by 3% with each millisecond of abdominal muscle shut-off latency. On average, this latency was 14 milliseconds longer for athletes who sustained LBI in comparison to athletes who did not sustain LBI (77 [36] vs. 63 [31]). There were no significant changes in any of the muscle response latencies on retest following the injury. Conclusions. The delayed muscle reflex response significantly increases the odds of sustaining an LBI. These delayed latencies appear to be a preexisting risk factor and not the effect of an LBI.
Determining dental checkup frequency.

BACKGROUND The authors assessed the dental checkup frequency of adults living in the Detroit tricounty area and identified demographic, access and subjective factors associated with visits to a dentist made not because of a dental problem. METHODS Data are from a 1994 probability-based sample of adults who were interviewed and received an in-home oral examination. The authors used the variables of age, sex, education level, income level, dental insurance status, usual place for care, objective measures of oral health, and subjective assessments of health, pain and dental anxiety to predict the frequency of dental checkups. RESULTS The authors found that differences in dental checkup behavior were related to demographics, access to dental care, subjective ratings of oral and general health and other self-assessments, and clinical parameters of oral health. In multiple logistic regression analysis considering all variables simultaneously, sex, income, having a usual place for care and level of dental care anxiety were found to be associated with having dental checkups. The authors determined the statistical significance level at P < . 05. CONCLUSIONS A total of 69.7 percent of the study population reported having had a dental checkup at least once a year in the past five years. The authors found that four factors associated with infrequent dental checkups: being male, having lower income levels, not having a usual place for care and being anxious about receiving dental care. PRACTICE IMPLICATIONS Dental health professionals should consider the correlates of dental checkup frequency identified in this study and the usefulness of proposed strategies to increase and sustain regular preventive visitation patterns in their own patient populations.
Inverse agonist exposure enhances ligand binding and G protein activation of the human MT1 melatonin receptor, but leads to receptor down‐regulation

Abstract: Melatonin binds and activates G protein‐coupled melatonin receptors. The density and affinity of the endogenous melatonin receptors change throughout the 24‐hr day, and the exposure of recombinant melatonin receptors to melatonin often results in desensitization of the receptors. Receptor density, G protein activation and expression level were analyzed in CHO cell lines stably expressing the human MT1 receptors after 1 or 72 hr of exposure to melatonin (agonist, 10 nm) and luzindole (antagonist/inverse agonist, 10 μm). The 72‐hr exposure to luzindole significantly increased the apparent receptor density in cell lines with both high and low MT1 receptor expression levels (MT1high and MT1low cells, respectively). In the constitutively active MT1high cells, luzindole pretreatment also stimulated the functional response to melatonin in [35S]GTPγS binding assays, whereas melatonin pretreatment attenuated the functional response at both time points. Receptor ELISA was used to analyze the cell membrane and total expression level of the MT1 receptor in intact and permeabilized cells, respectively. Luzindole pretreatment decreased the total cellular level of MT1 receptor in the MT1high cells at both time points but increased the cell surface expression of MT1 receptor at 72 hr. Melatonin significantly decreased MT1 receptor cell surface expression only in MT1high cells after a 1‐hr treatment. These results indicate that melatonin treatment desensitizes MT1 receptors, whereas luzindole increases ligand binding and G‐protein activation. Luzindole also stimulates downregulation of the MT1 receptor protein, interfering with the synthesis and/or degradation of the receptor.
Function Approximation for Continuous Constrained MDPs

In this work we apply function approximation techniques to solve continuous, constrained Markov Decision Processes (MDPs). Many real-world robot planning problems are best represented as MDPs with a continuous state space. However, in many scenarios constraints must be accounted for as well. These constraints are treated probabilistically, with a bound on the constraint violation probability. Existing function approximation literature does not account for constraints, and existing constrained MDP work assumes a discrete state space. We seek to bridge this gap by maintaining two continuous value functions one for the reward and one for the constraint violation probability and approximate these value functions by writing them as a linear combination of a set of basis functions (not necessarily the same set for both value functions). We present some simulation results and investigate the impact of choice of basis functions on the quality of policies generated.
Two randomized trials of linaclotide for chronic constipation.

BACKGROUND Linaclotide is a minimally absorbed peptide agonist of the guanylate cyclase C receptor. In two trials, we aimed to determine the efficacy and safety of linaclotide in patients with chronic constipation. METHODS We conducted two randomized, 12-week, multicenter, double-blind, parallel-group, placebo-controlled, dual-dose trials (Trials 303 and 01) involving 1276 patients with chronic constipation. Patients received either placebo or linaclotide, 145 μg or 290 μg, once daily for 12 weeks. The primary efficacy end point was three or more complete spontaneous bowel movements (CSBMs) per week and an increase of one or more CSBMs from baseline during at least 9 of the 12 weeks. Adverse events were also monitored. RESULTS For Trials 303 and 01, respectively, the primary end point was reached by 21.2% and 16.0% of the patients who received 145 μg of linaclotide and by 19.4% and 21.3% of the patients who received 290 μg of linaclotide, as compared with 3.3% and 6.0% of those who received placebo (P<0.01 for all comparisons of linaclotide with placebo). Improvements in all secondary end points were significantly greater in both linaclotide groups than in the placebo groups. The incidence of adverse events was similar among all study groups, with the exception of diarrhea, which led to discontinuation of treatment in 4.2% of patients in both linaclotide groups. CONCLUSIONS In these two 12-week trials, linaclotide significantly reduced bowel and abdominal symptoms in patients with chronic constipation. Additional studies are needed to evaluate the potential long-term risks and benefits of linaclotide in chronic constipation. (Funded by Ironwood Pharmaceuticals and Forest Research Institute; ClinicalTrials.gov numbers, NCT00765882 and NCT00730015.).
Shape- and Texture-Based Fish Image Recognition System

Thisresearchdevelopedacomputersystemcapableofrecognizingsomefishimages. �The� systemknownasthe�"shape-�andtexture-basedfishimagerecognitionsystem"�(FIRS)�consistsoffive� subsystems—namely: 1) image acquisition, 2) image preprocessing 3) feature extraction, 4) image recognitionand�5)�resultpresentation. �Theexperimentwasconductedon�30�fishspecies,�whichconsisted� of�600�fishimagesasthetrainingdatasetand�300�fishimagesfortesting. �Thesystemcomparedtwo� recognitiontechniques—aEuclideandistancemethod�(EDM)�andartificialneuralnetworks�(ANN). � Thesystemwasabletorecognizeall�30�speciesofthetrainingfishimageswithaprecisionof�99.00� and 81.67% for the ANN and the EDM techniques, respectively. The average access times were 24.4 and 154.43 sec per image for the EDM and ANN techniques, respectively.
BMP 4 Gene and Pathophysiology of Cleft Lip and Palate

The rapid proliferative expansion and complex morphogenetic events that coordinate the development of face underpin the sensitivity of the structure to genetic and environmental insult and provide an explanation for the high incidence of midfacial malformation. Most notable of these malformations is cleft lip with or without palate. Despite the global impact of the disorder and some recent progress in identifying the causative genes for the non syndromic forms of CLP, our knowledge on the key genetic factors and the environmental mutants therein contributing to CLP remains still remarkably patchy. The current understanding of the molecular and cellular processes that orchestrate morphogenesis of the midface, with emphasis on events leading to the fusion of the lip and primary palate is detailed in this review. The role of the candidate gene BMP4 in nsCLP, identified from relevant animal model systems and the likely events perturbed by the key gene pin pointed in human studies are discussed in this light. In this present review the normal craniofacial patterning and morphogenesis of lip and palate are discussed with a focus on the role of BMP signaling therein.
CITRIC ACID PRODUCTION BY Candida SPECIES GROWN ON A SOY-BASED CRUDE GLYCEROL

Citric acid was produced by five species of the yeast Candida after growth on a medium containing soy biodiesel-based crude glycerol. After growth on a medium containing 10 g L−1 or 60 g L−1 crude glycerol for 168 hr at 30°C, Candida parapsilosis ATCC 7330 and C. guilliermondii ATCC 9058 produced the highest citric acid levels. On 10 g L−1 or 60 g L−1 crude glycerol for 168 hr at 30°C, the citric acid level produced by C. parapsilosis ATCC 7330 was 1.8 g L−1 or 11.3 g L−1, respectively, while C. guilliermondii ATCC 9058 produced citric acid concentrations of 3.0 g L−1 or 10.4 g L−1, respectively. Biomass production by C. guilliermondii ATCC 9058 on 10 g L−1 or 60 g L−1 crude glycerol for 168 hr at 30°C was highest at 1.2 g L−1 or 6.9 g L−1, respectively. The citric acid yields observed for C. guilliermondii ATCC 9058 after growth on 10 g L−1 or 60 g L−1 crude glycerol (0.35 g g−1 or 0.21 g g−1, respectively) were generally higher than for the other Candida species tested. When similar crude glycerol concentrations were present in the culture medium, citric acid yields observed for some of the Candida species utilized in this study were about the same or higher compared to citric acid yields by Yarrowia lipolytica strains. Based on the findings, it appeared that C. guilliermondii ATCC 9058 was the most effective species utilized, with its citric acid production being similar to what has been observed when citric acid-producing strains of Y. lipolytica were grown on crude glycerol under batch conditions that could be of significance to biobased citric acid production.
Designing Energy-Efficient Data Center Networks Using Space-Time Optical Interconnection Architectures

This paper considers a space-time interconnection architecture (STIA) based on optical devices and proposes its introduction in data center networks. The power consumption of the STIA is modeled, accounting for the energy proportionality of the optical devices in the STIA. Using such a model, a STIA-based network is designed using three different topologies, tree, folded Clos, and flattened butterfly, and optimized for power efficiency. Results show that, for a fixed topology, small-size STIAs are an energy-efficient solution for data center networks and allow a power reduction of more than an order of magnitude with respect to the Ethernet-based network. The comparison for the same bisection bandwidth shows that folded Clos and flattened butterfly outperform tree, whose power consumption is strongly dependent on the oversubscription ratio selected.
To fast or feed: an alternative life history for anadromous brook trout Salvelinus fontinalis overwintering within a harbour.

The seasonal feeding pattern of sea-run brook trout Salvelinus fontinalis was studied from November to May 2010-2012 in Antigonish Harbour, Nova Scotia, Canada (45° 38' N; 61° 55' W). Sixty-three S. fontinalis (mean ± s.d. fork length = 330 ± 70 mm and mass = 536 ± 351 g) captured had fed predominantly on fishes (Fundulidae and Gasterosteidae). Percentage of empty stomachs was highest during autumn (18%) and winter (22%) and lowest in spring (7%). Stomach fullness increased from autumn to a maximum during winter, relating to near-zero body temperatures which may have effectively stopped gastric evacuation. Although feeding occurred during winter (December to March), consumption rates were calculated as negative values, and subsequently returned to positive values in spring (April to May). The over-winter life-history strategy of this sea-run S. fontinalis population appears to be a feeding marine migration in which fish continually increase body condition, representing an alternative to the more common overwintering strategy of starvation in fresh water until spring.
Diurnal and Circadian Oscillations in Expression of Kisspeptin, Kisspeptin Receptor and Gonadotrophin‐Releasing Hormone 2 Genes in the Grass Puffer, A Semilunar‐Synchronised Spawner

In seasonally breeding animals, the circadian and photoperiodic regulation of neuroendocrine system is important for precisely‐timed reproduction. Kisspeptin, encoded by the Kiss1 gene, acts as a principal positive regulator of the reproductive axis by stimulating gonadotrophin‐releasing hormone (GnRH) neurone activity in vertebrates. However, the precise mechanisms underlying the cyclic regulation of the kisspeptin neuroendocrine system remain largely unknown. The grass puffer, Takifugu niphobles, exhibits a unique spawning rhythm: spawning occurs 1.5–2 h before high tide on the day of spring tide every 2 weeks, and the spawning rhythm is connected to circadian and lunar‐/tide‐related clock mechanisms. The grass puffer has only one kisspeptin gene (kiss2), which is expressed in a single neural population in the preoptic area (POA), and has one kisspeptin receptor gene (kiss2r), which is expressed in the POA and the nucleus dorsomedialis thalami. Both kiss2 and kiss2r show diurnal variations in expression levels, with a peak at Zeitgeber time (ZT) 6 (middle of day time) under the light/dark conditions. They also show circadian expression with a peak at circadian time 15 (beginning of subjective night‐time) under constant darkness. The synchronous and diurnal oscillations of kiss2 and kiss2r expression suggest that the action of Kiss2 in the diencephalon is highly dependent on time. Moreover, midbrain GnRH2 gene (gnrh2) but not GnRH1 or GnRH3 genes show a unique semidiurnal oscillation with two peaks at ZT6 and ZT18 within a day. The cyclic expression of kiss2, kiss2r and gnrh2 may be important in the control of the precisely‐timed diurnal and semilunar spawning rhythm of the grass puffer, possibly through the circadian clock and melatonin, which may transmit the photoperiodic information of daylight and moonlight to the reproductive neuroendocrine centre in the hypothalamus.
From PID to Extended Learning Control

It has been recently shown in Marino, Tomei, and Verrelli (2011) that the output error feedback regulation problem with (unknown) periodic reference and/or disturbance signals of known common period can be effectively solved for the class of single-input, single-output, minimum phase, nonlinear, time-invariant systems in output feedback form (of known relative degree one or two) which are affected by unknown parameters and unknown output-dependent nonlinearities. The resulting nonlinear control, which relies on advanced learning control techniques, can be interpreted as a generalization of the classical PID control which solves the problem when both reference and disturbance signals are constant. In this paper, we present sophisticated analytical arguments which prove that the learning control designed in Marino, Tomei, and Verrelli (2011) can be endowed with a period identifier when the output reference signal is periodic of uncertain period but available at each time instant. The generalized resulting control preserves the achievement of the closed loop properties obtained in Marino, Tomei, and Verrelli (2011) while maintaining an overall simple structure. The application of the presented control techniques to the position synchronization problem for current-fed permanent magnet step motors with non-sinusoidal flux distribution and uncertain position-dependent load torque allows us to provide a solution to a yet unsolved problem.