Miracle-dz/UniFAR-FTUs huggingface dataset:
Assembly of the small ribosomal subunit in yeast: mechanism and regulation

The eukaryotic ribosome is made of four intricately folded ribosomal RNAs and 79 proteins. During rapid growth, yeast cells produce an incredible 2000 ribosomes every minute. Ribosome assembly involves more than 200 trans-acting factors, intervening from the transcription of the preribosomal RNA in the nucleolus to late maturation events in the cytoplasm. The biogenesis of the small ribosomal subunit, or 40S, is especially intricate, requiring more than four times the mass of the small subunit in assembly factors for its full maturation. Recent studies have provided new insights into the complex assembly of the 40S subunit. These data from cryo-electron microscopy, X-ray crystallography, and other biochemical and molecular biology methods, have elucidated the role of many factors required in small subunit maturation. Mechanisms of the regulation of ribosome assembly have also emerged from this body of work. This review aims to integrate these new results into an updated view of small subunit biogenesis and its regulation, in yeast, from transcription to the formation of the mature small subunit.
STAR3D: Simultaneous Tracking and Reconstruction of 3D Objects Using RGB-D Data

We introduce a probabilistic framework for simultaneous tracking and reconstruction of 3D rigid objects using an RGB-D camera. The tracking problem is handled using a bag-of-pixels representation and a back-projection scheme. Surface and background appearance models are learned online, leading to robust tracking in the presence of heavy occlusion and outliers. In both our tracking and reconstruction modules, the 3D object is implicitly embedded using a 3D level-set function. The framework is initialized with a simple shape primitive model (e.g. a sphere or a cube), and the real 3D object shape is tracked and reconstructed online. Unlike existing depth-based 3D reconstruction works, which either rely on calibrated/fixed camera set up or use the observed world map to track the depth camera, our framework can simultaneously track and reconstruct small moving objects. We use both qualitative and quantitative results to demonstrate the superior performance of both tracking and reconstruction of our method.
Removal of Estrone from Water by Adsorption on Zeolites with Regeneration by Direct UV Photolysis

Estrone is an endocrine-disrupting compound (EDC) that is suspected to have adverse effects on aquatic organisms. This work investigated the removal of estrone from water by adsorption onto hydrophobic molecular sieve zeolites followed by ultraviolet light (UV) photolysis to destroy the adsorbed estrone. A solvent-free analytical method employing solid phase micro-extraction (SPME) and gas chromatography (GC-FID) was utilized to analyze low estrone concentrations in water. Two types of zeolites, dealuminated Y (DAY) and silicalite-1, were evaluated for adsorption capacity and compared with Centaur® activated carbon (CAC). DAY showed the highest adsorption capacity, while silicalite-1 was the least effective in removing estrone. Moreover, DAY required four hours to reach adsorption equilibrium; much less than the eight days needed for CAC to reach equilibration. The Freundlich adsorption isotherm was found to best represent the data for adsorption of estrone on DAY. UV at λ = 254 nm degraded estrone in wat.
User capacity scaling laws for fading multiple-access channels

In this paper, the maximum number of simultaneous active transmitters (i.e. user capacity) is obtained in the many user case for fading multiple-access channels in which a minimum rate must be maintained for all active users. The results are presented in the form of scaling laws as the number of transmitters increases and three commonly used fading models, namely, Rayleigh, Rician and Nakagami are considered. It is shown that in all three cases, the user capacity scales double logarithmically with the number of users and differs only by constants depending on the distributions. We also show that the scheduling policy maximizing the number of simultaneous active transmitters can be implemented in a distributed fashion.
An Empirical Test of Warranty Theories in the U.S. Computer Server and Automobile Markets

Four theories on the economic rationale for warranty provision have been proposed in the literature: (1) Warranties provide insurance to customers and work as a risk-sharing mechanism, (2) warranties are a sorting mechanism and work as a means for second-degree price discrimination among customers with different risk preferences, (3) warranties work as a signal of product quality to consumers under information asymmetry, and (4) warranties work as an incentive mechanism for firms to reveal and improve product quality. The authors examine the conditions under which each theory would apply and derive testable implications from the data. They then assess whether these theories have empirical support in the U.S. computer server and automobile markets in the context of manufacturer base warranties. The results indicate that in both markets, warranties primarily provide customers with insurance against product failure, and warranties of different durations work as a sorting mechanism across customers with different levels of risk aversion. Warranties are not used to signal product quality or to provide an incentive for manufacturers to reveal or improve product quality.
Dynamic Software Updating Using a Relaxed Consistency Model

Software is inevitably subject to changes. There are patches and upgrades that close vulnerabilities, fix bugs, and evolve software with new features. Unfortunately, most traditional dynamic software updating approaches suffer some level of limitations; few of them can update multithreaded applications when involving data structure changes, while some of them lose binary compatibility or incur nonnegligible performance overhead. This paper presents POLUS, a software maintenance tool capable of iteratively evolving running unmodified multithreaded software into newer versions, yet with very low performance overhead. The main idea in POLUS is a relaxed consistency model that permits the concurrent activity of the old and new code. POLUS borrows the idea of cache-coherence protocol in computer architecture and uses a ”bidirectional write-through” synchronization protocol to ensure system consistency. To demonstrate the applicability of POLUS, we report our experience in using POLUS to dynamically update three prevalent server applications: vsftpd, sshd, and Apache HTTP server. Performance measurements show that POLUS incurs negligible runtime overhead on the three applications-a less than 1 percent performance degradation (but 5 percent for one case). The time to apply an update is also minimal.
The Ghost of Stochastic Resonance

Pablo Balenzuela, Holger Braun and Dante R. Chialvo ∗ Departamento de F́ısica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Cient́ıficas y Tecnológicas (CONICET), Buenos Aires, Argentina; Department of Physiology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Santa Fé, Argentina; Heidelberg Academy of Sciences and Humanities, Heidelberg, Germany; f Centre of Ice and Climate, Niels-Bohr Institute, University of Copenhagen, Copenhagen, Denmark;
POLD2 and KSP37 (FGFBP2) Correlate Strongly with Histology, Stage and Outcome in Ovarian Carcinomas

Background Epithelial ovarian cancer (EOC) constitutes more than 90% of ovarian cancers and is associated with high mortality. EOC comprises a heterogeneous group of tumours, and the causes and molecular pathology are essentially unknown. Improved insight into the molecular characteristics of the different subgroups of EOC is urgently needed, and should eventually lead to earlier diagnosis as well as more individualized and effective treatments. Previously, we reported a limited number of mRNAs strongly upregulated in human osteosarcomas and other malignancies, and six were selected to be tested for a possible association with three subgroups of ovarian carcinomas and clinical parameters. Methodology/Principal Findings The six selected mRNAs were quantified by RT-qPCR in biopsies from eleven poorly differentiated serous carcinomas (PDSC, stage III–IV), twelve moderately differentiated serous carcinomas (MDSC, stage III–IV) and eight clear cell carcinomas (CCC, stage I–IV) of the ovary. Superficial scrapings from six normal ovaries (SNO), as well as biopsies from three normal ovaries (BNO) and three benign ovarian cysts (BBOC) were analyzed for comparison. The gene expression level was related to the histological and clinical parameters of human ovarian carcinoma samples. One of the mRNAs, DNA polymerase delta 2 small subunit (POLD2), was increased in average 2.5- to almost 20-fold in MDSC and PDSC, respectively, paralleling the degree of dedifferentiation and concordant with a poor prognosis. Except for POLD2, the serous carcinomas showed a similar transcription profile, being clearly different from CCC. Another mRNA, Killer-specific secretory protein of 37 kDa (KSP37) showed six- to eight-fold higher levels in CCC stage I compared with the more advanced staged carcinomas, and correlated positively with an improved clinical outcome. Conclusions/Significance We have identified two biomarkers which are markedly upregulated in two subgroups of ovarian carcinomas and are also associated with stage and outcome. The results suggest that POLD2 and KSP37 might be potential prognostic biomarkers.
Intensity-dependent phase-matching effects in harmonic generation

In high-order harmonic generation by an intense laser, intrinsic phases can develop at the atomic level between the laser field and the individual emitted harmonics. Because intrinsic phases can vary rapidly with the laser intensity, they can strongly influence phase matching to the extent that the laser intensity varies within the generating medium. Previously reported measurements of broad far-field harmonic emission patterns as well as measured asymmetries in the emission with respect to the axial positioning of the medium in the focus can be explained by intrinsic phases. An experimental method for further study of intrinsic phases is proposed that involves harmonic generation in two counterpropagating laser beams. The periodic intensity modulation created by the two beams coupled with the intensity-dependent intrinsic phases allows harmonic light to propagate in directions with otherwise extremely poor phase-matching conditions.
Periopathogenic bacteria in dental plaque of Congolese patients with periodontitis: A pilot study

Background Periopathogenic bacteria play an important role in the etiology of periodontal disease. At present, no study screening for periopathogens in the DR Congo was carried out. The aim of this pilot study was to investigate the prevalence of five periopathogens in Congolese patients with periodontitis and to determine the association between these bacteria. Material and Methods Twelve patients (eight women and four men) with a mean age of 45 ± 19 years from those consulted in dental services of two medical centers of Kinshasa from April 2017 to October 2017 were included. Full mouth examination was registered, the probing pocket depth and clinical attachment level were assessed at six sites per tooth. Dental subgingival plaque samples were taken in the deepest pocket per arch in the maxilla and mandible. DNA analysis was performed using DNA-strip technology. The Fisher Exact test and Pearson correlation were used for statistical analysis. Results Porphyromonas gingivalis and Tannerella forsythia were detected at high level of 92%, Prevotella intermedia at a rate of 75% whereas Treponema denticola was detected in all patients. Aggregatibacter actinomycetemcomitans was not detected. Strong associations were found between three bacteria of the red complex and between T. denticola and P. intermedia (r=1). Conclusions This first study investigating periopathogens in subgingival plaque of Congolese with periodontitis demonstrated a high prevalence of the red complex (P. gingivalis, T. forsythia and T. denticola). Associations between different bacteria of this complex were strong. Key words:Association, bacteria, periopathogen, periodontitis, prevalence.
Characterization of Arbuscular Mycorrhizal Fungus Communities of Aquilaria crassna and Tectona grandis Roots and Soils in Thailand Plantations

Aquilaria crassna Pierre ex Lec. and Tectona grandis Linn.f. are sources of resin-suffused agarwood and teak timber, respectively. This study investigated arbuscular mycorrhizal (AM) fungus community structure in roots and rhizosphere soils of A. crassna and T. grandis from plantations in Thailand to understand whether AM fungal communities present in roots and rhizosphere soils vary with host plant species and study sites. Terminal restriction fragment length polymorphism complemented with clone libraries revealed that AM fungal community composition in A. crassna and T. grandis were similar. A total of 38 distinct terminal restriction fragments (TRFs) were found, 31 of which were shared between A. crassna and T. grandis. AM fungal communities in T. grandis samples from different sites were similar, as were those in A. crassna. The estimated average minimum numbers of AM fungal taxa per sample in roots and soils of T. grandis were at least 1.89 vs. 2.55, respectively, and those of A. crassna were 2.85 vs. 2.33 respectively. The TRFs were attributed to Claroideoglomeraceae, Diversisporaceae, Gigasporaceae and Glomeraceae. The Glomeraceae were found to be common in all study sites. Specific AM taxa in roots and soils of T. grandis and A. crassna were not affected by host plant species and sample source (root vs. soil) but affected by collecting site. Future inoculum production and utilization efforts can be directed toward the identified symbiotic associates of these valuable tree species to enhance reforestation efforts.
Young women’s retrospective accounts of their experience of same-sex sexual desire in adolescence

Seven women aged 19-25 participated in this qualitative study on young women's retrospective accounts of their experience of same-sex sexual desire in adolescence. Each woman participated in an open-ended, audiotaped interview. Each interview was transcribed and then analyzed using Arvay's (2002) narrative method of analysis. A narrative was developed from the analysis of each interview to represent the experience of same-sex desire in adolescence. Upon completion, each narrative was returned to the participant for feedback. Questions were also asked of each participant for clarification or new information. Five themes were identified upon reading across the narratives, based on their consistency across most or all the participants. These were: Growing up in a homophobic and heterosexist environment, denial and repression of same-sex desire, unfulfilled desire, secrecy and self-silencing, and reaching self-acceptance. It is anticipated that this research will help to redress the 'missing discourse of desire' in research and in social constructions of young women's sexuality, and contribute to the development of knowledge and implementation of counselling practice related to adolescent women's same-sex desire. T A B L E OF C O N T E N T S Abstract ii Table of
The Application of an Enamel Matrix Protein Derivative (Emdogain®) in Regenerative Periodontal Therapy: A Review

Regenerative periodontal therapy aims at reconstitution of the lost periodontal structures such as new formation of root cementum, periodontal ligament and alveolar bone. Findings from basic research indicate that enamel matrix protein derivative (EMD) has a key role in periodontal wound healing. Histological results from animal and human studies have shown that treatment with EMD promotes periodontal regeneration. Moreover, clinical studies have indicated that treatment with EMD positively influences periodontal wound healing in humans. This review aims to present an overview of evidence-based clinical indications for regenerative therapy with EMD.
Characterization and analysis on the solder ball shear testing conditions

This paper presents both experimental investigation and computational analysis on the solder ball shear testing conditions for ball grid array (BGA) packages. The experimental data of solder ball shear tests indicate that the ram height and the shear speed have substantial effects on the solder ball shear strength. The general trend shows that lower ram height and faster shear speed can result in higher ball shear strength. A two-dimensional finite element model is established to simulate the solder ball shear tests. The results in terms of load-displacement curve from computational analysis are in good agreement with the experimental data. Based on the computational stress analysis, an effort is made to interpret the failure mode of solder balls subject to the ball shear test.
Sexist Humor and Beliefs that Justify Societal Sexism

Research suggests that sexist humor creates a context that justifies the expression of prejudice against women. The present research investigates whether sexist humor has broader social consequences related to societal sexism. An experiment supported our hypothesis that men higher in hostile sexist attitudes express beliefs that justify the gender status-quo to a greater degree after exposure to sexist humor versus neutral humor or non-humorous sexist material. Specifically, male participants higher in hostile sexism reported greater acceptance of current gender relations and greater acceptance of societal devaluation of women after reading sexist jokes than after reading neutral (nonsexist) jokes or non-humorous sexist material.
Utilization of adjuvant arthritis model for evaluation of new approaches in rheumatoid arthritis therapy focused on regulation of immune processes and oxidative stress

Utilization of adjuvant arthritis model for evaluation of new approaches in rheumatoid arthritis therapy focused on regulation of immune processes and oxidative stress As a number of disease-modifying anti-rheumatic drugs often have side effects at high doses and/or during long-term administration, increased efficacy without increased toxicity is expected for combination therapy of rheumatoid arthritis (RA). The safety of longterm therapy of RA is very important as patients with RA are usually treated for two or more decades. This experimental overview is focused on some promising substances and their combinations with the standard antirheumatic drug - methotrexate (Mtx) for treatment of rheumatoid arthritis. The adjuvant arthritis model in Lewis rats was used for evaluation of antiinflammatory efficacy of the substances evaluated. Mtx was administered in the oral dose of 0.3 mg/kg b.w. twice a week. Natural and synthetic antioxidants were administered in the daily oral dose of 20 mg/kg b.w for coenzyme Q10 (CoQ10), 150 mg/kg b.w for carnosine (Carn), 15 mg/kg b.w. for stobadine dipalmitate (Stb) and its derivative SMe1.2HCl (SMe1), and 30 mg/kg b.w. for pinosylvin (Pin) or pterostilbene (Pte). Mtx in the oral dose of 0.4 mg/kg b.w. twice a week was combined with Pin in the oral daily dose of 50 mg/kg b.w. Clinical (hind paw volume - HPV), biochemical (activity of GGT in joint and level of TBARS in plasma), and immunological (IL-1 in plasma) parameters were assessed. Our results achieved with different antioxidants in monotherapies showed a reduction of oxidative stress in adjuvant arthritis independently of the chemical structure of the compounds. Pin was the most effective antioxidant tested in decreasing HPV. All combinations tested showed a higher efficacy in affecting biochemical or immunological parameters than Mtx administered in monotherapy. The findings showed the benefit of antioxidant compounds for their use in combination therapy with methotrexate.
Inference in the FO(C) Modelling Language

Recently, FO(C), the integration of C-LOG with classical logic, was introduced as a knowledge representation language. Up to this point, no systems exist that perform inference on FO(C), and very little is known about properties of inference in FO(C). In this paper, we study both of the above problems. We define normal forms for FO(C), one of which corresponds to FO(ID). We define transformations between these normal forms, and show that, using these transformations, several inference tasks for FO(C) can be reduced to inference tasks for FO(ID), for which solvers exist. We implemented this transformation and hence, created the first system that performs inference in FO(C). We also provide results about the complexity of reasoning in FO(C).
UNIQ : Uniform Noise Injection for non-uniform Quantization of neural networks

We present a novel method for training a neural network amenable to inference in low-precision arithmetic with quantized weights and activations. The training is performed in full precision with random noise injection emulating quantization noise. In order to circumvent the need to simulate realistic quantization noise distributions, the weight distributions are uniformized by a non-linear transformation, and uniform noise is injected. This procedure emulates a non-uniform k-quantile quantizer at inference time, which adapts to the specific distribution of the quantized parameters. As a by-product of injecting noise to weights, we find that activations can also be quantized to as low as 8-bit with only a minor accuracy degradation. The method achieves state-of-the-art results for training low-precision networks on ImageNet. In particular, we observe no degradation in accuracy for MobileNet and ResNet-18/34/50 on ImageNet with as low as 4-bit quantization of weights. Our solution achieves the state-of-the-art results in accuracy, in the low computational budget regime, compared to similar models.
Fuzzy Logic Controller for Enhancement of Transient Stability in Multi Machine AC-DC Power Systems

This paper discusses the impact of HVDC on Power System Stability and proposes a new type of control mechanism based on Fuzzy set theory to augment dynamic performance of a multi-machine power system. To have good damping characteristics over a wide range of operating conditions, speed deviation (¿ω = error1) and acceleration (¿¿ = error3 ), of the machines are chosen as the input signals to the fuzzy controller. These input signals are first characterized by a set of linguistic variables using fuzzy set notations. The fuzzy relation matrix allows a set of fuzzy logic operations that are performed on controller inputs to obtain the desired output. The effectiveness of the proposed controller is demonstrated by a multi-machine system example. The superior performance of this fuzzy controller in comparison to the conventional fixed gain controller proves the efficiency of this new fuzzy PID controller.