Miracle-dz/UniFAR-FTUs huggingface dataset:
3D structure stability of RNA hairpin controlled by loop size

The thermodynamic stability of RNAs, which is important for unravelling structure-function relationships for RNAs, can be controlled by loops. To predict RNA 3D structure and stability, we have previously proposed a three-bead coarse-grained model. In this work, we further employ the model to predict the stability of RNA hairpins with different lengths of hairpin loops in monovalent/divalent ion solutions. The melting temperatures for the hairpins predicted by the present model are in correspondence with the extensive experiments. Our results suggest that RNA hairpin stability decreases with the length of hairpin loops, and the change is slowed down gradually as the increases of ion concentration and loop-size.
Barium ions induce prolonged plateau depolarizations in neurosecretory neurones of the adult rat supraoptic nucleus.

The occurrence and ionic basis of prolonged plateau depolarizations were studied during intracellular recordings obtained from thirty‐nine supraoptic nucleus (s.o.n.) neurosecretory neurones in perfused explants of rat hypothalamus. Replacement of Ca2+ by Ba2+ in the perfusion media enhanced the shoulder on the repolarization phase of the action potentials in all of eleven cells tested. In Ba2+, spike durations increased as the holding membrane potential was made more positive, resulting in plateaux lasting up to 100 s. These plateaux were characterized by a sustained but slowly decaying absolute potential near 0 mV from which there appeared frequent spontaneous hyperpolarizing transients. A membrane resistance decrease of more than 50% was observed at the onset of a plateau, with gradual restoration during the plateau. Injection of Cs+ into twenty‐one cells abolished the spike frequency adaptation and after‐hyperpolarization associated with current‐evoked bursts of action potentials. Mean spike duration after Cs+ injection increased from 2.5 +/‐ 0.3 ms to 68 +/‐ 9 ms (S.E. of mean). Addition of 4‐5 mM‐tetraethylammonium (TEA) to the perfusion media further increased the spike duration of nine Cs+‐injected cells to 320 +/‐ 70 ms. No further increase could be obtained by doubling the concentration of TEA and/or by the addition of 0.2‐0.5 mM‐4‐aminopyridine to the media. Although spike duration was greatly prolonged during such extensive blockade of K+ channels, plateau potentials lasting for longer than 1 s were observed only when Ba2+ was eventually added to the perfusion media. The special property of Ba2+ that leads to the formation of plateau potentials in s.o. n. neurones is therefore not restricted to its ability to reduce K+ conductances but may reside in its reduced effectiveness as a mediator of Ca2+‐dependent inactivation of Ca2+ channels. Injection of Cs+ into s.o. n. neurones increased the slope of their current‐voltage relationship below ‐60 mV from 148 +/‐ 15 to 257 +/‐ 41 M omega (S.E. of mean) and eliminated the outward rectification present at potentials above ‐60 mV. K+ currents are presumably active near the resting potential of these cells. Addition of Ba2+ to the perfusion media revealed a Cd2+‐sensitive inward rectification above but not below ca. ‐55 mV. A slowly inactivating Ba2+ current is therefore carried through Ca2+ channels at potentials above ‐55 mV. (ABSTRACT TRUNCATED AT 400 WORDS)
Conditionally Immortal Slc4a11−/− Mouse Corneal Endothelial Cell Line Recapitulates Disrupted Glutaminolysis Seen in Slc4a11−/− Mouse Model

Purpose To establish conditionally immortal mouse corneal endothelial cell lines with genetically matched Slc4a11+/+ and Slc4a11−/− mice as a model for investigating pathology and therapies for SLC4A11 associated congenital hereditary endothelial dystrophy (CHED) and Fuchs' endothelial corneal dystrophy. Methods We intercrossed H-2Kb-tsA58 mice (Immortomouse) expressing an IFN-γ dependent and temperature-sensitive mutant of the SV40 large T antigen (tsTAg) with Slc4a11+/+ and Slc4a11−/− C57BL/6 mice. The growth characteristics of the cell lines was assessed by doubling time. Ion transport activities (Na+/H+ exchange, bicarbonate, lactate, and Slc4a11 ammonia transport) were analyzed by intracellular pH measurement. The metabolic status of the cell lines was assessed by analyzing TCA cycle intermediates via gas chromatography mass spectrometry (GC-MS). Results The immortalized Slc4a11+/+ and Slc4a11−/− mouse corneal endothelial cells (MCECs) remained proliferative through passage 49 and maintained similar active ion transport activity. As expected, proliferation was temperature sensitive and IFN-γ dependent. Slc4a11−/− MCECs exhibited decreased proliferative capacity, reduced NH3:H+ transport, altered expression of glutaminolysis enzymes similar to the Slc4a11−/− mouse, and reduced proportion of TCA cycle intermediates derived from glutamine with compensatory increases in glucose flux compared with Slc4a11+/+ MCECs. Conclusions This is the first report of the immortalization of MCECs. Ion transport of the immortalized endothelial cells remains active, except for NH3:H+ transporter activity in Slc4a11−/− MCECs. Furthermore, Slc4a11−/− MCECs recapitulate the glutaminolysis defects observed in Slc4a11−/− mouse corneal endothelium, providing an excellent tool to study the pathogenesis of SLC4A11 mutations associated with corneal endothelial dystrophies and to screen potential therapeutic agents.
Analysis of outsourcing pricing for fourth party logistics enterprise based on bilateral bargaining game with asymmetric information

The fourth party logistics(4PL) must outsource the logistic tasks after obtaining them from the manufacturer, therefore, we use bargaining game to analyze the outsourcing. In the bargaining game, 4PL and manufacturer's earnings will not be zero when both sides can not reach an agreement. This is due to the fact that manufacturer will spend money to search, inspect and assess the new 4PL who can provide logistic service for him after that. And it will also cost 4PL some money to search for new customers. We call these costs cause by failure of the deal conversion costs. Using asymmetric information Bilateral bargaining game, we analyze the factors that affect the deal price and the dealing conditions between 4PL and manufacturer. Comparing the game with switching cost and without switching cost, we conclude that in the game without switching cost, manufacturer with a high degree of patience will get a smaller earning if a deal is concluded in the first phase. Once we take into account switching cost, manufacturer and 4PL get different earning in different domain.
The RBMX gene as a candidate for the Shashi X‐linked intellectual disability syndrome

A novel X‐linked intellectual disability (XLID) syndrome with moderate intellectual disability and distinguishing craniofacial dysmorphisms had been previously mapped to the Xq26‐q27 interval. On whole exome sequencing in the large family originally reported with this disorder, we identified a 23 bp frameshift deletion in the RNA binding motif protein X‐linked (RBMX) gene at Xq26 in the affected males (n = 7), one carrier female, absent in unaffected males (n = 2) and in control databases (7800 exomes). The RBMX gene has not been previously causal of human disease. We examined the genic intolerance scores for the coding regions and the non‐coding regions of RBMX; the findings were indicative of RBMX being relatively intolerant to loss of function variants, a distinctive pattern seen in a subset of XLID genes. Prior expression and animal modeling studies indicate that loss of function of RBMX results in abnormal brain development. Our finding putatively adds a novel gene to the loci associated with XLID and may enable the identification of other individuals affected with this distinctive syndrome.
Approach-withdrawal behavior of peach-faced lovebirds, Agapornis roseicolis, and its modification by brain lesions.

I. The frequency of mobbing vocalizations (chips, squeaks, chitters) and wing-beating was increased by the presence of a strange object (a small wooden cylinder) in the cage. The relative increase produced by the cylinder was much greater in birds that were partially isolated from the sounds as well as the sight of others than in birds only visually isolated. 2. The number of mobbing displays given by 20-hour food-deprived birds in response to the cylinders was sharply reduced by simultaneous presentation of food (even though the birds did not eat) but remained significantly above that given to food alone. This effect was observed in all lesioned birds as well as in intact controls. 3. A peculiar vocalization is described and termed "singing" because of some resemblance to subsong of passerines. It included all the vocalizations encountered in mobbing but occurred mostly in birds that appeared drowsy and was inhibited by stimuli that produced mobbing. 4. Brain lesions that destroyed the medial archistriatum bilaterally greatly reduced the frequency of mobbing displays in response to unfamiliar objects, and simultaneously decreased withdrawal and avoidance and increased some approach behavior. 5. Lesions of the hyperstriatum increased mobbing displays and probably increased the inhibitory effect of the cylinders on feeding compared to intact birds.
Gluconeogenesis and related aspects of glycolysis.

PERSPECTIVES AND SUMMARy 618 GENERAL PROPERTIES OF GLUCONEOGENESIS AND GLYCOLYSIS IN THE LIVER 619 Gluconeogenesis 619 Glycolysis 619 Control Steps 620 ENZYME PROPERTIES 620 Pyruvate Carboxylase and Other Mitochondrial Involvement 620 Phosphoenolpyruvate Carboxykinase 623 Pyruvate Kinase 625 Fructose 1,6-Bisphosphatase 626 Fructose 2,6-Bisphosphatase 629 6-Phosphofructokinases 629 Glucose 6-Phosphatase 633 Glucokinase 634 THE CONTROL OF METABOLIC FLUX BY HORMONES AND OTHER EFFECTORS . 634 Cyclic AMP, Glucagon, and f3-Adrenergic Agents 634 Fructose 2,6-Bisphosphate 639 ex-Adrenergic Agents, Vasopressin, and Angiotensin 641 Glucocorticoids 643 Glucose 643 THE FUTILE CYCLES 644 Glucose/Glucose 6-Phosphate Cycle 644 Fructose 6-Phosphate/Fructose 1,6-Bisphosphate Cycle 646 Pyruvate/Phosphoenolpyruvate Cycle 647
Glutamine as a pathogenic factor in hepatic encephalopathy

Hepatic encephalopathy (HE) results from acute or chronic liver dysfunction and is associated with hyperammonemia. Ammonium ions penetrate from blood to brain, where they form glutamine (Gln) in the reaction with glutamate catalyzed by an astroglia‐specific enzyme, glutamine synthetase (GS). Experimental data suggest that many manifestations of HE can be ascribed to increased Gln synthesis and accumulation in the brain. In HE resulting from acute liver failure (“fulminant hepatic failure”), the osmotic action of Gln appears to be in a large degree responsible for cerebral edema and edema‐associated disturbances of cerebral blood flow and ionic homeostasis. In chronic HE not accompanied by cerebral edema, Gln contributes to impairment of cerebral energy metabolism, and its increased transport from brain to the periphery accelerates the blood‐to‐brain transport of aromatic amino acids, of which tryptophen (Trp) is converted to metabolites directly implicated in HE. Most of the evidence that Gln participates in pathological events has been derived from their disappearance or amelioration in HE rats in which the cerebral Gln content was reduced by treatment with a GS inhibitor, methionine sulfoximine. J. Neurosci. Res. 65:1–5, 2001. © 2001 Wiley‐Liss, Inc.
Agents for Social Media

While currently intended for sharing personal content, future social media applications could support broader interactions, including business and government. Such applications could use agents that form communities, foster communications, vote, and collaborate to formulate policies and reach decisions. This special issue addresses several of the ways that software agent capabilities intersect with the demands of social media.
Fast proton spectroscopic imaging of human brain using multiple spin‐echoes

We introduce a multi‐echo multi‐slice MR proton spectroscopic imaging method, which allows for a dramatic reduction of the measurement time by acquiring multiple spin‐echoes within a single repetition time. In the multi‐echo multi‐slice experiment discussed in this paper, a threefold reduction in measurement time is obtained by sacrificing some spectral resolution. Signal‐to‐noise ratio and spatial resolution are preserved. Metabolite images of N‐acetyl aspartate, and total choline + total creatine from multiple slices through the human brain are presented and compared with images obtained with a conventional single‐echo multi‐slice method.
Effects of long‐term in vitro incubation of human spermatozoa: functional parameters and catalase effect

Summary. Prolonged incubation of human spermatozoa can have deleterious effects on sperm function. The aim of this paper was to describe the effects of a prolonged in vitro incubation, under similar conditions to those employed in human assisted reproduction, on various sperm functional parameters, and to investigate the effect of an antioxidant (catalase) on this system. Freshly collected ejaculates from 20 healthy donors were studied. Samples were divided into two aliquots: the first was incubated with Ham's F10 containing 3.5% HAS, and the second was incubated in the same medium plus catalase (100 units ml−1). All experiments were carried out with spermatozoa isolated using the swim‐up technique. Spermatozoa recovered from the supernatant after 1 h (T1) of incubation in 5% CO2 in air at 37 °C, and after 5 h (T6), 23 h (T24) and 47 h (T48), were evaluated for concentration, motion parameters including hyperactivation (computer‐assisted analysis), viability, ATP concentration, reactive oxygen species (ROS) generation, DNA integrity (acridine orange), and acrosome reaction (AR). The major alteration observed in sperm function during the prolonged in vitro incubation was a reduction in the number of motile spermatozoa, together with an impairment in the quality of sperm movement. ROS levels increased with the incubation time. No substantial modifications of sperm viability, chromatin condensation and AR inducibility were observed. The addition of catalase to the medium, while keeping ROS values within baseline levels, did not prevent the loss of motility or the corresponding increase in ATP.
Data-Driven Earthquake Location Method Project Report

Earthquake is one of the most commonly happened disasters with devastating consequences and poses significant risks to human society. The ability to determine the time and location of an earthquake can provide valuable information for rescue guidance, hazard assessment and scientific study. After a destructive earthquake, an accurate earthquake location is the most importtance information needed for rescue. Earthquakes also provide valuable information for scientists to study our Earth: the movement of plates, the property of rock in Earth’s interior and local geological background.
A microscope for the data centre

Data centres are large energy consumers. A large portion of this power consumption is due to the control of physical parameters of the data centre such as temperature and humidity. However, these physical parameters are tightly coupled with computations, and even more so in upcoming data centres, where the location of workloads can vary substantially due, for example, to workloads being moved in the cloud infrastructure hosted in the data centre. Therefore, managing the physical and compute infrastructure of a large data centre is an embodiment of a cyber-physical system CPS. In this paper, we describe a data collection and distribution architecture that enables gathering physical parameters of a large data centre at a very high temporal and spatial resolution of the sensor measurements. We detail this architecture and define the structure of the underlying messaging system that is used to collect and distribute the data.
Linear and nonlinear optical properties of chalcogenide microstructured optical fibers

Chalcogenide glasses are known for their large transparency in the mid-infrared and their high linear refractive index (>2). They present also a high non-linear coefficient (n2), 100 to 1000 times larger than for silica, depending on the composition. we have developed a casting method to prepare the microstructured chalcogenide preform. This method allows optical losses as low as 0.4 dB/m at 1.55 µm and less than 0.05 dB/m in the mid IR. Various chalcogenide MOFs operating in the IR range has been fabricated in order to associate the high non-linear properties of these glasses and the original MOF properties. For example, small core fibers have been drawn to enhance the non linearities for telecom applications such as signal regeneration and generation of supercontinuum sources. On another hand, in the 3-12 µm window, single mode fibers and exposed core fibers have been realized for Gaussian beams propagation and sensors applications respectively.
Implementing antiretroviral therapy in resource-constrained settings: opportunities and challenges in integrating HIV and tuberculosis care

Highly active antiretroviral therapy (HAART) can transform the natural course of HIV infection by reducing morbidity and mortality as has been observed in many industrialized countries. The increasing availability of antiretroviral therapy through resources from among others the Global Fund to fight AIDS tuberculosis (TB) and malaria is a major step forward in the global effort to make HAART available in the developing world. There is therefore an urgent need to develop simple and sustainable strategies for initiation and delivery of HIV care and therapy to large numbers of patients in the context of the existing under-developed health care delivery systems. Among the various models of HIV care provision one proposed strategy is to integrate this care including HAART provision into the existing TB directly observed therapy (DOT) programs. This would allow for the opportunity to initiate HIV care and HAART for patients identified as HIV infected during TB treatment as well as to be able to continue such management for those who develop TB during HIV treatment. (excerpt)
Optimizing Subspace SVM Ensemble for Hyperspectral Imagery Classification

In hyperspectral remote sensing image classification, ensemble systems with support vector machine (SVM), such as the Random Subspace SVM Ensemble (RSSE), have significantly outperformed single SVM on the robustness and overall accuracy. In this paper, we introduce a novel subspace mechanism, the Optimizing Subspace SVM Ensemble (OSSE), to improve RSSE by selecting discriminating subspaces for individual SVMs. The framework is based on Genetic Algorithm (GA), adopting the Jeffries-Matusita (JM) distance as a criterion, to optimize the selected subspaces. The combination of optimizing subspaces is more suitable for classification than the random one, at the same time having the ability to accommodate requisite diversity within the ensemble. The modifications have improved the accuracies of individual classifiers; as a result, better overall accuracies are present. Experiments on the classification of two hyperspectral datasets reveal that our proposed OSSE obtains sound performances compared with RSSE, single SVM, and other ensemble with GA to optimize SVM.
Power Minimization-Based Robust OFDM Radar Waveform Design for Radar and Communication Systems in Coexistence

This paper considers the problem of power minimization-based robust orthogonal frequency division multiplexing (OFDM) radar waveform design, in which the radar coexists with a communication system in the same frequency band. Recognizing that the precise characteristics of target spectra are impossible to capture in practice, it is assumed that the target spectra lie in uncertainty sets bounded by known upper and lower bounds. Based on this uncertainty model, three different power minimization-based robust radar waveform design criteria are proposed to minimize the worst-case radar transmitted power by optimizing the OFDM radar waveform, which are constrained by a specified mutual information requirement for target characterization and a minimum capacity threshold for communication system. These criteria differ in the way the communication signals scattered off the target are considered: 1) as useful energy, 2) as interference, or 3) ignored altogether at the radar receiver. Numerical simulations demonstrate that the radar transmitted power can be efficiently reduced by exploiting the communication signals scattered off the target at the radar receiver. It is also shown that the robust waveforms bound the worst-case power-saving performance of radar system for any target spectra in the uncertainty sets.
The female athlete triad: Components, nutrition issues, and health consequences

Abstract This paper, which was part of the International Association of Athletics Federations (IAAF) 2007 Nutritional Consensus Conference, briefly reviews the components of the female athlete triad (Triad): energy availability, menstrual status, and bone health. Each component of the Triad spans a continuum from health to disease, and female athletes can have symptoms related to each component of the Triad to different degrees. Low energy availability is the primary factor that impairs menstrual dysfunction and bone health in the Triad. We discuss nutritional issues associated with the Triad, focusing on intakes of macronutrients needed for good health, and stress fractures, the most common injury associated with the Triad. Finally, we briefly discuss screening and treatment for the Triad and the occurrence of the Triad in men.
An Evolutionary Fuzzy Hybrid System for Educational Purposes

When the Fuzzy Set Theory was proposed by Lotfi Zadeh in a seminal paper published in 1965, he noted that the technological resources available until then were not able to automate the activities related to industrial, biological or chemical problems. These activities use typically analog data which are inappropriate to be handled in a digital computer that works with well-defined numerical data, i.e. , discrete values.
Tinnitus with a Normal Audiogram: Physiological Evidence for Hidden Hearing Loss and Computational Model

Ever since Pliny the Elder coined the term tinnitus, the perception of sound in the absence of an external sound source has remained enigmatic. Traditional theories assume that tinnitus is triggered by cochlear damage, but many tinnitus patients present with a normal audiogram, i.e., with no direct signs of cochlear damage. Here, we report that in human subjects with tinnitus and a normal audiogram, auditory brainstem responses show a significantly reduced amplitude of the wave I potential (generated by primary auditory nerve fibers) but normal amplitudes of the more centrally generated wave V. This provides direct physiological evidence of “hidden hearing loss” that manifests as reduced neural output from the cochlea, and consequent renormalization of neuronal response magnitude within the brainstem. Employing an established computational model, we demonstrate how tinnitus could arise from a homeostatic response of neurons in the central auditory system to reduced auditory nerve input in the absence of elevated hearing thresholds.
Early literacy in South Africa: the promise of book-sharing

It has been estimated, conservatively, that 200 million young children, predominantly from Asia and sub-Saharan Africa, are failing to achieve their developmental potential as a consequence of poverty. These children are multiply disadvantaged, suffering adverse consequences in terms of their growth, physical health, socioemotional competence, and cognitive skills. While all of these adverse outcomes carry clear disadvantage, arguably it is the deficits in cognitive skills, including literacy, and the associated educational failure, that serve especially to exacerbate the entrenchment of cycles of deprivation. This occurs, not only through their impact on later earnings, but also, especially in mothers, through their association with high fertility, poor child care, and poor child health and survival rates (GranthamMcGregor et al. 2007).