Miracle-dz/UniFAR-FTUs huggingface dataset:
Activity Switches of Rhodopsin †

Rhodopsin, the visual pigment of the rod photoreceptor cell contains as its light‐sensitive cofactor 11‐cis retinal, which is bound by a protonated Schiff base between its aldehyde group and the Lys296 side chain of the apoprotein. Light activation is achieved by 11‐cis to all‐trans isomerization and subsequent thermal relaxation into the active, G protein‐binding metarhodopsin II state. Metarhodopsin II decays via two parallel pathways, which both involve hydrolysis of the Schiff base eventually to opsin and released all‐trans retinal. Subsequently, rhodopsin's dark state is regenerated by a complicated retinal metabolism, termed the retinoid cycle. Unlike other retinal proteins, such as bacteriorhodopsin, this regeneration cycle cannot be short cut by light, because blue illumination of active metarhodopsin II does not lead back to the ground state but to the formation of largely inactive metarhodopsin III. In this review, mechanistic details of activating and deactivating pathways of rhodopsin, particularly concerning the roles of the retinal, are compared. Based on static and time‐resolved UV/Vis and FTIR spectroscopic data, we discuss a model of the light‐induced deactivation. We describe properties and photoreactions of metarhodopsin III and suggest potential roles of this intermediate for vision.
Relationship between kinesiophobia and pain, quality of life, functional status, disease activity, mobility, and depression in patients with ankylosing spondylitis

Background/aim: Our aim was to investigate the association of kinesiophobia with pain, quality of life, clinical measures, and depression in patients with ankylosing spondylitis (AS). Materials and methods: Patients with AS (n: 163) were enrolled in the study. Kinesiophobia was evaluated with the Tampa Scale of Kinesiophobia (TSK), pain with a visual analog scale (VAS), mobility with Bath Ankylosing Spondylitis Metrology Index (BASMI), disease activity with the Bath AS Disease Activity Index (BASDAI), functional status with the Bath AS Functional Index (BASFI), depression level with Beck's Depression Inventory (BDI), and quality of life with the AS Quality of Life Questionnaire (ASQoL). Besides correlation analysis, outcome measures were compared between patients with (TSK ? 37) and without (TSK < 37) kinesiophobia. Results: Kinesiophobia was found to be common with a percentage of 66.6%. TSK scores were correlated with VAS, BASFI, ASQoL, and BDI scores (r = 0.259, r = 0.294, r = 0.392, and r = 0.398, respectively; P < 0.05 for each). There were no correlations between TSK and the BASDAI and BASMI scores (r = 0.142, r = 0.198, respectively; P > 0.05). Patients with kinesiophobia had more pain and poorer BASFI, ASQoL, and BDI scores than patients without kinesiophobia (P < 0.05). Conclusion: Our study is the first study that investigated the relationship between kinesiophobia and other clinical measures in AS patients. Pain and psychological status have an impact on fear of movement and thus functional status and quality of life.
Between- and within-breed genetic analysis of calving traits and survival to weaning in beef cattle.

Data for gestation length, birth weight, calving difficulty (percent assisted) and survival from birth to weaning were analyzed from 4,639 calves by 290 sires of 14 Bos taurus breeds (Hereford, Angus, Jersey, South Devon, Limousin, Simmental, Charolais, Red Poll, Brown Swiss, Gelbvieh, Maine Anjou, Chianina, Pinzgauer and Tarentaise) mated to Hereford and Angus cows. The calves were produced over a 7-yr period in a germ plasm evaluation program. Variance components were estimated for breed of sire (sigma 2b), sire within breed of sire (sigma 2s) and progeny within sire (sigma 2w) random effects. Estimates of sigma 2b and sigma 2s direct genetic variance were similar for gestation length and calf survival. Estimates of sigma 2b genetic variance were greater than for sigma 2s for birth weight and calving difficulty. Estimates of total heritability [h2t = 4(sigma 2b + sigma 2s)/(4 sigma 2b + sigma 2s + sigma 2w)] and within-breed heritability (h2w = 4 sigma 2s/sigma 2s + sigma 2w) indicated that gestation length (h2t = .77, h2w = 64) and birth weight (h2t = .79, h2w = .46) are under a high degree of direct genetic control, calving difficulty (h2t = .42, h2w = .21) is under a moderate degree of direct genetic control and calf survival (h2t = .11, h2w = .07) is under a low degree of direct genetic control. Estimates of genetic correlation for between (rb) - and within-breed (rg) sources of genetic variation were comparable in direction, but tended to be stronger between than within breeds. (ABSTRACT TRUNCATED AT 250 WORDS)
Expression of cyclooxygenase-2 and 12-lipoxygenase in human breast cancer and their relationship with HER-2/neu and hormonal receptors: impact on prognosis and therapy.

BACKGROUND A number of studies have shown over-expression of cox-2 in breast cancer. Also it has been recorded that human breast cancer expresses high level of cox-2 and 12-lipoxygenase which may be beneficial in future therapy plan for those patients. AIMS The present study aims to examine the level of transcripts of cox-2 and 12-lipoxygenase in Egyptian breast cancer patients and to compare between the expressions of both enzymes and TNM staging, hormone receptors status (including estrogen and progesterone) and HER2/neu expression. MATERIALS AND METHODS Total cellular RNA was extracted from 64 frozen tissue samples of breast carcinoma and their corresponding normal adjacent tissues. Cox-2 and 12-lipooxygenase expressions were detected using RT-PCR. Hormonal receptors as well as HER2/neu were detected immuno-histochemically for each patient. RESULTS About 47 and 62.5% of carcinoma samples showed over-expression of cox-2 and 12-lipooxygenase respectively as compared to their corresponding normal tissues. The results revealed that cox-2 significantly associated with TNM staging (P = 0.0047) and hormonal receptors status (P = 0.0201). The relationship between cox-2 and HER2/neu expression was close to a significant value (P = 0.0747). 12-lipooxygenase showed only significant association with TNM staging (P = 0.0076). Neither hormonal receptors nor HER2/neu showed significant association with this enzyme. CONCLUSION Elevated levels of cox-2 and 12-lipoxygenase expression were detected in human breast cancer. Also, the results revealed that cox-2 and 12-lipooxygenase mRNA expressions are associated with TNM staging in human breast cancer. Furthermore, there is an inverse association between cox-2 expression and hormonal receptor status. This observation may drive us to the possible role of those two enzymes in determining the plan of therapy of breast cancer patients.
Regulation of Dictyostelium myosin II by phosphorylation: what is essential and what is important?

M UCH Can be inferred about the function of a protein in vivo from its biochemical properties and its intracellular localization. The acid test for function in vivo, however, is the creation of mutant cell lines in which the protein of interest is either missing or nonfunctional and the analysis of the behavioral abnormalities exhibited by these mutant cells. One of the most dramatic successes in the use of this approach for the study of cell motility was the demonstration in 1987 that Dictyostelium ceils which lack the heavy chain polypeptide for the conventional form of nonmuscle myosin, myosin 11, have profound blocks in cytokinesis when grown in suspension and in multicellnlar development (6, 12). This elegant work was greatly aided by the simple fact that in Dictyostelium there is a single gene for the heavy chain of conventional myosin, so ablation of this gene or suppression of its expression with antisense RNA renders a cell that is missing an entire class of nonmuscle myosin. Subsequent work by a number of labs has shown that myosin IIcells are also unable to cap surface receptors crosslinked with Con A (22), have greatly reduced cortical stiffness (22), and are inefficient in cell locomotion and chemotaxis (37) (for review see reference 28). The fact that myosin 11cells exhibit these striking phenotypes, that wild type and mutated copies of the myosin II gene can be introduced into myosin IIcells, and that rescue of the behavioral abnormalities can be readily assayed, has opened the door to in vivo structure/function analyses of the myosin 1I heavy chain (7, 26, 35). Dictyostelium myosin 11 is phosphorylated in vivo on both its heavy and light chains (1, 2, 15), and in vitro data indicate that these phosphorylations regulate the actin-activated ATPase, self-assembly properties, and motility properties of the molecule (for review see references 13 and 31). In the last several years, therefore, efforts by several labs have been directed at ascertaining the relative importance of these phosphorylations in vivo. In this short review, I will summarize the current in vitro data regarding the effects of heavy and light chain phosphorylation on Dictyostelium myosin 11, and recent efforts to define the significance of these phosphorylations in living cells. For heavy chain phosphorylation, a myosin II heavy chain kinase expressed in vegetative ceils phosphorylates three
Inhibitory and excitatory subtypes of cochlear nucleus neurons are defined by distinct bHLH transcription factors, Ptf1a and Atoh1

The cochlear nucleus (CN), which consists of dorsal and ventral cochlear nuclei (DCN and VCN), plays pivotal roles in processing and relaying auditory information to the brain. Although it contains various types of neurons, the origins of the distinct subtypes and their developmental molecular machinery are still elusive. Here we reveal that two basic helix-loop-helix transcription factors play crucial roles in specifying neuron subtypes in the CN. Pancreatic transcription factor 1a (Ptf1a) and atonal homolog 1 (Atoh1) were found to be expressed in discrete dorsolateral regions of the embryonic neuroepithelia of the middle hindbrain (rhombomeres 2-5). Genetic lineage tracing using mice that express Cre recombinase from the Ptf1a locus or under the control of the Atoh1 promoter revealed that inhibitory (GABAergic and glycinergic) or excitatory (glutamatergic) neurons of both DCN and VCN are derived from the Ptf1a- and Atoh1-expressing neuroepithelial regions, respectively. In the Ptf1a or Atoh1 null embryos, production of inhibitory or excitatory neurons, respectively, was severely inhibited in the CN. These findings suggest that inhibitory and excitatory subtypes of CN neurons are defined by Ptf1a and Atoh1, respectively and, furthermore, provide important insights into understanding the machinery of neuron subtype specification in the dorsal hindbrain.
Effects of HIF-1α and HIF2α on Growth and Metabolism of Clear-Cell Renal Cell Carcinoma 786-0 Xenografts

In cultured clear-cell renal carcinoma (CCRCC) 786-0 cells transfected with HIF1α (HIF-1+), HIF-2α (HIF-2+), or empty vector (EV), no significant differences were observed in the growth rates in vitro, but when grown in vivo as xenografts HIF-2α significantly increased, and HIF-1α significantly decreased growth rates, compared to EV tumors. Factors associated with proliferation were increased and factors associated with cell death were decreased in HIF-2+ tumors. Metabolite profiles showed higher glucose and lower lactate and alanine levels in the HIF-2+ tumors whilst immunostaining demonstrated higher pyruvate dehydrogenase and lower pyruvate dehydrogenase kinase 1, compared to control tumors. Taken together, these results suggest that overexpression of HIF-2α in CCRCC 786-0 tumors regulated growth both by maintaining a low level of glycolysis and by allowing more mitochondrial metabolism and tolerance to ROS induced DNA damage. The growth profiles observed may be mediated by adaptive changes to a more oxidative phenotype.
Revisiting Hospital Readmissions

Is your hospital addressing the readmission rate? Maybe efforts are underway, but pharmacy is not directly involved. Although many believe the readmission reduction program needs changes to better reflect quality care, the program is in place and likely impacts your institution. We provide a broad overview of the program and try to sensitize you to the technologies that can support medication-related efforts.
Synthesis and characterization of Escherichia coli O18 O-polysaccharide conjugate vaccines

Nontoxic, serologically reactive O polysaccharide was derived from Escherichia coli O18 lipopolysaccharide by acid hydrolysis, extraction with organic solvents, and gel filtration chromatography. Oxidized O polysaccharide was covalently coupled to either Pseudomonas aeruginosa toxin A or cholera toxin by using adipic acid dihydrazide as a spacer molecule in the presence of carbodiimide. The resulting conjugates were composed of approximately equal amounts of O polysaccharide and protein and were nontoxic and nonpyrogenic. Both conjugates engendered an immunoglobulin G antibody response in rabbits that recognized native O18 lipopolysaccharide. Such antibody was able to promote the uptake and killing of an E. coli O18 strain bearing the K1 capsule by human polymorphonuclear leukocytes. Immunoglobulin G isolated from the sera of rabbits immunized with either conjugate afforded protection against an E. coli O18 challenge when passively transferred to mice.
The selectivity of rostroventral medulla descending control of spinal sensory inputs shifts postnatally from A fibre to C fibre evoked activity

Brainstem descending pathways control the balance of excitation and inhibition in spinal sensory networks. In adult rodents, descending inhibition is targeted to spinal neurons with a strong afferent C fibre input. Descending inhibitory control matures slowly; the first postnatal weeks are characterized by greater descending facilitation than inhibition. We report that, in contrast to adults, brainstem descending facilitation of spinal sensory neurons in young rats (postnatal day 21) is targeted to A fibre inputs. The selective inhibition of C fibre inputs observed in adults is absent at postnatal day 21. In both young and adult rats, descending inhibition or facilitation is correlated with the excitability of individual neurons, as measured by ‘wind‐up’ to repeated C fibre stimulation. The facilitation of A fibre input in early life is likely to enhance innocuous, tactile sensory inputs to the dorsal horn in the critical early postnatal weeks and thus promote activity‐dependent development of sensory networks.
ISOLATION OF ENTERIC PATHOGENS FROM BATS IN TRINIDAD

Bats are one of the most widely distributed mammals in the world, and they are reservoirs or carriers of several zoonoses. Bats were trapped in 27 geographic locations across Trinidad and Tobago, and following euthanasia, gastrointestinal tracts were aseptically removed. Contents were subjected to bacteriologic analysis to detect Salmonella spp. , Escherichia coli, and Campylobacter spp. Isolates of Salmonella were serotyped, and E. coli isolates were screened for O157 strains and antimicrobial sensitivity to eight antimicrobial agents; phenotypic characteristics also were determined. Of 377 tested bats, representing 12 species, four bats (1.1%) were positive for Samonella spp, 49 (13.0%) were positive for E. coli, and no bats were positive for E. coli O157 strain or Campylobacter spp. Isolated serotypes of Salmonella included Rubislaw and Molade, both from Noctilio leporinus, a fish-eating bat, Caracas recovered from Molossus major, and Salmonella Group I from Molossus ater, both insect-eating bats. Of the 49 isolates of E. coli tested, 40 (82%) exhibited resistance to one or more antimicrobial agents, and the prevalence of resistant strains was comparatively high to erythromycin (61%) and streptomycin (27%) but lower to gentamycin (0%) and sulphamethozaxole/trimethoprim (2%).
Motion capture using joint skeleton tracking and surface estimation

This paper proposes a method for capturing the performance of a human or an animal from a multi-view video sequence. Given an articulated template model and silhouettes from a multi-view image sequence, our approach recovers not only the movement of the skeleton, but also the possibly non-rigid temporal deformation of the 3D surface. While large scale deformations or fast movements are captured by the skeleton pose and approximate surface skinning, true small scale deformations or non-rigid garment motion are captured by fitting the surface to the silhouette. We further propose a novel optimization scheme for skeleton-based pose estimation that exploits the skeleton's tree structure to split the optimization problem into a local one and a lower dimensional global one. We show on various sequences that our approach can capture the 3D motion of animals and humans accurately even in the case of rapid movements and wide apparel like skirts.
Making Time-Series Classification More Accurate Using Learned Constraints

It has long been known that Dynamic Time Warping (DTW) is superior to Euclidean distance for classification and clustering of time series. However, until lately, most research has utilized Euclidean distance because it is more efficiently calculated. A recently introduced technique that greatly mitigates DTWs demanding CPU time has sparked a flurry of research activity. However, the technique and its many extensions still only allow DTW to be applied to moderately large datasets. In addition, almost all of the research on DTW has focused exclusively on speeding up its calculation; there has been little work done on improving its accuracy. In this work, we target the accuracy aspect of DTW performance and introduce a new framework that learns arbitrary constraints on the warping path of the DTW calculation. Apart from improving the accuracy of classification, our technique as a side effect speeds up DTW by a wide margin as well. We show the utility of our approach on datasets from diverse domains and demonstrate significant gains in accuracy and efficiency. E u clid ean D istan c e D yn am ic T im e W arp in g D is tan ce Figure 1: Note that while the two time series have an overall similar shape, they are not aligned in the time axis. Euclidean distance, which assumes the i point in one sequence is aligned with the i point in the other, will produce a pessimistic dissimilarity measure. The non-linear Dynamic Time Warped alignment allows a more intuitive distance measure to be calculated.
A new training algorithm using artificial neural networks to classify gender-specific dynamic gait patterns

The aim of this study was to present a new training algorithm using artificial neural networks called multi-objective least absolute shrinkage and selection operator (MOBJ-LASSO) applied to the classification of dynamic gait patterns. The movement pattern is identified by 20 characteristics from the three components of the ground reaction force which are used as input information for the neural networks in gender-specific gait classification. The classification performance between MOBJ-LASSO (97.4%) and multi-objective algorithm (MOBJ) (97.1%) is similar, but the MOBJ-LASSO algorithm achieved more improved results than the MOBJ because it is able to eliminate the inputs and automatically select the parameters of the neural network. Thus, it is an effective tool for data mining using neural networks. From 20 inputs used for training, MOBJ-LASSO selected the first and second peaks of the vertical force and the force peak in the antero-posterior direction as the variables that classify the gait patterns of the different genders.
Best Approximation to a Reversible Process in Black-Hole Physics and the Area Spectrum of Spherical Black Holes

The assimilation of a quantum (finite size) particle by a Reissner-Nordstr¨ black hole inevitably involves an increase in the black-hole surface area. It is shown that this increase can be minimized if one considers the capture of the lightest charged particle in nature. The unavoidable area increase is attributed to two physical reasons: the Heisenberg quantum uncertainty principle and a Schwinger-type charge emission (vacuum polarization). The fundamental lower bound on the area increase is 4¯ h, which is smaller than the value given by Bekenstein for neutral particles. Thus, this process is a better approximation to a reversible process in black-hole physics. The universality of the minimal area increase is a further evidence in favor of a uniformly spaced area spectrum for spherical quantum black holes. Moreover, this universal value is in excellent agreement with the area spacing predicted by Mukhanov and Bekenstein and independently by Hod.
Spectral karyotyping and interphase FISH reveal abnormalities not detected by conventional G‐banding

Abstract: Seventy uniformly treated children with acute lymphoblastic leukemia were analysed for chromosomal abnormalities with conventional G‐banding, spectral karyotyping (SKY) and interphase fluorescent in situ hybridisation (FISH) using probes to detect MLL,BCR/ABL, TEL/AML1 rearrangements and INK4 locus deletions. Numerical and/or structural changes could be identified in 80% of the patients by the use of molecular cytogenetic techniques, whereas abnormalities could be detected in 60% of the patients using G‐banding alone. Altogether, 106 structural aberrations were defined by FISH compared to 34 using G‐banding. Seventy‐four percent of the patients had numerical aberrations, 54% structural aberrations and 20% had no identified aberrations. Twelve cases had prognostically unfavourable chromosomal aberrations that had not been detected in the G‐banded analysis. We identified three novel TEL partner breakpoints on 1q41, 8q24 and 21p12, and a recurrent translocation t(1;12)(p32;p13) was found. In addition, two cases displayed amplification (7–15 copies) of AML1. Our results demonstrate the usefulness of SKY and interphase FISH for the identification of novel chromosome aberrations and cytogenetic abnormalities that provide prognostically important information in childhood ALL.
Foundations of timed concurrent constraint programming

We develop a model for timed, reactive computation by extending the asynchronous, untimed concurrent constraint programming model in a simple and uniform way. In the spirit of process algebras, we develop some combinators expressible in this model, and reconcile their operational, logical and denotational character. We show how programs may be compiled into finite-state machines with loop-free computations at each state, thus guaranteeing bounded response time. <<ETX>>