Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of two dominant alleles of the major rhodopsin-encoding gene ninaE in Drosophila

Purpose In this study we investigated the biochemical and cell biologic characteristics of flies expressing two novel dominant alleles of the major rhodopsin encoding gene neither inactivation nor afterpotential E (ninaE) in a heterozygous background. Methods Presence of the deep pseudopupil in flies was assayed 5 days post eclosion. For structural analysis, 1-μm-retinal cross sections were obtained from fixed and resin-embedded Drosophila heads. Confocal microscopy was performed on dissected retinas stained with antibodies specific for rhodopsin, NinaA, and F-actin. Rhodopsin levels were determined by western and slot blot analysis. Results Dominant rhodopsin mutants showed progressive age-dependent and light-independent loss of the deep pseudopupil, without any apparent retinal degeneration at the morphological level. Expression of mutant rhodopsin caused rhodopsin to mislocalize to the cell body and the endoplasmic reticulum compartment. Mutant rhodopsin also caused loss of solubility of wild-type rhodopsin and its accumulation presumably as a high molecular mass complex in the photoreceptor cell body. Conclusions In heterozygous mutant flies, there is loss of wild-type rhodopsin immunoreactivity on a western assay but less reduction using slot blot analysis. This suggests that mutant rhodopsin is likely inducing the misfolding and insolubility of wild-type rhodopsin. Localization of rhodopsin revealed that in mutant flies, wild-type rhodopsin is mislocalized to the cell body and the endoplasmic reticulum.
Cerebral hemodynamics during cerebral ischemia induced by acute hypotension.

The extreme dependence of the brain upon its circulation for substrates essential for the maintenance of its metabolic activity is well recognized. A cessation of the cerebral circulation for only a few minutes, as occurs in cardiac arrest, results in irreversible brain damage. The brain, for the most part, is an aerobic organ and its large oxygen demands probably account for its unusual susceptibility to circulatory disturbances. The oxygen consumed by the normal adult brain (3.5 cc. per 100 Gm. per min.) is extracted from approximately 800 cc. of blood passing through it each minute. The minimum blood flow requirements of the brain, i.e., the rate at which signs of cerebral ischemia become manifest, have not been accurately determined. Previous efforts to estimate the critical rate have been made both in animals (1) and in man (2) but the procedures utilized for the determination of cerebral blood flow were not sufficiently quantitative to warrant definite conclusions. In order to study this problem, cerebral hemodynamic and metabolic changes were determined before and during acute reductions in arterial pressure induced by drug administration and/or postural adjustments.
Effects of muscle immobilization at different lengths on tetrodotoxin-induced disuse atrophy

Previous studies have shown that immobilization causes muscle atrophy and that the rate of atrophy depends on the length at which the muscle is immobilized. However, most studies have been carried out in neurologically intact animals that were capable of generating at least some voluntary muscle activation. In this study, terrodotoxin was applied chronically to the rat sciatic nerve to produce complete paralysis of distal muscles for seven days, and the ankle was immobilized to hold the muscles at long or short lengths. Paralysis without immobilization resulted in relative weight losses of 36% for soleus, 19% for tibialis anterior (TA), and 17% for lateral gastrocnemius (LG) muscles. Casting the ankle in plantarflexion stretched TA and reduced its weight loss to 10%. Soleus and LG were shortened by this intervention and had increased losses of 43% and 28%, respectively. Fixing the limb in dorsiflexion resulted in a posture similar to that adopted by the unrestrained rats and had no significant effect on the amount of muscle atrophy compared to that in unrestrained paralyzed animals.
Alkaline decontamination of sputum specimens adversely affects stability of mycobacterial mRNA

Reverse transcriptase PCR (RT-PCR) is an important tool for Mycobacterium tuberculosis research and diagnostics. A standard procedure using N-acetyl-L-cysteine (NALC) and NaOH has been widely adopted for digestion and decontamination of sputum specimens for mycobacterial culture. The objective of this study was to determine the compatibility of this method with the recovery of RNA for RT-PCR assays. Nineteen sputum specimens were collected from smear-positive, pretreatment tuberculosis patients. After homogenization with NALC and glass beads, specimens were further processed by the addition of either NaOH, as per the standard decontamination protocol, or phosphate buffer. RNA was prepared by using a modified guanidine-phenol extraction method developed specifically for sputum sediments. DNA was isolated from the same specimens. Reverse transcriptions of alpha antigen (85B protein) mRNA and 16S rRNA were performed together, and aliquots were removed for separate PCRs. In all specimens, the 85B mRNA target was greatly diminished by treatment with NaOH; however, the 16S rRNA target remained unaffected. Storing sputum specimens for 48 h at 4 degrees C before processing did not seem to affect the integrity or yield of RNA; however, some degradation occurred by 72 h. Data suggest that the NaOH-NALC method for processing sputum samples is not suitable for detecting mRNA targets in RT-PCR assays.
Combining Speech Fragment Decoding and Adaptive Noise Floor Modeling

This paper presents a novel noise-robust automatic speech recognition (ASR) system that combines aspects of the noise modeling and source separation approaches to the problem. The combined approach has been motivated by the observation that the noise backgrounds encountered in everyday listening situations can be roughly characterized as a slowly varying noise floor in which there are embedded a mixture of energetic but unpredictable acoustic events. Our solution combines two complementary techniques. First, an adaptive noise floor model estimates the degree to which high-energy acoustic events are masked by the noise floor (represented by a soft missing data mask). Second, a fragment decoding system attempts to interpret the high-energy regions that are not accounted for by the noise floor model. This component uses models of the target speech to decide whether fragments should be included in the target speech stream or not. Our experiments on the CHiME corpus task show that the combined approach performs significantly better than systems using either the noise model or fragment decoding approach alone, and substantially outperforms multicondition training.
Effect of Vaginal Administration of Nitric Oxide Donor Isosorbide Mononitrate on Cervical Ripening Before Induction in Term Pregnancy: A Randomized Controlled Study

Introduction: Nitric oxide donors have been shown to cause cervical ripening. The aim of this study was to investigate whether sustained-release isosorbide mononitrate (ISMN-SR) 60 mg administered vaginally is effective for preinduction cervical ripening in term pregnancy and any effect on mother and fetus. Materials and Methods: A single-blinded study was conducted in Raja Mirasudar Hospital, Thanjavur for a period of 12-month. This study was conducted in 200 patients with uncomplicated singleton pregnancies at term. These patients were randomly allocated to receive either ISMN-SR 60 mg (n = 100) or vitamin C 100 mg (n = 100) vaginally. Modifi ed Bishop’s Score was evaluated after 24 h in each group. Results: At the commencement of the study, there were no differences between mean ages, Bishop score of the two groups. In the ISMN-SR group, there was a signifi cantly higher increase in the mean modifi ed Bishop score (2.466 vs. 0.561) P < 0.05 after 24 h. Percentage of those requiring additional ripening agent found to be lower in the study group (56.7%) compared to control group (91.7%). Cesarean section rates were similar in both groups.
Spatial distribution of soil water repellency in a grassland located in Lithuania

Soil water repellency (SWR) it is recognized to be very heterogeneous in time in space and depends on soil type, climate, land use, vegetation and season (Doerr et al., 2002). It prevents or reduces water infiltration, with important impacts on soil hydrology, influencing the mobilization and transport of substances into the soil profile. The reduced infiltration increases surface runoff and soil erosion. SWR reduce also the seed emergency and plant growth due the reduced amount of water in the root zone. Positive aspects of SWR are the increase of soil aggregate stability, organic carbon sequestration and reduction of water evaporation (Mataix-Solera and Doerr, 2004; Diehl, 2013). SWR depends on the soil aggregate size. In fire affected areas it was founded that SWR was more persistent in small size aggregates (Mataix-Solera and Doerr, 2004; Jordan et al., 2011). However, little information is available about SWR spatial distribution according to soil aggregate size. The aim of this work is study the spatial distribution of SWR in fine earth (<2 mm) and different aggregate sizes, 2-1 mm, 1-0.5 mm, 0.5-0.25 mm and <0.25 mm. The studied area is located near Vilnius (Lithuania) at 54◦ 42’ N, 25◦ 08 E, 158 masl. A plot with 400 m2 (20 x 20 m with 5 m space between sampling points) and 25 soil samples were collected in the top soil (0-5 cm) and taken to the laboratory. Previously to SWR assessment, the samples were air dried. The persistence of SWR was analysed according to the Water Drop Penetration Method, which involves placing three drops of distilled water onto the soil surface and registering the time in seconds (s) required for the drop complete penetration (Wessel, 1988). Data did not respected Gaussian distribution, thus in order to meet normality requirements it was log-normal transformed. Spatial interpolations were carried out using Ordinary Kriging. The results shown that SWR was on average in fine earth 2.88 s (Coeficient of variation % (CV%)=44.62), 2-1mm 1.73 s (CV%=45.10), 1-0.5 mm 2.02 s (CV%=93.75), 0.5-0.25 mm 3.12 s (CV%=233.68) and in <0.25 mm 15.54 mm (CV%=240.74). This suggests that SWR persistence and CV% is higher in small size aggregates than in the coarser aggregate sizes. The interpolated maps showed that in fine earth SWR was higher in the western part of the studied plot and lower in the central area. In the 2-1 mm aggregate size it was higher in the southwest and lower at north and northwest area. In the 1-0.5 mm aggregate size it was lower in the central area and higher in the southwest. In the 0.5-0.25 mm aggregate size it was higher in the west part and lower in the north of the plot and. In the <0.25 mm no specific pattern was identified and the SWR was heterogeneously distributed. This suggests that the spatial distribution of SWR is very different according to the aggregate size. Future studies are needed in order to identify the causes and consequences of such dynamic.
NMDA Receptors Mediate Poly- Motoneurons of Rat Embryos and Monosynaptic Potentials

We determined the contribution of glutamate receptor subtypes to developing excitatory synaptic transmission in isolated spinal cord of rat embryos. Using electrophysiological and morphological techniques, we studied the pattern of development of synapses between dorsal root afferents and motoneurons in lumbar spinal cords of 15 to Pl-d-old rat embryos. Motoneuron dendritic fields and afferent projections onto motoneurons were identified by labeling with HRP. Afferents first entered the gray matter at Day 15 of gestation, and by Day 16 they terminated close to motoneuron dendritic trees. Afferent axons projected onto motoneuron dendritic fields at Day 17, when boutons were detected on motoneuron dendrites that were crossed by afferent axons. To determine the time course of formation of functional sensorimotor synapses and their pharmacological properties, a dorsal root was stimulated while recording intracellularly from segmental motoneurons. At Day 16, excitatory postsynaptic potentials (EPSPs) with long latencies, slow rates of rise, and long durations were recorded. The amplitudes of these EPSPs increased with membrane depolarization and in the absence of extracellular Mg2+. These EPSPs were blocked by D-2-amino-5-phosphonovalerate (APV) and ketamine, which are selective antagonists of N-methyl-oaspartate (NMDA) receptors. These findings suggest that initial synaptic transmission in embryonic motoneurons is mediated solely by NMDA receptors. Short-latency EPSPs with fast rates of rise were first recorded in most motoneurons by Day 17. These EPSPs were composed of fast- and slow-rising potentials. The slow component was blocked by APV, while the fast component was eliminated by 6-cyano-7-nitroquinoxaline-2,3-dione and kynurenate. This indicates that the short-latency EPSPs are mediated by both NMDA and non-NMDA receptors. Dose-response curves of motoneurons to L-glutamate, NMDA, and kainate demonstrated that motoneurons are sensitive to these agonists prior to the formation of synapses between afferents and motoneurons. Motoneuron responses to NMDA and kainate increased immediately after the onset
Genome sequence of a rice pest, the white-backed planthopper (Sogatella furcifera)

Abstract Background: Sogatella furcifera is an important phloem sap-sucking and plant virus-transmitting migratory insect of rice. Because of its high reproductive potential, dispersal capability and transmission of plant viral diseases, S. furcifera causes considerable damage to rice grain production and has great economical and agricultural impacts. Comprehensive studies into ecological aspects and virus–host interactions of S. furcifera have been limited because of the lack of a well-assembled genome sequence. Findings: A total of 241.3 Gb of raw reads from the whole genome of S. furcifera were generated by Illumina sequencing using different combinations of mate-pair and paired-end libraries from 17 insert libraries ranging between 180 bp and 40 kbp. The final genome assembly (0.72 Gb), with average N50 contig size of 70.7 kb and scaffold N50 of 1.18 Mb, covers 98.6 % of the estimated genome size of S. furcifera. Genome annotation, assisted by eight different developmental stages (embryos, 1st-5th instar nymphs, 5-day-old adults and 10-day-old adults), generated 21 254 protein-coding genes, which captured 99.59 % (247/248) of core CEGMA genes and 91.7 % (2453/2675) of BUSCO genes. Conclusions: We report the first assembled and annotated whole genome sequence and transcriptome of S. furcifera. The assembled draft genome of S. furcifera will be a valuable resource for ecological and virus–host interaction studies of this pest.
MMSE based power allocation for broadband cooperative communication with amplify-and- forward protocol

This paper proposes a subcarrier power allocation scheme for broadband OFDM cooperative communications, in the typical single-relay scenario with the amplify-and-forward protocol. The design criterion is to minimize the mean square error (MSE) of the received signal at the destination. Relying on the Lagrange multiplier techniques we derive a closed-form solution of the optimal power loading factors. Numerical simulation result shows that the proposed scheme significantly improves the bit-error-rate performance when compared with the systems without power loading.
Rapid Assessment Shore Survey for Exotic Species in San Francisco Bay - May 2004

Andrew N. Cohen, San Francisco Estuary Institute, Oakland, CA Dale R. Calder, Royal Ontario Museum, Toronto, Ontario James T. Carlton, Williams College/Mystic Seaport–Maritime Studies Program, Mystic, CT John W. Chapman, Oregon State University/Hatfield Marine Science Center, Newport, OR Leslie H. Harris, Natural History Museum of Los Angeles County, Los Angeles, CA Taiju Kitayama, Tokyo National Science Museum, Tokyo, Japan Charles C. Lambert, University of Washington/Friday Harbor Laboratory, Friday Harbor, WA Gretchen Lambert, University of Washington/Friday Harbor Laboratory, Friday Harbor, WA Christina Piotrowski, California Academy of Science, San Francisco, CA Michelle Shouse, U.S. Geological Survey, Menlo Park, CA Luis A. Solorzano, U.S. Food and Drug Administration, Alameda, CA
Preparation of Silica Particles Encapsulating Retinol Using O/W/O Multiple Emulsions.

Retinol, a cosmetic ingredient, was entrapped within inorganic microspheres obtained from sol-gel reaction of TEOS in o/w/o multiple emulsions as microreactors. In o/w/o multiple emulsions, the retinol was emulsified as an internal oil phase in a aqueous solution of 3.0 wt% Tween 20 prior to emulsification into an external oil phase. The multiple emulsions appeared to be stable enough in the presence of HPC polymer in the external oil phase. In sol-gel reaction, the hydrolysis and condensation rate of TEOS were greatly dependent upon the catalyst and the molar ratio of H(2)O to TEOS (R(W)). In this study, sphere-like microspheres entrapping retinol were best formed with the addition of NH(4)OH as a catalyst when the concentration of TEOS was at the R(W) value of 4. Microspheres obtained under these conditions were 15-40 &mgr;m with very dense surfaces containing a few globules 1.17-2.35 &mgr;m. Also, they showed the slower release of retinol into the external ethanol phase and higher loading and encapsulation efficiency. Copyright 2001 Academic Press.
Role of the lateral line mechanosensory system in directionality of goldfish auditory evoked escape response

SUMMARY Goldfish (Carassius auratus) escape responses to sudden auditory stimuli are mediated by a pair of reticulospinal neurons, the Mauthner (M-) cells, which integrate mechanosensory inputs from the inner ear and the lateral line (LL) to initiate a fast directional response away from the aversive stimulus. This behavior is context dependent; when near an obstruction the fish may rather turn towards the sound to avoid hitting the object. Mechanisms underlying this directionality remain unknown. Here we investigate the contribution of the LL system to auditory evoked escapes and provide behavioral evidence that it transmits stimulus – and environmental-dependent information that determines the initial response direction of the escape. We quantified escape latency, probability and directionality following abrupt sound stimuli before and after removal of the entire LL with 0.03 mmol l–1 cobalt chloride (CoCl2), 0.002% gentamicin or selective posterior LL nerve (pLLn) transection. CoCl2 significantly increased escape onset latency without affecting probability and reduced open field directionality from 77% to chance, 52%. This effect on directionality was also observed with gentamicin. Transection of the pLLn had no effect on directionality, indicating the anterior LL nerve (aLLn) afferents are more likely to transmit directional information to the M-cell. When the fish were near a wall, the error rate was quadrupled by both CoCl2 and pLLn transection. Visual elimination had no influence on directionality unless combined with LL elimination.
Interactive Haptic Rendering of Deformable Surfaces Based on the Medial Axis Transform

We present a new method for interactive deformation and haptic rendering of viscoelastic surfaces. Objects are defined by a discretized Medial Axis Transform (MAT), which consists of an ordered set of circles (in 2D) or spheres (in 3D) whose centers are connected by a skeleton. The skeleton and physical properties of the object, including the radii of the spheres centered on the skeleton and material properties, are encapsulated in a single high dimensional parametric surface. To compute the force upon deformation, we use a mass-spring-damper model that takes into account both normal and shear surface forces. Our implementation attains real time 3D haptic and graphic rendering rates, making it appropriate to model deformation in complex haptic virtual environments. The algorithm is appealing because it takes advantage of single-point haptic interaction to render efficiently while maintaining a very low memory footprint.
The role of the meridional sea surface temperature gradient in controlling the Caribbean low‐level jet

The Caribbean low‐level jet (CLLJ) is an important modulator of regional climate, especially precipitation, in the Caribbean and Central America. Previous work has inferred, due to their semiannual cycle, an association between CLLJ strength and meridional sea surface temperature (SST) gradients in the Caribbean Sea, suggesting that the SST gradients may control the intensity and vertical shear of the CLLJ. In addition, both the horizontal and vertical structure of the jet have been related to topographic effects via interaction with the mountains in Northern South America (NSA), including funneling effects and changes in the meridional geopotential gradient. Here we test these hypotheses, using an atmospheric general circulation model to perform a set of sensitivity experiments to examine the impact of both SST gradients and topography on the CLLJ. In one sensitivity experiment, we remove the meridional SST gradient over the Caribbean Sea and in the other, we flatten the mountains over NSA. Our results show that the SST gradient and topography have little or no impact on the jet intensity, vertical, and horizontal wind shears, contrary to previous works. However, our findings do not discount a possible one‐way coupling between the SST and the wind over the Caribbean Sea through friction force. We also examined an alternative approach based on barotropic instability to understand the CLLJ intensity, vertical, and horizontal wind shears. Our results show that the current hypothesis about the CLLJ must be reviewed in order to fully understand the atmospheric dynamics governing the Caribbean region.
Thread-Aware Logic Programming for Data-Driven Parallel Programs

Declarative programming in the style of functional and logic programming has been hailed as an alternative parallel programming style where computer programs are automatically parallelized without programmer control. Although this approach removes many pitfalls of explicit parallel programming, it hides important information about the underlying parallel architecture that could be used to improve the scalability and efficiency of programs. In this paper, we present a novel programming model that allows the programmer to reason about thread state in data-driven declarative programs. This abstraction has been implemented on top of Linear Meld, a linear logic programming language that is designed for writing graphbased programs. We present several programs that show the flavor of our new programming model, including graph algorithms and a machine learning algorithm. Our goal is to show that it is possible to take advantage of architectural details without losing the key advantages of logic programming.
Realistic compilation by partial evaluation

Two key steps in the compilation of strict functional languages are the conversion of higher-order functions to data structures (closures) and the transformation to tail-recursive style. We show how to perform both steps at once by applying first-order offline partial evaluation to a suitable interpreter. The resulting code is easy to transliterate to low-level C or native code. We have implemented the compilation to C; it yields a performance comparable to that of other modern Scheme-to-C compilers. In addition, we have integrated various optimizations such as constant propagation, higher-order removal, and arity raising simply by modifying the underlying interpreter. Purely first-order methods suffice to achieve the transformations. Our approach is an instance of semantics-directed compiler generation.