Miracle-dz/UniFAR-FTUs huggingface dataset:
Measurements of mRNA Degradation in Borrelia burgdorferi

ABSTRACT The importance of gene regulation in the enzootic cycle of Borrelia burgdorferi, the spirochete that causes Lyme disease, is well established. B. burgdorferi regulates gene expression in response to changes in environmental stimuli associated with changing hosts. In this study, we monitored mRNA decay in B. burgdorferi following transcriptional arrest with actinomycin D. The time-dependent decay of transcripts encoding RNA polymerase subunits (rpoA and rpoS), ribosomal proteins (rpsD, rpsK, rpsM, rplQ, and rpsO), a nuclease (pnp), outer surface lipoproteins (ospA and ospC), and a flagellar protein (flaB) have different profiles and indicate half-lives ranging from approximately 1 min to more than 45 min in cells cultured at 35°C. Our results provide a first step in characterizing mRNA decay in B. burgdorferi and in investigating its role in gene expression and regulation.
Obesity and the economy: from crisis to opportunity.

To the authors of this article, the economic stimulus program in Washington provides a unique opportunity to develop and institute a comprehensive national obesity initiative with immediate and long-term benefits to public health and the economy. They believe that part of the estimated $700 billion economic stimulus program should be invested in a national initiative to prevent obesity. This article provides an overview of the factors responsible for the obesity epidemic and highlights lifestyle choices among Americans that lead inevitably to obesity and obesity-related diseases, thereby addressing the need for a long-term national initiative to prevent obesity. An increasingly unhealthful lifestyle among the US population in the last 50 years has led to an obesity epidemic as a consequence of national economic, social, and policy decisions. During this time, government subsidies to industrial agriculture have supported low-cost high-calorie commodities―highly processed fat and sugar-based products―that have largely displaced a wide range of more expensive nutritious whole foods, such as fresh fruits and vegetables, once grown at low cost on family farms. One consequence of these policies is the increasing popularity of low cost fast food that contains a high amount of fat and low-quality carbohydrates and has little nutritional value or fiber. Coincident with increased energy consumption, the level of energy expenditure in the form of physical activity has sharply declined. In cities and suburban communities, there has been a reduction in consumer use of recreational or other facilities involving physical activity and limited money allocated to build or improve upon such facilities. Changes in family lifestyle contribute to obesity. Parents prepare few meals at home due to busy work schedules and the need to commute. Children have little time for recreational physical activities because of academic pressure; any free time available is used for sedentary activities such as television or computers. Reduced physical activity combined with psychosocial stress leads to an unhealthy diet, overeating and ultimately to increased fat deposition and obesity and greatly increase the risk of chronic diseases such as diabetes, myocardial infarction, and cancer. Current obesity-related costs amount to more than $100 billion per year, which represents 5% to 7% of annual health care expenditures. The authors suggest implementation of several projects that could be part of a planned national strategy to promote a healthy life style and reduce obesity. For Americans, addressing the obesity crisis will require a long-term integrated national program involving restructuring of US food production and distribution, together with major investments in social infrastructure. The authors believe that failure to act now will have devastating consequences for society much worse than the mortgage crisis.
'Allowable Limits of Performance' for External Quality Assurance Programs - an Approach to Application of the Stockholm Criteria by the RCPA Quality Assurance Programs.

External quality assurance (EQA) has been described as the ‘fifth pillar’ of laboratory standardisation, added to the four pillars of reference materials, reference methods, reference laboratories and traceable reference intervals and decision points.1 One vital component of an EQA program is to provide criteria to allow participating laboratories to assess their performance. These criteria, also described as quality standards, may be based on statistical comparison with peers, expert opinion, clinical need or other criteria. In Australia, the RCPA Quality Assurance Programs (RCPAQAP) quality standards are known as the Allowable Limits of Performance (ALP) and are used to assist with interpretation of all numerical QAP results in the program. The stated goal of these limits is that they are clinically based to provide warning of clinically important changes in assay performance. As these limits were derived some years ago2 it is appropriate to review them. This document describes the assessment and implementation of a hierarchical approach to setting quality standards for EQA programs using the approach used by the RCPAQAP Chemical Pathology as an example.
A Comment on the Functional Localization of the Phonological Storage Subsystem of Working Memory

Working memory, as defined by Baddeley and Hitch, is an interactive set of cognitive processes responsible for holding information online and available for analysis. Part of that system is a specialized subsystem devoted to maintaining verbal information; the verbal "slave" subsystem has as a core component a phonological store. For many years, the anatomical locus of the phonological store has been thought to be in the supramarginal and angular gyri of the speech dominant hemisphere, and functional neuroimaging studies provide broad support for this localization. However, a finer grained analysis of published experiments reveals two possible foci for the phonological store within the parietal lobe, neither of which has a pattern of functional activation that is fully consistent with the Baddeley and Hitch model. The purpose of the present paper is to review several studies relevant to the question of the localization of the phonological store and to suggest possible reasons the results are discrepant.
A Synchronous Chinese Language Corpus from Different Speech Communities: Construction and Applications

Similar to other languages such as English, Spanish and Arabic, Chinese is used by a large number of speakers in distinct speech communities which, despite sharing the unity of language, vary in interesting ways, and a systematic study of such linguistic variation is invaluable to appreciate the diversity and richness of the underlying cultures. This paper describes Project LIVAC (Linguistic Variation in Chinese Communities), which focuses on the development of a Chinese corpus, based on data taken concurrently at regular intervals from multiple Chinese speech communities. The resulting database and computerized concordance from the approximately 20 million word corpus with uniform time reference points extending across two years enable linguists and social scientists to undertake meaningful qualitative and quantitative comparative analysis of the development of linguistic and cultural variation. To facilitate these studies, a framework for integrating the corpus with specific corpus analysis applications is proposed. Based on this framework, a prototype retrieval system, which supports longitudinal studies on word and concept distribution, as well as lexical and other linguistic variation, is designed and implemented.
Overexpression of Mycobacterium tuberculosis manB, a phosphomannomutase that increases phosphatidylinositol mannoside biosynthesis in Mycobacterium smegmatis and mycobacterial association with human macrophages

Mycobacterium tuberculosis (M. tb) pathogenesis involves the interaction between the mycobacterial cell envelope and host macrophage, a process mediated, in part, by binding of the mannose caps of M. tb lipoarabinomannan (ManLAM) to the macrophage mannose receptor (MR). A presumed critical step in the biosynthesis of ManLAM, and other mannose‐containing glycoconjugates, is the conversion of mannose‐6‐phosphate to mannose‐1‐phosphate, by a phosphomannomutase (PMM), to produce GDP‐mannose, the primary mannose‐donor in mycobacteria. We have identified four M. tb H37Rv genes with similarity to known PMMs. Using in vivo complementation of PMM and phosphoglucomutase (PGM) deficient strains of Pseudomonas aeruginosa, and an in vitro enzyme assay, we have identified both PMM and PGM activity from one of these genes, Rv3257c (MtmanB). MtmanB overexpression in M. smegmatis produced increased levels of LAM, lipomannan, and phosphatidylinositol mannosides (PIMs) compared with control strains and led to a 13.3 ± 3.9‐fold greater association of mycobacteria with human macrophages, in a mannan‐inhibitable fashion. This increased association was mediated by the overproduction of higher order PIMs that possess mannose cap structures. We conclude that MtmanB encodes a functional PMM involved in the biosynthesis of mannosylated lipoglycans that participate in the association of mycobacteria with macrophage phagocytic receptors.
A new method for determining meteoroid mass from head echo data

[1] A head echo is the radar reflection from the plasma immediately surrounding a meteoroid upon its entry into the Earth's atmosphere; analysis of these plasmas can help determine a parent meteoroid's inherent properties, such as mass. In the past, meteoroid mass was calculated using head echo velocity and deceleration data by assuming momentum conservation between the meteoroid and air molecule. We refer to such masses as “dynamical masses. ” This method, however, can only be used to determine meteoroid mass if either the meteoroid radius or density is assumed. In this paper, we expound upon a new method for determining a meteoroid's mass by utilizing our new spherical scattering theory. This theory allows us to use head echo measurements to calculate head echo plasma density. Then, by using the plasma density in an established formula that estimates the ratio of unionized to ionized material produced by an ablating meteoroid, we can determine a meteoroid's mass. We refer to such masses as “scattering masses. ” We show that our new mass determination method applies to head echoes detected simultaneously at VHF and UHF and verify that the meteoroid mass is the same at both frequencies. We conclude with a comparison between dynamical and scattering masses and show that in general, these methods agree to within an order of magnitude.
A randomized clinical trial of combination chemotherapy with and without low‐molecular‐weight heparin in small cell lung cancer

Summary. Background Small cell lung cancer (SCLC) is a chemotherapy‐responsive tumor type but most patients ultimately experience disease progression. SCLC is associated with alterations in the coagulation system. The present randomized clinical trial (RCT) was designed to determine whether addition of low‐molecular‐weight heparin (LMWH) to combination chemotherapy (CT) would improve SCLC outcome compared with CT alone. Methods Combination CT consisted of cyclophosphamide, epirubicine and vincristine (CEV) given at 3‐weekly intervals for six cycles. Eighty‐four patients were randomized to receive either CT alone (n = 42) or CT plus LMWH (n = 42). LMWH consisted of dalteparin given at a dose of 5000 U once daily during the 18 weeks of CT. Results Overall tumor response rates were 42.5% with CT alone and 69.2% with CT plus LMWH (P = 0.07). Median progression‐free survival was 6.0 months with CT alone and 10.0 months with CT plus LMWH (P = 0.01). Median overall survival was 8.0 months with CT alone and 13.0 months with CT plus LMWH (P = 0.01). Similar improvement in survival with LMWH treatment occurred in patients with both limited and extensive disease stages. The risk of death in the CT + LMWH group relative to that in the CT group was 0.56 (95% confidence interval 0.30, 0.86) (P = 0.012 by log rank test). Toxicity from the experimental treatment was minimal and there were no treatment‐related deaths. Conclusions These results support the concept that anticoagulants, and particularly LMWH, may improve clinical outcomes in SCLC. Further clinical trials of this relatively non‐toxic treatment approach are indicated.
Hepatocyte Growth Factor Expression in EGFR Mutant Lung Cancer with Intrinsic and Acquired Resistance to Tyrosine Kinase Inhibitors in a Japanese Cohort

Seiji Yano, MD, PhD,* Tadaaki Yamada, MD, PhD,* Shinji Takeuchi, MD, PhD,* Keisei Tachibana, MD, PhD,† Yuko Minami, MD, PhD,† Yasushi Yatabe, MD, PhD,‡ Tetsuya Mitsudomi, MD, PhD,§ Hidenori Tanaka, MD, PhD, Tatsuo Kimura, MD, PhD, Shinzoh Kudoh, MD, PhD, Hiroshi Nokihara, MD, PhD,¶ Yuichiro Ohe, MD, PhD,¶ Jun Yokota, MD, PhD,# Hidetaka Uramoto, MD, PhD,** Kosei Yasumoto, MD, PhD,** Katsuyuki Kiura, MD, PhD,†† Masahiko Higashiyama, MD, PhD,‡‡ Makoto Oda, MD, PhD,§§ Haruhiro Saito, MD, PhD, Junji Yoshida, MD, PhD,¶¶ Kazuya Kondoh, MD, PhD,## and Masayuki Noguchi, MD, PhD†
Predicting global atmospheric ice nuclei distributions and their impacts on climate

Knowledge of cloud and precipitation formation processes remains incomplete, yet global precipitation is predominantly produced by clouds containing the ice phase. Ice first forms in clouds warmer than -36 °C on particles termed ice nuclei. We combine observations from field studies over a 14-year period, from a variety of locations around the globe, to show that the concentrations of ice nuclei active in mixed-phase cloud conditions can be related to temperature and the number concentrations of particles larger than 0.5 μm in diameter. This new relationship reduces unexplained variability in ice nuclei concentrations at a given temperature from ∼103 to less than a factor of 10, with the remaining variability apparently due to variations in aerosol chemical composition or other factors. When implemented in a global climate model, the new parameterization strongly alters cloud liquid and ice water distributions compared to the simple, temperature-only parameterizations currently widely used. The revised treatment indicates a global net cloud radiative forcing increase of ∼1 W m-2 for each order of magnitude increase in ice nuclei concentrations, demonstrating the strong sensitivity of climate simulations to assumptions regarding the initiation of cloud glaciation.
Scientific dependence in Africa today

In the African universities where I was trained, there was a scientific teaching quite valid in the subject matters I had to learn, but it taught dependence rather than real science. I mean that, for three years I was told how biology had developed through experiments that necessitated the use of facilities unavailable on the spot. Therefore in order to do biology, students had to go abroad. Such and such scientific results were pubiished in such and such journals, but these journals were European or American, and one had to read them abroad. In short, during three years, thanks to teachers who were good ones and of whom up to sixty percent were African, I received good teaching and learned, at the same time? but for me, this was, of course, not as serious as it was for my fellow students who did not return to France? I learned that, in the end, all I could do as a biologist in the future would have to be done under the control of American centers, American periodicals, with European facilities, and that all I could ever do at the University of Dakar was to duplicate European experiments, or to conduct minor experiments that would have to be submitted, for publication, to European journals. All this apparently
Initial code synchronization of W-CDMA mobile systems exploiting local phase coherence and Pisarenko estimation

Noncoherent techniques can be adopted for pseudonoise code synchronization in the presence of random phase. Differentially coherent methods conversely operate with linear phase shifts, such as when a systematic frequency error occurs. This letter presents a method exploiting local phase coherence (inspired by the Pisarenko estimation), allowing global frequency estimation in the presence of random phase noise. Its accuracy is numerically compared with noncoherent and differential techniques for the initial stage of wideband code-division multiple-access code synchronization.
Space‐time block coded spatial modulation with labeling diversity

Space‐time block coded spatial modulation (STBC‐SM) exploits the advantages of both spatial modulation and the Alamouti space‐time block code. Meanwhile, space‐time labeling diversity has demonstrated an improved bit error rate (BER) performance in comparison to the latter. Hence, in this paper, we extend the application of labeling diversity to STBC‐SM, which is termed STBC‐SM‐LD. Under identical channel assumptions, STBC‐SM‐LD exhibits superior BER performance compared to STBC‐SM. For example, with 4 × 4, 64‐quadrature amplitude modulation (64‐QAM), STBC‐SM‐LD has a BER performance gain of approximately 2.6 dB over STBC‐SM. Moreover, an asymptotic bound is presented to quantify the average BER performance of M‐ary QAM STBC‐SM‐LD over independent and identically distributed Rayleigh frequency‐flat fading channels. Monte Carlo simulations for STBC‐SM‐LD agree well with the analytical framework. In addition to the above, low‐complexity (LC) near‐maximum‐likelihood detectors for space‐time labeling diversity and STBC‐SM‐LD are presented. Complexity analysis of the proposed LC detectors shows a substantial reduction in computational complexity compared to their ML detector counterparts. For example, the proposed detector for STBC‐SM‐LD achieves a 91.9% drop in computational complexity for a 4 × 4, 64‐QAM system. The simulations further validate the near‐maximum‐likelihood performance of the LC detectors.
Improving Prediction Accuracy in Trust-Aware Recommender Systems

Trust-aware recommender systems are intelligent technology applications that make use of trust information and user personal data in social networks to provide personalized recommendations. Earlier research in trust-aware systems have shown that the ability of trust-based systems to make accurate predictions coupled with their robustness from shilling attacks make them a better alternative than traditional recommender systems. In this paper we propose an approach for improving accuracy of predictions in trust-aware recommender systems. In our approach, we first reconstruct the trust network. Trust network is reconstructed by removing trust links between users having correlation coefficient below a specified threshold value. For prediction calculation we compare three different approaches based on trust and correlation. We show through experiments on real life Epinions data set that our proposed approach of reconstructing the trust network gives substantially better prediction accuracy than the original approach of using all trust statements in the network.
Association Between the NFKB1-94ins/del ATTG Polymorphism and Cancer Risk: An Updated Meta-Analysis

To assess the effect of the NFKB1 -94ins/del polymorphism on cancer, we conducted a meta-analysis based on 25 studies including 8,750 cases and 9,170 controls. Overall, the -94ins/del polymorphism was associated with cancer risk in the pooled analysis and in Asian population, whereas no association was observed in Caucasian population. Stratified analysis by subtypes of cancer showed that the -94ins/del polymorphism was associated with oral squamous cell carcinoma and ovarian cancer risk, but had no association with colorectal cancer, bladder cancer, and renal cell cancer. Our meta-analysis suggests the NFKB1 -94ins/del polymorphism affects cancer susceptibility, and the association is ethnic-specific.
A Multilab Preregistered Replication of the Ego-Depletion Effect

Good self-control has been linked to adaptive outcomes such as better health, cohesive personal relationships, success in the workplace and at school, and less susceptibility to crime and addictions. In contrast, self-control failure is linked to maladaptive outcomes. Understanding the mechanisms by which self-control predicts behavior may assist in promoting better regulation and outcomes. A popular approach to understanding self-control is the strength or resource depletion model. Self-control is conceptualized as a limited resource that becomes depleted after a period of exertion resulting in self-control failure. The model has typically been tested using a sequential-task experimental paradigm, in which people completing an initial self-control task have reduced self-control capacity and poorer performance on a subsequent task, a state known as ego depletion. Although a meta-analysis of ego-depletion experiments found a medium-sized effect, subsequent meta-analyses have questioned the size and existence of the effect and identified instances of possible bias. The analyses served as a catalyst for the current Registered Replication Report of the ego-depletion effect. Multiple laboratories (k = 23, total N = 2,141) conducted replications of a standardized ego-depletion protocol based on a sequential-task paradigm by Sripada et al. Meta-analysis of the studies revealed that the size of the ego-depletion effect was small with 95% confidence intervals (CIs) that encompassed zero (d = 0.04, 95% CI [−0.07, 0.15]. We discuss implications of the findings for the ego-depletion effect and the resource depletion model of self-control.
Analytical Characterization of Optical Pulse Propagation in Polarization-Sensitive Semiconductor Optical Amplifiers

In this paper, we perform analytical characterization of optical pulses propagating through a polarization-sensitive semiconductor optical amplifier (SOA). We derive analytical expressions for the carrier density, gain and phase evolution along the SOA and show how these expressions prove useful in optical signal processing applications. The propagation of counter-propagating pulses as well as pulse streams across SOAs have been analysed and expressions for energy gain have been derived in all these cases. We also show that our analytical results reduce to corresponding results of polarization insensitive SOAs already published. The analytical results are in excellent agreement with detailed numerical simulations done in MATLAB using the NIMROD portal. The analytical calculations lead to significant savings with regard to simulation time and processing capacity requirements. We further prove that the energy gain difference for counter-propagating pulse streams is directly proportional to the difference delay between in them and hence can be used as a measure of the delay difference. This theoretical result agrees well with experimental results