Miracle-dz/UniFAR-FTUs huggingface dataset:
Signal Recognition Particle-ribosome Binding Is Sensitive to Nascent Chain Length*

Background: The initial step of the signal recognition particle (SRP) targeting pathway requires binding to actively translating ribosomes. Results: SRP-ribosome binding kinetics and affinities are affected by nascent chain length. Conclusion: SRP targeting is likely modulated at the initial ribosome-binding step, which is influenced by translation of nascent chain. Significance: Understanding signal recognition particle-ribosome binding provides insights into the constraints of co-translational targeting. The signal recognition particle (SRP) directs ribosome-nascent chain complexes (RNCs) displaying signal sequences to protein translocation channels in the plasma membrane of prokaryotes and endoplasmic reticulum of eukaryotes. It was initially proposed that SRP binds the signal sequence when it emerges from an RNC and that successful binding becomes impaired as translation extends the nascent chain, moving the signal sequence away from SRP on the ribosomal surface. Later studies drew this simple model into question, proposing that SRP binding is unaffected by nascent chain length. Here, we reinvestigate this issue using two novel and independent fluorescence resonance energy transfer assays. We show that the arrival and dissociation rates of SRP binding to RNCs vary according to nascent chain length, resulting in the highest affinity shortly after a functional signal sequence emerges from the ribosome. Moreover, we show that SRP binds RNCs in multiple and interconverting conformations, and that conversely, RNCs exist in two conformations distinguished by SRP interaction kinetics.
Intralayer Communication for Tree-Based Overlay Networks

While various HPC tools use Tree-Based Overlay Networks (TBONs) to increase their scalability, some use cases do not map well to a tree-based hierarchy. We provide the concept of intralayer communication to improve this situation, where nodes in a specific hierarchy layer may exchange messages directly with each other. This concept targets data preprocessing that allows tool developers to avoid load imbalances in higher hierarchy levels. We implement intralayer communication within the Generic Tools Infrastructure (GTI) that provides TBON services, as well as a high-level abstraction to ease the creation of scalable runtime tools. An extension of GTI's abstractions allows simple and efficient use of intralayer communication. We demonstrate this capability with a runtime message matching tool for MPI's point-to-point communication, which we evaluate in an application study with up to 16,384 processes. Low overheads for two benchmark suites show the applicability of our approach, while a stress test demonstrates close to constant overheads across scales. The stress test measurements demonstrate that intralayer communication reduces application slowdown by two orders of magnitude at 2,048 processes, compared to a previous TBON-based implementation.
A Super-Logarithmic Lower Bound for Shuffle-Unshuffle Sorting Networks 1

Shuffle-unshuffle sorting networks are a class of comparator networks whose structure maps efficiently to the hypercube and any of its bounded degree varia nts. Recently,n-input shuffleunshuffle sorting networks with depth 2O(plg lgn) lgn have been discovered. These networks are the only known sorting networks of depth o(lg2 n) that are not based on expanders, and their existence raises the question of whether a depth of O(lg n) can be achieved by any shuffle-unshuffle sorting network. In this paper, we resolve this question by e stablishing an lgn lg lgn lg lg lgn lower bound on the depth of any n-input shuffle-unshuffle sorting network. Our lower bound ca n be extended to certain restricted classes of non-oblivious sort ing algorithms on hypercubic machines. 1 A preliminary version of this paper was presented at the 21st International Colloquium on Automata, Languages, and Programming (ICALP), 1994. 2 Department of Computer Science, University of Texas, Austi n, TX 78712. Email:plaxton@cs.utexas. edu. Supported by NSF Research Initiation Award CCR–9111591, an d the Texas Advanced Research Program under Grant Nos. 003658–480 and 003658–461. 3 CIS Department, Polytechnic University, Brooklyn, NY 1120 . Email:suel@photon.poly. edu. Part of this work was performed while the author was a graduate student at the University of Texas, and was supported by the Texas Advanced Research Program under Grant Nos. 003658–48 0 and 003658–461, and by a Schlumberger Graduate Fellowship.
The interphotoreceptor retinoid-binding protein (IRBP) of the chicken (Gallus gallus domesticus).

PURPOSE Despite decades of investigation, the function of interphotoreceptor retinoid binding protein (IRBP), the most abundant protein in the interphotoreceptor matrix of vertebrates, remains enigmatic. Roles for IRBP in the visual cycle of rod photoreceptors and in the independent visual cycle of cone photoreceptors have been suggested, yet very little is known of the biology of IRBP in cone-dominant retinas, such as those of diurnal birds. Our aim was to identify and characterize expression of the IRBP of the cone-dominant chicken (Gallus gallus domesticus). METHODS Chicken IRBP mRNA was identified by PCR cloning. Primary protein structure, genomic organization, and phylogenies were determined through comparative sequence analyses. Expression of IRBP mRNA was characterized by northern analysis and by in situ hybridization on cryosectioned chicken retina. Expression of the IRBP protein was characterized by western blotting and by indirect immunofluorescence on cryosectioned retina and on retinal whole mounts. RESULTS The chicken IRBP gene encodes a secreted protein with a predicted 1,252 amino acid length. The gene structure for chicken IRBP resembles that of most other vertebrates, with four homologous, modular repeats and introns within only the fourth module. Each module is more homologous with the corresponding module in other species than it is with the remaining chicken modules. Chicken retinal tissue contains a single IRBP mRNA transcript of approximately 4.8 kb and western analysis of chicken retina shows a single major band of 140 kDa. Chicken IRBP mRNA is expressed exclusively by retinal photoreceptor cells and the intensity of the hybridization signal shows light/dark rhythmicity. The IRBP protein is localized to the interphotoreceptor matrix of the chicken retina and to intracellular regions of photoreceptors, with a spatial distribution indicating an association with cone outer segments. CONCLUSIONS The high degree of conservation of IRBP's primary structure, genomic organization, and cell-specific expression within the retinas of all vertebrates examined to date, including those with cone-dominant retinas, implies a conserved role for IRBP in photoreceptor function and/or health. Expression of chicken IRBP and its mRNA are functionally regulated. This report provides a necessary first step to explore a specific function for IRBP in the cone visual cycle.
Exploring variability within and between corpora: some methodological considerations

The results usually reported in corpus-linguistic studies are quantitative: frequencies, percentages, model parameters, etc. However, given that no corpora are alike, and that sometimes different results are reported for very similar corpora (or even the same corpus), three central issues are: (i) how to identify and quantify the degree of variation coming with one's results; (ii) how to investigate the source of the observed variation in corpora; and, (iii) how homogeneous one's corpus is with respect to a particular phenomenon. In this paper, I shall present a methodology that addresses these issues, providing data from ICE-GB on the frequency of the English present perfect, the alternation of transitive phrasal verbs and the semantics of the English ditransitive. Specifically, I will show how applying resampling methods and exploratory data analysis to corpus data allows for, (i) providing interval estimates for one's findings that show how superficially different results may reflect similar underlying.
From Hope in Palliative Care to Hope as a Virtue and a Life Skill

Abstract: This paper aims at explicating a theory of hope that is also suitable for gravely ill people and based on virtue ethics, research in the psychology of “well-being,” and the philosophy of palliative care. The working hypotheses of the theory are that hope is conditioned neither by past events nor by present needs, but is not necessarily oriented toward the future, especially the distant future; that hope is related to personal agency and to freedom; and that hope is deliberative, hence evaluative, motivatory, and rationally critical. Following Higgins’ distinction between “prevention-focus” and “promotion-focus” strategies of coping, and Rawls’ notion of the “Aristotelian principle,” it is argued that hope is the valuation of and personal identification with “promotion-focus” goals with an attitude of nonattachment to any one goal.
Conditions of Endoplasmic Reticulum Stress Favor the Accumulation of Cytosolic Prion Protein*

After signal sequence-dependent targeting to the endoplasmic reticulum (ER), prion protein (PrP) undergoes several post-translational modifications, including glycosylation, disulfide bond formation, and the addition of a glycosylphosphatidylinositol anchor. As a result, multiple isoforms are generated. Because of the intrinsic weakness of the PrP signal sequence, a fraction of newly synthesized molecules fails to translocate and localizes to the cytosol. The physiopathologic role of this cytosolic isoform is still being debated. Here we have shown that, in both cultured cell lines and primary neurons, ER stress conditions weaken PrP co-translational translocation, favoring accumulation of aggregation-prone cytosolic species, which retain the signal sequence but lack N-glycans and disulfides. Inhibition of proteasomes further increases the levels of cytosolic PrP. Overexpression of spliced XBP1 facilitates ER translocation, suggesting that downstream elements of the Ire1-XBP1 pathway are involved in PrP targeting. These studies reveal a link between ER stress and the formation of cytosolic PrP isoforms potentially endowed with novel signaling or cytotoxic functions.
THE RELATIONSHIP BETWEEN PRESEASON RANGE OF MOTION AND MUSCLE STRAIN INJURY IN ELITE SOCCER PLAYERS

The purpose of the study was to determine the influence of preseason lower-extremity range of motion (ROM) on the risk of muscle strain injury during a competitive season for elite soccer players. Thirty-six elite male soccer players (age, 25.6 = 4.7 years) had maximum static ROM for 6 movements of the lower extremity measured prior to the 2003–2004 English Premier League season. Player age, body size, dominant limb, and playing position were documented also. All lower-extremity muscle strain injuries were recorded prospectively during the competitive season, as was the total amount of time spent in training and games for each player. Soccer players sustaining a muscle strain injury in the hip flexors or knee flexors had lower pre- season ROM (p ≤ 0.05) in these muscle groups compared with uninjured players. Similar trends were observed for the remaining muscle groups, but all failed to reach statistical significance (p ≥ 0.05). Most significantly, soccer players with lower preseason ROM in the hip flexors and knee flexors had a statistically higher risk for a muscle strain injury to these muscle groups during a competitive season. Age, body size, limb dominance, and playing position were not significant intrinsic risk factors for the development of muscle strain injuries. Screening of flexibility for soccer players should be conducted during preseason, and flexibility training should be prescribed to players with reduced ROM to lower the risk of developing a muscle strain injury.
Training Multi-Classifiers for Chinese Unknown Word Detection

According to a survey in a corpus, majority of the unknown words in Chinese texts are numbers, time nouns and person names. Detection of numbers and time nouns are trivial tasks. These three types of unknown words may need different feature sets and parameters to achieve optimal results. For example, characters used in Chinese family names help in Chinese person name detection. Therefore, we propose a hierarchical model, with multiple classifiers (same model but different feature sets and parameters) for the detection. We create one classifier for each unknown word type: numbers, time nouns, person names and others. The experimental results show that our model can get higher precision (89%) comparing with only using one classifier (86%). Furthermore, this model enables us to detect the three unknown word types straightaway with high accuracy so that we can concentrate only on POS tag guessing for the other unknown types.
Apatinib for the treatment of gastric cancer

ABSTRACT Introduction: Apatinib, a small-molecule inhibitor of vascular endothelial growth factor receptor 2, has demonstrated encouraging anti-cancer activity in gastric cancer within both in vitro and in vivo models. Areas covered: Apatinib's efficacy, tolerability and safety have been evaluated in one Phase II and one Phase III study in metastatic/advanced gastric cancer. In this review, we focus on the mechanism of action of apatinib, its pharmacokinetic profile and its clinical activity in the treatment of advanced/metastatic gastric cancer. Expert commentary: Unfortunately, as yet, there is no definitive biomarker data for apatinib in gastric cancer.
Electronic pan-tilt-zoom: a solution for intelligent room systems

Choosing the appropriate type of video input is an important issue for any vision-based system, and the right decision must take into account the specific requirements of the intended application. We present GlobeAll, a modular four-component prototype for a vision-based intelligent room: a video input component that uses an electronic pan-tilt-zoom camera array, a background learning and foreground extraction component, a tracking component and an interpretation component. In the context of intelligent room systems, we establish several qualitative criteria to evaluate their video input components. We use these principles to compare our electronic pan-tilt-zoom camera with two other current solutions-mobile pan-tilt-zoom and wide-angle lens cameras-and we show that electronic pan-tilt-zoom systems best satisfy our criteria.
Approaching Difficult Communication Tasks in Oncology 1

Effective communication skills enable physicians to improve patients' understanding of their illnesses, improve patient adherence to treatment regimens, use time efficiently, avoid burnout, and increase professional fulfillment. Common communication pitfalls include blocking, lecturing, depending on a routine, collusion, and premature reassurance. Fundamental communication skills include “ask‐tell‐ask,” “tell me more,” and responding empathetically. Key communication tasks that are linked to the illness trajectory include: the first visit, giving bad news, making anticancer treatment decisions, offering clinical trials, completing anticancer therapy, and discontinuing palliative chemotherapy. While enhancing or acquiring new skills ultimately requires practice and feedback over time, this article provides a cognitive map for important communication skills that physicians need over the course of caring for a person with cancer.
Risk factors for patients developing a fulminant course with acute myocarditis.

BACKGROUND A fulminant course can be difficult to predict at the onset of acute myocarditis, so the aim of the present study was to identify the predictive clinical symptoms/signs or laboratory findings. METHODS AND RESULTS Thirty-nine patients with acute lymphocytic myocarditis, excluding 8 who manifested shock at admission, were studied. The fulminant group was defined as 12 patients who developed shock after admission, requiring intraaortic balloon pumping or percutaneous cardiopulmonary support, and the non-fulminant group comprised the 27 patients without shock. Various parameters at admission were compared between the 2 groups, together with multiple logistic regression analysis, excluding 6 patients with partially missing values. In the fulminant group, C-reactive protein (7.0 +/- 7.0 vs 2.3 +/- 2.2 mg/dl, p<0.01) and creatine kinase (1,147 +/- 876 vs 594 +/- 568 IU/L, p<0.05) concentrations were higher, intraventricular conduction disturbances were more frequent (9/12 vs 7/27 patients, p<0.01) and the left ventricular ejection fraction was lower (40.7 +/- 13.9 vs 50.1 +/- 10.6%, p<0.05) than in the non-fulminant group. In the multiple logistic regression analysis model with the presence/absence of a fulminant course considered as the independent variable, and C-reactive protein, creatine kinase, intraventricular conduction disturbances, and left ventricular ejection fraction as dependent variables, a high-risk group (expected proportion of fulminant course > or = 0.5) and a low-risk group (<0.5) could be differentiated. A fulminant course occurred in 9/13 (69%) patients in the high-risk group, but in only 2/20 (10%) patients in the low risk group (p<0.001). CONCLUSIONS The risk of a fulminant course of acute myocarditis was high in patients with elevated C-reactive protein, and creatine kinase concentrations, decreased left ventricular ejection fraction, and intraventricular conduction disturbances at the time of admission.
New 2-Arylbenzofurans from the Root Bark of Artocarpus lakoocha

Three new prenylated 2-arylbenzofurans – artolakoochol, 4-hydroxy-artolakoochol and cycloartolakoochol – have been isolated from the root bark of Artocarpus lakoocha Roxb. , Their structures were elucidated through analysis of their spectroscopic data, and their antiherpetic potential was evaluated by the plaque reduction assay.
Gender differences in nonverbal communication of emotion

There is a large accumulation of research on gender differences in nonverbal communication. By nonverbal communication we mean specific behaviors such as smiling or gazing, as well as accuracy in nonverbal communication. Summaries of these gender differences are available (Hall, 1978, 1984, 1987; LaFrance & Hecht, this volume; Vrugt & Kerkstra, 1984). The present chapter is also concerned with gender and nonverbal communication, but differs from earlier treatments in that we discuss a selected group of nonverbal behaviors with specific interest in analyzing the role of emotion in understanding the gender differences. Before beginning, it is important to make several points. First, nonverbal behavior does not necessarily signify emotion. Some examples will easily make this point. Smiles can serve the function of “listener responses” that signal comprehension and cue the other person to keep speaking (Brunner, 1979). Gaze is used to help coordinate the intricate process of turn-taking in conversation (Cappella, 1985). Hand movements aid in the process of speech encoding (Krauss, Chen, & Chawla, 1996). These are but a few examples of non-emotional meanings and functions of nonverbal cues. Second, even when nonverbal cues do indicate emotion, it is often difficult to identify what emotion is being felt. Nonverbal cues do not have fixed, dictionary-like meanings. So, a smile might convey either joy or anxiety, looking at someone might signify hostility or fascination, and so forth. Although someday we might understand the relations among contextual factors, motivational states, and specific muscle configurations well enough to permit a confident identification of which particular emotions are being conveyed by which nonverbal behaviors, in our present state of knowledge we are often unable to do so.
EFFECTS OF SHRIMP (MACROBRACIUM ROSENBERGII)‐DERIVED CHITOSAN ON PLASMA LIPID PROFILE AND LIVER LIPID PEROXIDE LEVELS IN NORMO‐ AND HYPERCHOLESTEROLAEMIC RATS

1 The effects of chitosan (CS) derived from the exoskeleton of the shrimp Macrobracium rosenbergii on bodyweight, plasma lipid profile, fatty acid composition, liver lipid peroxide (LPO) levels and plasma levels of glutamate pyruvate transaminase (GPT) were determined in normocholesterolaemic (NC) and hypercholesterolaemic (HC) Long Evans rats. 2 The NC rats were fed a diet containing 2% CS and the HC rats were fed a diet containing 2 and 4% CS for 8 weeks. Chitosan significantly reduced bodyweight gain only in HC + 4% CS rats compared with HC rats, but not in NC + 2% CS or HC + 2% CS rats. 3 Chitosan reduced plasma total cholesterol in the HC + 2% CS, HC + 4% CS and NC + 2% CS rats; however, low density lipoprotein–cholesterol decreased only in the first two groups. High‐density lipoprotein–cholesterol (HDL‐C) increased in the HC + 4% CS rats by 24% compared with the HC + 2% CS group and by 30% compared with HC rats; however, HDL‐C did not increase in the NC + 2% CS group compared with NC rats. The level of plasma triglycerides decreased significantly only in HC + 2% CS rats compared with HC rats. 4 Chitosan significantly decreased plasma levels of arachidonic acid in the HC + 2% CS and HC + 4% CS groups, with a concurrent increase in the molar ratio of total unsaturated fatty acid (TUFA) to total saturated fatty acid (TSFA). 5 Moreover, CS increased liver LPO levels without affecting plasma levels of GPT. Liver LPO levels were positively correlated with the TUFA/TSFA molar ratio. 6 The present study suggests that dietary CS decreases the atherogenic lipid profiles of both NC and HC rats and reduces the bodyweight gain of HC rats.
Photothermal Imaging of Nanometer-Sized Metal Particles Among Scatterers

Ambient optical detection of labeled molecules is limited for fluorescent dyes by photobleaching and for semiconducting nanoparticles by “blinking” effects. Because nanometer-sized metal particles do not optically bleach, they may be useful optical labels if suitable detection signals can be found. We demonstrate far-field optical detection of gold colloids down to diameters of 2.5 nanometers with a photothermal method that combines high-frequency modulation and polarization interference contrast. The photothermal image is immune to the effects of scattering background, which limits particle imaging through Rayleigh scattering to diameters larger than 40 nanometers.
Culturing nerve cells

Part 1 A user's guide: getting started, Gary Banker, Kimberly Goslin. Part 2 General principles: types of nerve cell cultures, their advantages and limitations, Gary Banker, Kimberly Goslin primary dissociated cell cultures, Dennis Higgins, Gary Banker transfecting cultured neurons, Ann Marie Craig characterizing and studying neuronal cultures, Ginger S. Withers, Gary Banker. Part 3 Culture of specific cell types - choosing the right system: culture and experimental use of the PC12 rat pheochromocytoma cell line, Lloyd A. Greene et al neuronlike cells derived in culture from P19 embryonal carcinoma and embryonic stem cells, Gerard Bain et al culturing the large neurons of aplasia, Daniel J. Goldberg, Samuel Schacher culturing spinal neurons and muscle cells from xenopus embryos, Nacira Tabti et el cultures from chick peripheral ganglia, Carolyn L. Smith culturing mammalian sympathoadrenal derivatives, Nagesh K. Mahanthappa, Paul H. Patterson mass cultures and microislands of neurons from postnatal rat brain, Michael M. Segal et al rat hippocampal neurons in low-density culture, Kimberley Goslin et al rat striatal neurons in low-density, serum-free culture, Roseann Ventimiglia, Ronald M. Lindsay cell culture of cholinergic and cholinoceptive neurons from the medial habenulae, Raul Krauss, Gerald D. Fischbach the cerebellum - purification and coculture of identified cell populations, Mary Beth Hatten et al organotypic slice cultures of neural tissue, Beat H. Gahwiler et al culture of astrocytes, oligodendrocytes, and O-2A progenitor cells, Mark Noble, Margot Mayer-Proschel tissue culture methods for the study of myelination, Naomi Kleitman et al.