Miracle-dz/UniFAR-FTUs huggingface dataset:
Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking.

The catabolite activator protein (CAP) makes no direct contact with the consensus base-pair T:A at position 6 of the DNA half-site 5'-A(1)A(2)A(3)T(4)G(5)T(6)G(7)A(8)T(9)C(10)T(11)-3' but, nevertheless, exhibits strong specificity for T:A at position 6. Binding of CAP results in formation of a sharp DNA kink, with a roll angle of approximately 40 degrees and a twist angle of approximately 20 degrees, between positions 6 and 7 of the DNA half-site. The consensus base-pair T:A at position 6 and the consensus base-pair G:C at position 7 form a T:A/G:C step, which is known to be associated with DNA flexibility. It has been proposed that specificity for T:A at position 6 is a consequence of formation of the DNA kink between positions 6 and 7, and of effects of the T:A(6)/G:C(7) step on the geometry of DNA kinking, or the energetics of DNA kinking. In this work, we determine crystallographic structures of CAP-DNA complexes having the consensus base-pair T:A at position 6 or the non-consensus base-pair C:G at position 6. We show that complexes containing T:A or C:G at position 6 exhibit similar overall DNA bend angles and local geometries of DNA kinking. We infer that indirect readout in this system does not involve differences in the geometry of DNA kinking but, rather, solely differences in the energetics of DNA kinking. We further infer that the main determinant of DNA conformation in this system is protein-DNA interaction, and not DNA sequence.
Structural insights into translational recoding by frameshift suppressor tRNASufJ

The three-nucleotide mRNA reading frame is tightly regulated during translation to ensure accurate protein expression. Translation errors that lead to aberrant protein production can result from the uncoupled movement of the tRNA in either the 5′ or 3′ direction on mRNA. Here, we report the biochemical and structural characterization of +1 frameshift suppressor tRNASufJ, a tRNA known to decode four, instead of three, nucleotides. Frameshift suppressor tRNASufJ contains an insertion 5′ to its anticodon, expanding the anticodon loop from seven to eight nucleotides. Our results indicate that the expansion of the anticodon loop of either ASLSufJ or tRNASufJ does not affect its affinity for the A site of the ribosome. Structural analyses of both ASLSufJ and ASLThr bound to the Thermus thermophilus 70S ribosome demonstrate both ASLs decode in the zero frame. Although the anticodon loop residues 34–37 are superimposable with canonical seven-nucleotide ASLs, the single C31.5 insertion between nucleotides 31 and 32 in ASLSufJ imposes a conformational change of the anticodon stem, that repositions and tilts the ASL toward the back of the A site. Further modeling analyses reveal that this tilting would cause a distortion in full-length A-site tRNASufJ during tRNA selection and possibly impede gripping of the anticodon stem by 16S rRNA nucleotides in the P site. Together, these data implicate tRNA distortion as a major driver of noncanonical translation events such as frameshifting.
Prevention of Bone Loss in Ovariectomized Rats by Combined Treatment With Risedronate and 1α,25‐Dihydroxyvitamin D3

Bisphosphonates inhibit bone loss through inhibition of osteoclast‐mediated bone resorption. At low doses, vitamin D metabolites can prevent bone loss in models of osteopenia in rats by an antiresorptive effect, while at high doses they also stimulate osteoblast activity and show an anabolic effect. Therefore, combined therapy with bisphosphonates and vitamin D analogs might be expected to be more effective than either treatment alone. It was the aim of this study to compare the efficacy of risedronate and of the naturally occurring vitamin D hormone 1α,25‐dihydroxyvitamin D3 (calcitriol), alone and in combination, for the prevention of ovariectomy‐induced bone loss in rats. One hundred ten female 4‐month‐old Sprague‐Dawley rats were used for this experiment. Ninety rats were bilaterally ovariectomized (OVX), 10 rats were sham‐operated (SHAM), and 10 rats were killed at the time of surgery as a baseline control. Groups of rats (10 rats/group) received vehicle or daily doses of 0.1 mg or 0.5 mg of risedronate or 0.05 μg or 0.1 μg of calcitriol/kg body weight, alone and in combination. Both compounds were administered orally via gavage, commencing on the day after surgery. Although estrogen deficiency‐induced bone loss was prevented by individual prophylactic administration of risedronate or calcitriol, OVX rats treated with a combination of risedronate and calcitriol had higher bone mineral density (BMD), cancellous bone area (B.Ar), and bone strength in long bones and vertebrae compared with rats receiving risedronate alone. Furthermore, calcitriol enhanced the suppressive effects of risedronate on osteoclast number and partially counteracted the suppressive effects of risedronate on bone formation and histomorphometric indices of osteoblast team performance. Risedronate did not reduce the anabolic effect of calcitriol, and at the high dose it normalized hypercalcemia in calcitriol‐treated OVX rats. Therefore, this study in OVX rats suggests that combined therapy with bisphosphonates and vitamin D analogs may offer advantages over the treatment with bisphosphonates or vitamin D analogs alone.
Pitfalls in comparing modern hair and fossil bone collagen C and N isotopic data to reconstruct ancient diets: a case study with cave bears (Ursus spelaeus)†

Stable isotope analyses provide one of the few means to evaluate diet of extinct taxa. However, interpreting isotope data from bone collagen of extinct animals based on isotopic patterns in different tissues of modern animal proxies is precarious. For example, three corrections are needed before making comparisons of recent hair and ancient bone collagen: calibration of carbon-13 variations in atmospheric CO2, different isotopic discrimination between diet–hair keratin and diet–bone collagen, and time averaging of bone collagen versus short-term record in hair keratin. Recently, Robu et al. [Isotopic evidence for dietary flexibility among European Late Pleistocene cave bears (Ursus spelaeus). Can J Zool. 2013;91:227–234] published an article comparing extant carbon (δ13C) and nitrogen (δ15N) stable isotopic data of European cave bear bone collagen with those of Yellowstone Park grizzly bear hair in order to test the prevailing assumption of a largely vegetarian diet among cave bears. The authors concluded that cave bears were carnivores. This work is unfortunately unfounded as the authors failed to consider the necessary corrections listed above. When these corrections are applied to the Romanian cave bears, these individuals can be then interpreted without involving consumption of high trophic-level food, and environmental changes are probably the reason for the unusual isotopic composition of these cave bears in comparison with other European cave bears, rather than a change of diet. We caution researchers to pay careful attention to these factors when interpreting feeding ecology of extinct fauna using stable isotope techniques.
Characterization of nine novel microsatellite markers from Brandt's vole (Lasiopodomys brandtii)

Highly polymorphic microsatellite markers are the most powerful tools to infer kinship relations. In this study, a library enriched for (AC)n (AG)n and (AGAT)n was constructed for screening microsatellite markers in Brandt's vole (Lasiopodomys brandtii), and nine novel polymorphic microsatellite markers were developed and characterized. The number of alleles ranged from 4 to 11 per locus and the mean polymorphism information content was 0.7535. The observed and the expected heterozygosity values averaged 0.760 (0.554–0.908) and 0.7914 (0.718–0.845), respectively. Average nonexclusion probability for one candidate parent varied from 0.485 to 0.716. These nine novel markers are highly polymorphic and powerful enough for our future kinship analysis.
Independent validation of software safety requirements for systems of systems

As one can only reason about the safety of software within the system context in which the software is executing, traditional independent validation and verification approaches which focus on the assurance of satisfaction of requirements by the delivered software are not sufficient in the assurance of software safety requirements. This paper presents an extension to an approach to assurance that relies on the use of a system reference model to capture an independent verification and validation team's understanding of a system's requirements. Here we describe how to apply the approach in conjunction with hazard analysis to evaluate the sufficiency of the software safety requirements early in the software development process. We explain this approach using examples of the safe hold requirements for a spacecraft system.
Quality of diurnal intraocular pressure control in primary open-angle patients treated with latanoprost compared with surgically treated glaucoma patients: a prospective trial

Purpose: To compare the intraocular pressure (IOP) diurnal fluctuations of glaucoma patients treated with latanoprost 0.005% once a day with patients with controlled IOP after deep sclerectomy or trabeculectomy. Methods: The trial included 60 prospectively recruited subjects with primary open-angle glaucoma. The medical group consisted of 20 patients with controlled IOP (<18 mm Hg) under latanoprost 0.005% monotherapy and with no history of previous intraocular surgery or argon laser trabeculoplasty; the surgical groups included 20 patients after trabeculectomy, and 20 patients after deep sclerectomy with collagen implant (DSCI). The patients in the surgical groups had a controlled IOP without any ocular hypotensive medications. All patients underwent a diurnal tension curve (08:00–17:00/three-hour intervals), followed by a water-drinking test (WDT) with the last IOP measurement taken at 21:00 hours. The between-group differences were tested for significance by means of analysis of variance (ANOVA). Results: Baseline IOP was significantly different between the trabeculectomy group (10.1 mm Hg (3.4 SD)), the DSCI group (13.9 mm Hg (2.8)) and the latanoprost group (15.5 mm Hg (2.0); p = 0.005). The average IOP during the diurnal tension curve (10.1, 13.7, and 15.7 mm Hg, respectively, for the trabeculectomy, DSCI, and latanoprost groups) differed significantly between groups (ANOVA; p<0.0001), but the variation was comparable in the three groups (ANOVA; p = 0.13). After the WDT, elevation of IOP was significantly greater among patients treated with latanoprost (p = 0.003). Conclusion: Trabeculectomy patients had a statistically significant lower average IOP in the diurnal tension curve compared with the other two groups. No wider variation in diurnal IOP with latanoprost compared with the surgical procedures was found. The IOP increase during the WDT was most marked in patients under latanoprost therapy.
Lifestyle habits and compression of morbidity.

BACKGROUND There has been much debate regarding the degree to which healthy lifestyles can increase longevity and whether added years will be offset by increased morbidity at older ages. This study was designed to test the compression of morbidity hypothesis, proposing that healthy lifestyles can reduce and compress disability into a shorter period toward the end of life. METHODS Functional status in 418 deceased members of an aging cohort was observed between 1986 and 1998 in relationship to lifestyle-related risk factors, including cigarette smoking, physical inactivity, and under- or overweight. Three risk groups were created based on the number of these factors at study entry. Disability scores prior to death were modeled for each risk group to compare levels and rates of change, as well as to determine if and when acceleration in functional decline occurred. RESULTS The risk-factor-free group showed average disability scores near zero 10-12 years before death, rising slowly over time, without evidence of accelerated functional decline. In contrast, those with two or more factors maintained a greater level of disability throughout follow-up and experienced an increase in the rate of decline 1.5 years prior to death. For those at moderate risk, the rate of decline increased significantly only in the last 3 months of life. Other differences between groups provided no alternative explanations for the findings. CONCLUSIONS These results make a compelling argument for the reduction and postponement of disability with healthier lifestyles as proposed by the compression of morbidity hypothesis.
A Two-Stage Charge Transfer Active Pixel CMOS Image Sensor With Low-Noise Global Shuttering and a Dual-Shuttering Mode

A complementary metal-oxide-semiconductor (CMOS) image sensor with low-noise global shuttering and a dual-shuttering mode is presented. The developed two-stage charge transfer pixel enables noise canceling by means of true correlated double sampling. The implemented prototype demonstrates for the first time that a noise level of less than three electrons can be achieved in a global-shutter CMOS image sensor while attaining high shutter efficiency of 99.7%. In the dual-shuttering mode, both a pinned storage diode signal and a floating diffusion signal are used for desirable functions such as wide-dynamic-range imaging, motion detection, and dual consecutive snapshot imaging.
Effectiveness of incentivized social media campaigns for a Fortune 500 company’s brand

Purpose The purpose of this paper is to determine how best to build online advocates for a food company’s brand based on data available from the brand’s Facebook pages. Specific research objectives are to study examine whether incentivizing actions such as “liking,” sharing or commenting on a brand’s Facebook impacts the brand community’s sentiment and engagement with the brand, and whether such engagement is different for different actions (e.g. liking vs sharing). Design/methodology/approach To achieve the objectives of this research, sentiment analysis is performed on Facebook insight data from a Fortune 500 company, consisting of fans’ comments, shares and “likes” for promotional and fan posts pertaining to one of its brands. Paired samples t-tests are performed to assess differences in sentiment and engagement before and after each promotional post. Findings The results do not support a strong impact of promotional posts on overall sentiment. However, there is evidence in support of a positive impact of the campaigns on overall wall-level engagement with the brand. Moreover, the levels of engagement are not the same for all promotional posts. Rather, some posts resulted in much higher engagement levels than others, suggesting that not all incentivized campaigns are created equal. Research limitations/implications The study used the data from only one of company’s many brands. Therefore, similar studies on other brands are warranted. Practical implications Social networking sites are increasing in numbers, and more and more businesses are embracing social networks and/or blogs as part of their marketing platforms. Many companies offer coupons and incentives on social media to entice customers to engage with their social media platforms as well as buy products. The study results provide valuable insight into the effectiveness of different kinds of social media promotional campaigns, and can help managers decide which campaigns to implement to achieve specific objectives. Originality/value This research adds to the literature in two ways. First, it contributes to the limited literature on the effectiveness of incentivized social media campaign. Second, it contributes to the social media analytics literature by demonstrating how sentiment analysis can be used along with other statistical procedures to make sense of qualitative social media data.
The PABITRA Project: Island Landscapes under Global Change1

ABSTRACT The Pacific-Asia Biodiversity Transect (PABITRA) is a network of the Ecosystem Division in the Pacific Science Association's Task Force on Biodiversity. The PABITRA project seeks to develop a network of ocean-to-mountain transects on islands across the Pacific to test hypotheses about biodiversity and promote sustainable use of island ecosystems under the influence of global change. A specific objective of PABITRA was to establish an ocean-to-mountain transect in Fiji with major involvement of the resident islanders. Along this transect, a number of biodiversity study sites were to be selected for further research. The transect was established during two consecutive field workshops, from 18 November to 3 December 2002. Involved were 25 University of the South Pacific (USP) students, eight local faculty including Fiji Government and nongovernmental organization officials, and seven overseas collaborators. The outcome was documented in a 69-page illustrated report issued by the USP Institute of Applied Sciences as well as at a special symposium presented during the 20th Pacific Science Congress in Bangkok (17–21 March 2003) titled “Island Landscapes under Global Change: the PABITRA Project. ” Seven papers presented by members of the Fijian PABITRA group are published here, following this introductory paper. In addition, five papers introducing PABITRA activities outside Fiji are included in this special issue. The PABITRA project is ongoing and it is hoped that these papers will stimulate broad interest and participation in PABITRA's key objectives of promoting integrative resource management in Pacific Island environments.
Systemic Macrophage Depletion Inhibits Helicobacter bilis-Induced Proinflammatory Cytokine-Mediated Typhlocolitis and Impairs Bacterial Colonization Dynamics in a BALB/c Rag2 −/− Mouse Model of Inflammatory Bowel Disease

ABSTRACT Helicobacter bilis, an enterohepatic helicobacter, is associated with chronic hepatitis in aged immunocompetent inbred mice and inflammatory bowel disease (IBD) in immunodeficient mice. To evaluate the role of macrophages in H. bilis-induced IBD, Rag2 −/− BALB/c or wild-type (WT) BALB/c mice were either sham dosed or infected with H. bilis Missouri strain under specific-pathogen-free conditions, followed by an intravenous injection of a 0.2-ml suspension of liposomes coated with either phosphate-buffered saline (control) or clodronate (a macrophage depleting drug) at 15 weeks postinfection (wpi). At 16 wpi, the ceca of H. bilis-infected Rag2 −/− mice treated with control liposomes had significantly higher histopathological lesional scores (for cumulative typhlitis index, inflammation, edema, epithelial defects, and hyperplasia) and higher counts of F4/80+ macrophages and MPO+ neutrophils compared to H. bilis-infected Rag2 −/− mice treated with clodronate liposomes. In addition, cecal quantitative PCR analyses revealed a significant suppression in the expression of macrophage-related cytokine genes, namely, Tnfa, Il-1β, Il-10, Cxcl1, and iNos, in the clodronate-treated H. bilis-infected Rag2 −/− mice compared to the H. bilis-infected Rag2−/− control mice. Finally, cecal quantitative PCR analyses also revealed a significant reduction in bacterial colonization in the clodronate-treated Rag2 −/− mice. Taken together, our results suggest that macrophages are critical inflammatory cellular mediators for promoting H. bilis-induced typhlocolitis in mice.
A study on people’s concepts associating community health exam interventions with their participation in future health examinations

This study primarily employed the health belief model (HBM) to identify the effect between health examination services and intentions to continue receiving health examinations. The research participants (n = 905) were people who received a health examination in a hospital in Central Taiwan in 2012. The study conducted an anonymous questionnaire survey to collect data and implemented cross-sectional research to examine the factors. The results for the threat construct the participants who showed concern regarding potential physical conditions, and the causes of diseases were more likely to anticipate in health examinations. The participants who indicated their intentions to modify dietary and exercise regimen according to their health examination reports were more likely to anticipate examinations. The results for the cues to action construct showed that the participants who considered advice from others were more inclined to undergo examinations. The results for the barriers construct found that factors, including anxiety, concern for personal-information disclosure. Providing community health examinations helps health care facilities understand people’s concepts regarding health examinations and ensures that hospitals enhance the delivery of health examinations to satisfy people’s demands and achieve community health.
Tumor‐derived exosomes and microvesicles in head and neck cancer: Implications for tumor biology and biomarker discovery

Exosomes and microvesicles (MVs) are nanometer‐sized, membranous vesicles secreted from many cell types into their surrounding extracellular space and into body fluids. These two classes of extracellular vesicles are regarded as a novel mechanism through which cancer cells, including virally infected cancer cells, regulate their micro‐environment via the horizontal transfer of bioactive molecules: proteins, lipids, and nucleic acids (DNA, mRNA, micro‐RNAs; oncogenic cargo hence often referred to as oncosomes). In head and neck cancer (HNC), exosomes and MVs have been described in Epstein Barr Virus (EBV)‐associated nasopharyngeal cancer (NPC), as well as being positively correlated with oral squamous cell carcinoma (OSCC) progression. It has therefore been suggested that HNC‐derived vesicles could represent a useful source for biomarker discovery, enriched in tumor antigens and cargo; hence fundamentally important for cancer progression. This current review offers an overall perspective on the roles of exosomes and MVs in HNC biology, focusing on EBV‐associated NPC and OSCC. We also highlight the importance of saliva as a proximal and easily accessible bio‐fluid for HNC detection, and propose that salivary vesicles might serve as an alternative model in the discovery of novel HNC biomarkers.
Implicit Analysis of Perceptual Multimedia Experience Based on Physiological Response: A Review

The exponential growth of popularity of multimedia has led to needs for user-centric adaptive applications that manage multimedia content more effectively. Implicit analysis, which examines users’ perceptual experience of multimedia by monit-oring physiological or behavioral cues, has potential to satisfy such demands. Particularly, physiological signals categorized into cerebral physiological signals (electroencephalography, functional magnetic resonance imaging, and functional near-infrared spectro-scopy) and peripheral physiological signals (heart rate, respiration, skin temperature, etc.) have recently received attention along with notable development of wearable physiological sensors. In this paper, we review existing studies on physiological signal analysis exploring perceptual experience of multimedia. Furthermore, we discuss current trends and challenges.