Miracle-dz/UniFAR-FTUs huggingface dataset:
Helix 69 Is Key for Uniformity during Substrate Selection on the Ribosome*

Structural studies of ribosome complexes with bound tRNAs and release factors show considerable contacts between these factors and helix 69 (H69) of 23 S rRNA. Although biochemical and genetic studies have provided some general insights into the role of H69 in tRNA and RF selection, a detailed understanding of these contributions remains elusive. Here, we present a pre- steady-state kinetic analysis establishing that two distinct regions of H69 make critical contributions to substrate selection. The loop of H69 (A1913) forms contacts necessary for the efficient accommodation of a subset of natural tRNA species, whereas the base of the stem (G1922) is specifically critical for UGA codon recognition by the class 1 release factor RF2. These data define a broad and critical role for this centrally located intersubunit helix (H69) in accurate and efficient substrate recognition by the ribosome.
Biosynthesis of poly(3-hydroxybutyrate-co-3-hydroxyvalerate-co-3-hydroxyhexanoate) by metabolically engineered Escherichia coli strains.

The recombinant Escherichia coli strain, equipped with the newly cloned Aeromonas PHA biosynthesis genes, could produce a terpolymer of 3-hydroxybutyrate (3HB), 3-hydroxyvalerate (3HV), and 3-hydroxyhexanoate (3HHx) [P(3HB-co-3HV-co-3HHx)] from dodecanoic acid plus odd carbon number fatty acid. In addition, the orf1 gene of Aeromonas hydrophila was found to play a critical role in assimilating the 3HV monomer and in regulating the monomer fraction in the terpolymer.
Parallelizing Big Data Machine Learning Applications with Model Rotation

This paper proposes model rotation as a general approach to parallelize big data machine learning applications. To solve the big model problem in parallelization, we distribute the model parameters to inter-node workers and rotate different model parts in a ring topology. The advantage of model rotation comes from maximizing the effect of parallel model updates for algorithm convergence while minimizing the overhead of communication. We formulate a solution using computation models, programming interfaces, and system implementations as design principles and derive a machine learning framework with three algorithms built on top of it: Latent Dirichlet Allocation using Collapsed Gibbs Sampling, Matrix Factorization using Stochastic Gradient Descent and Cyclic Coordinate Descent. The performance results on an Intel Haswell cluster with max 60 nodes show that our solution achieves faster model convergence speed and higher scalability than previous work by others.
Voltage-scaled integrated circuit technologies enable a new generation of power supply control IC's

This paper introduces a family of three voltage-scaled BiCMOS-DMOS integrated circuit technologies that integrate 45 V, 80 V or 100 V DMOS power switches with CMOS control logic and BiCMOS analog cells. A dual gate driver IC and forward active clamp PWM controller are presented as examples of the function and performance afforded by these new power IC technologies. The 5 A BiCMOS output stage and split-supply operation for negative VGS drive are key attributes of the gate driver. The controller features voltage feed-forward voltage-mode PWM with 100 V start-up regulator, 3 A BiCMOS gate driver and 40 ns current limit response time.
A frotograph-based design of quasi-cyclic spatially coupled LDPC codes

Spatially coupled (SC) low-density parity-check (LDPC) codes can achieve capacity approaching performance with low message recovery latency when using sliding window (SW) decoding. An SC-LDPC code constructed from a protograph can be generated by first coupling a chain of block protographs and then lifting the coupled protograph using permutation matrices. This paper introduces a systematic design of SC-LDPC codes to eliminate 4-cycles in the coupled photograph. Using a quasi-cyclic (QC) lifting, we obtain QC-SC-LDPC codes of girth at least eight. Coupling a chain of block protographs implies spreading edges from one protograph to the others. Our protograph-based design can be viewed as guiding the edge spreading and also the graph-lifting process. Simulation results show the design leads to improved decoding performance, particularly in the error floor, compared to random designs.
On the Foundations of Corporate Social Responsibility

Using corporate social responsibility (CSR) ratings for 23,000 companies from 114 countries, we find that a firm's CSR rating and its country's legal origin are strongly correlated. Legal origin is a stronger explanation than “doing good by doing well” factors or firm and country characteristics (ownership concentration, political institutions, and globalization): firms from common law countries have lower CSR than companies from civil law countries, with Scandinavian civil law firms having the highest CSR ratings. Evidence from quasi-natural experiments such as scandals and natural disasters suggests that civil law firms are more responsive to CSR shocks than common law firms.
New Innovations in Cervical Cancer Screening

Cervical cancer is a disease that results in devastating mortality, especially in third world countries where screening and treatment of the disease are not widely available, and is the leading cause of cancer mortality in women worldwide. With the introduction of cytologic cervical cancer screening more than 50 years ago, the mortality rate of cervical cancer has markedly decreased in areas where access to this technology is available. The National Cancer Institute Surveillance, Epidemiology, and End Results registry data show a 43% decrease in incidence and 46% decrease in mortality from invasive cervical cancer from 1973 to 1995. In fact, screening for cervical cancer has had a greater influence in reducing mortality than screening for any other malignancy. Despite the impact of screening on cervical cancer, it is expected that in the United States during 2001, 12,900 cases of invasive cervical cancer will have been diagnosed, and 4,400 women with cervical cancer will have died of their disease. Thus, other factors certainly contribute to the cases of invasive cervical cancer diagnosed in a population with access to screening and treatment of the disease. In this review, we discuss the failures of cervical cytology screening and new technological advances that aim to increase the sensitivity and specificity of cervical cancer screening techniques.
A Passive UHF RF Identification CMOS Tag IC Using Ferroelectric RAM in 0.35-$\mu{\hbox {m}}$  Technology

A passive UHF RF identification (RFID) tag IC with embedded 2-KB ferroelectric RAM (FeRAM) for rewritable applications enables a 2.9 times faster read-and-write transaction time over EEPROM-based tag ICs. The resulting FeRAM-based tag has a nominally identical communication range for both read and write operations, which is indispensable for data write applications. The evaluated tag communication range with a folded dipole antenna is from 0 m to 4.3 m, at the 953-MHz carrier frequency with 4-W transmitting Effective Isotropic Radiated Power (EIRP) from a reader/writer. The developed tag IC features two circuit blocks to maximize the communication range in 0.35-mum CMOS/FeRAM technology. First is a CMOS-only full-wave rectifier, which can improve the measured efficiency by up to 36.6% by reducing the input parasitic capacitances and optimization of multiplier structure. This efficiency is more than twice that of previously-published results. Second is a low-voltage current-mode ASK demodulator to accommodate a low-breakdown voltage of FeRAM, which converts the ASK power modulation into a linearly modulated current over an incoming power range of 27 dB, corresponding to the entire communication range. The developed demodulator can thus resolve the primary design tradeoff issue between device protection and detection sensitivity in the conventional voltage-mode demodulator
Isolation from human seminal plasma of an abundant 16-kDa protein originating from the prostate, its identification with a 94-residue peptide originally described as beta-inhibin.

In addition to other known markers of the human prostate, it was shown that the prostatic fraction of the split ejaculate was rich in a 16-kDa protein with properties not described previously. This protein was purified from human seminal plasma using ammonium sulfate precipitation, DEAE-Sepharose CL-6B ion exchange chromatography, and gel filtration on Sephadex G-100. The purified protein showed a single prominent spot on two-dimensional gel electrophoresis. The sequence of the first 40 amino acids that could be positively identified was identical to that of a prostatic secretory protein of 94 amino acids (PSP94) previously designated as beta-inhibin. Antibodies produced in rabbits against the purified protein were used to develop a radioimmunoassay. These antibodies appeared to recognize only the NH2-terminal portion of the native molecule since they did not react with a synthetic peptide composed of the 28 C-terminal residues. The radioimmunoassay showed that the concentration of the protein was 1320 +/- 183 micrograms/ml in the seminal plasma of adult fertile men and 1134 +/- 136 micrograms/ml in vasectomized patients. In hypertrophic and adenocarcinomatous prostates, the concentrations were 326 +/- 156 and 104 +/- 23 micrograms/ml, respectively, while values were lower than 0.060 micrograms/ml in the testis, epididymis, vas deferens and liver. The blood plasma concentration was 0.019 +/- microgram/ml in 23 asymptomatic men 45 to 65 years old and 0.115 +/- 0.036 microgram/ml in eight patients with prostate cancer. (ABSTRACT TRUNCATED AT 250 WORDS)
Par3 in chick lens placode development

The lens originates from a simple cuboidal epithelium, which, on its basal side, contacts the optic vesicle, whilst facing the extraembryonic environment on its apical side. As this epithelium changes into the pseudostratified lens placode, its cells elongate and become narrower at their apical ends. This is due to the formation of an apical actin network, whose appearance is restricted to cells of the placodal region, as a result of region‐specific signaling mechanisms that remain largely unknown. Here, we investigated the role of the polarity protein PAR3 and the phosphorylation state of its Threonine 833 (T833) aPKC‐binding site in the recruitment of aPKC and in the establishment of actin network in the chick lens placode. Overexpression of wild type PAR3 recruited aPKC and punctate actin clusters to the basolateral membranes of the placodal cells. Recruitment of aPKC depended on the charge of the residue that replaced the T833 residue. In contrast, induction of the ectopic actin spots was independent on the charge of this residue.
Cognitive Function and the Concordance Between Survey Reports and Medicare Claims in a Nationally Representative Cohort of Older Adults

Background:While age-related cognitive decline may affect all stages in the response process—comprehension, retrieval, judgment, response selection, and response reporting—the associations between objective cognitive tests and the agreement between self-reports and Medicare claims has not been assessed. We evaluate those associations using the Survey on Assets and Health Dynamics among the Oldest Old (AHEAD). Methods:Eight waves of reinterviews (1995–2010) were linked to Medicare claims for 3661 self-respondents yielding 12,313 person-period observations. Cognitive function was measured by 2 episodic memory tests (immediate and delayed recall of 10 words) and 1 mental status test (backward counting, dates, and names). Survey reports on 12 diseases and 4 health services were mapped to Medicare claims to derive counts of concordant reports, underreports, and overreports, as were the numbers of hospital episodes and physician visits. GEE negative binomial and logistic regression models were used. Results:Better mental status was associated with more concordant reporting and less underreporting on disease history and the number of hospital episodes. Better mental status and delayed word recall were associated with more concordant reporting and less underreporting on health services use. Better delayed recall was significantly associated with less underreporting on the number of physician visits. These associations were not appreciably altered by adjustment for demographic characteristics, socioeconomic status, self-rated health, or secular trends. Conclusion:We recommend that future surveys of older adults include an objective measure of mental status (rather than memory), especially when those survey reports cannot be verified by access to Medicare claims or chart review.
Quantifying Energy Usage in Data Centers through Instruction-count Overhead

Energy usage of data centers is rising quickly and the electricity cost can no longer be neglected. Most efforts to relieve the increase of energy usage concentrate on improving hardware efficiency, by improving the hardware itself or by turning to server virtualization. Yet, no serious effort is made to reduce electricity usage by targeting the software running in data centers. To be able to effectively target software, a quantification of software overhead is necessary. In this paper, we present a quantification of the sources of overhead in applications that are these days ubiquitous in data centers: web applications. Experiments with three web applications show that up to 90% of the instructions executed to generate web pages are non-essential, in other words overhead, and can be eliminated. Elimination of these non-essential instructions results in an approximately linear decrease in page generation time as well as significantly reduced energy usage. In order to get the rising energy cost of data centers under control it is obligatory to be able to quantify the source of energy cost. In this paper we present an approach how to quantify wasted energy based on a quantification of non-essential instructions that are executed.
Understanding the Privacy Issue in the Digital Age: An Expert Perspective

In The importance of privacy has been the subject of much debate for centuries. While the public opinion continues to value and desire privacy, the level of privacy afforded to citizens continues to diminish owing to the continued, rapid pace of technological advances. With the imminent transition to the Internet of Things (IoT), the future of privacy is uncertain and in danger. In order to understand what the future holds for privacy, we leverage the predictions made by 2511 privacy experts. Utilizing semantic analysis, we identify the emerging privacy-related concepts and explore the relationships between these concepts. The resultant framework will be compared to existing privacy frameworks to determine the influence of individual and external factors such as demographics and culture on experts’ predictions, and to identify fruitful avenues for future privacy research in the digital age.
Improving Online Marketing Experiments with Drifting Multi-armed Bandits

Restless bandits model the exploration vs. exploitation trade-off in a changing (non-stationary) world. Restless bandits have been studied in both the context of continuously-changing (drifting) and change-point (sudden) restlessness. In this work, we study specific classes of drifting restless bandits selected for their relevance to modelling an online website optimization process. The contribution in this work is a simple, feasible weighted least squares technique capable of utilizing contextual arm parameters while considering the parameter space drifting non-stationary within reasonable bounds. We produce a reference implementation, then evaluate and compare its performance in several different true world states, finding experimentally that performance is robust to time drifting factors similar to those seen in many real world cases.
Corrections for Type I Error in Social Science Research: A Disconnect between Theory and Practice

Type I errors are a common problem in factorial ANOVA and ANOVA based analyses. Despite decades of literature offering solutions to the Type I error problems associated with multiple significance tests, simple solutions such as Bonferroni corrections have been largely ignored by social scientists. To examine this discontinuity between theory and practice, a content analysis was performed on 5 flagship social science journals. Results indicate that corrections for Type I error are seldom utilized, even in designs so complicated as to almost guarantee erroneous rejection of null hypotheses.
The distribution of neuron‐specific gene family member 1 in brain and germ cells: Implications for the regulation of germ‐line development by brain

Vesicular acidification at early endosomes dissociates endocytosed receptor‐ligand complexes. The ligands, receptors, or both are then directed to late endosomes for degradation or recycled back to the plasma membrane. Of neuron‐specific gene (NSG) family members, early endosomal protein neuron‐specific gene family member 1 (NSG1) is the most important in receptor recycling. In this study, we characterized chicken NSG1 (cNSG1). We found several functional sites related to endocytotic machinery in cNSG1 that were highly conserved with most other vertebrate NSG1 proteins. We examined the tissue and duration specificity and the temporal and spatial patterns of cNSG1 expression. cNSG1 expression was preferentially located in all regions of the brain, neuroendocrine glands, and spinal cord. Unexpectedly, cNSG1 expression was strongly detected during male and female germ‐line development. Expression of NSG1 in two apparently unrelated cell types such as neurons and germ cells suggests NSG1 roles in neurons and germ‐cells chemotaxis and endocytotic machinery. Developmental Dynamics 240:850–861, 2011. © 2011 Wiley‐Liss, Inc.
RAPID BREAKING OF TOLERANCE AGAINST ESCHERICHIA COLI LIPOPOLYSACCHARIDE IN VIVO AND IN VITRO

The breaking of tolerance against the lipopolysaccharide from E. coli 055:B5 was studied. It was found that immune responsiveness recovered very slowly in vivo, tolerance still existing 3 wk after the last tolerizing injection. However, if spleen cells from tolerant mice were transferred into irradiated syngeneic recipients, the tolerant state was readily broken. Spleen cells transferred 3 days after the last tolerance-maintaining dose did not respond, whereas cells transferred on day 5 or 7 responded equally well as normal spleen cells. It was also possible to break tolerance by incubating tolerant spleen cells, which did not respond after transfer, for 20 hr in vitro before transfer into irradiated recipients. The results suggest that there exist reversibly inactivated cells in tolerant animals and that these cells can be reactivated upon removal of the cells to a neutral environment.
Time-Average Optimization With Nonconvex Decision Set and Its Convergence

This paper considers <italic>time-average optimization</italic>, where a decision vector is chosen every time step within a (possibly nonconvex) set, and the goal is to minimize a convex function of the time averages subject to convex constraints on these averages. Such problems have applications in networking, multiagent systems, and operation research, where decisions are constrained to a discrete set and the decision average can represent average bit rates or average agent actions. This time-average optimization extends traditional convex formulations to allow a nonconvex decision set. This class of problems can be solved by Lyapunov optimization. A simple drift-based algorithm, related to a classical dual subgradient algorithm, converges to an <inline-formula><tex-math notation="LaTeX">$\epsilon$ </tex-math></inline-formula>-optimal solution within <inline-formula><tex-math notation="LaTeX">$O(1/\epsilon ^2)$ </tex-math></inline-formula> time steps. Furthermore, the algorithm is shown to have a transient phase and a steady-state phase, which can be exploited to improve convergence rates to <inline-formula><tex-math notation="LaTeX"> $O(1/\epsilon)$</tex-math></inline-formula> and <inline-formula><tex-math notation="LaTeX">$O(1/{\epsilon ^{1.5}})$ </tex-math></inline-formula> when vectors of Lagrange multipliers satisfy locally polyhedral and locally smooth assumptions, respectively. Practically, this improved convergence suggests that decisions should be implemented after the transient period.
Overcoming Obstacles to Drug Repositioning in Japan

Drug repositioning (DR) is the process of identifying new indications for existing drugs. DR usually focuses on drugs that have cleared phase-I safety trials but has yet to show efficacy for the intended indication. Therefore, DR can probably skip the preclinical and phase-I study, which can reduce the cost throughout drug development. However, the expensive phase-II/III trials are required to establish efficacy. The obstacles to DR include identification of new indications with a high success rate in clinical studies, obtaining funding for clinical studies, patent protection, and approval systems. To tackle these obstacles, various approaches have been applied to DR worldwide. In this perspective, we provide representative examples of DR and discuss the ongoing efforts to overcome obstacles to DR in Japan.
The librarian 2.0: Identifying a typology of librarians’ social media literacy

This article reports on the identification of librarians’ social media literacy profiles. These profiles were developed through the construction of scales measuring social media competencies. An online questionnaire was developed and administered to a sample of 184 librarians working in Flemish public libraries. Cluster analysis revealed four social media literacy profiles: (1) social media workers; (2) social media laggards; (3) social media literates; and (4) social media spare-time users. This typology of social media literacy profiles is necessary information when developing a successful social media literacy strategy in libraries. Our research results further indicate that librarians who fit the social media literate or social media worker profiles are expected to play a central and facilitating role in the adoption and implementation of social media within public libraries.
Real-Time Attention for Robotic Vision

This paper discusses the development and real-time implementation of an algorithm to determine interest points in a scene. The algorithm models interest points as the points of intersection of lines of symmetry between edges in an image and is based on psychophysical experiments of human gaze fixation. A novel, real-time method of computing these interest points is achieved by adopting a symmetry measure which determines the loci of centers of co-circular edges.The algorithm has been implemented on a parallel network of Texas Instruments TMS320C40 (C40) processors. In addition, the implementation permits the algorithm to operate on non-uniformly mapped logÂ? polar images. This configuration facilitates near real-time performance on images covering a very large field of view.Results show that the algorithm has practical uses in a number of areas, including face recognition, object tracking and the positioning of an active vision sensor in real-time.