Miracle-dz/UniFAR-FTUs huggingface dataset:
Validation of an algorithm for delay stochastic simulation of transcription and translation in prokaryotic gene expression

The quantitative modeling of gene transcription and translation requires a treatment of two key features: stochastic fluctuations due to the limited copy numbers of key molecules (genes, RNA polymerases, ribosomes), and delayed output due to the time required for biopolymer synthesis. Recently proposed algorithms allow for efficient simulations of such systems. However, it is critical to know whether the results of delay stochastic simulations agree with those from more detailed models of the transcription and translation processes. We present a generalization of previous delay stochastic simulation algorithms which allows both for multiple delays and for distributions of delay times. We show that delay stochastic simulations closely approximate simulations of a detailed transcription model except when two-body effects (e.g. collisions between polymerases on a template strand) are important. Finally, we study a delay stochastic model of prokaryotic transcription and translation which reproduces observations from a recent experimental study in which a single gene was expressed under the control of a repressed lac promoter in E. coli cells. This demonstrates our ability to quantitatively model gene expression using these new methods.
Ranking of critical species to preserve the functionality of mutualistic networks using the k-core decomposition

Background Network analysis has become a relevant approach to analyze cascading species extinctions resulting from perturbations on mutualistic interactions as a result of environmental change. In this context, it is essential to be able to point out key species, whose stability would prevent cascading extinctions, and the consequent loss of ecosystem function. In this study, we aim to explain how the k-core decomposition sheds light on the understanding the robustness of bipartite mutualistic networks. Methods We defined three k-magnitudes based on the k-core decomposition: k-radius, k-degree, and k-risk. The first one, k-radius, quantifies the distance from a node to the innermost shell of the partner guild, while k-degree provides a measure of centrality in the k-shell based decomposition. k-risk is a way to measure the vulnerability of a network to the loss of a particular species. Using these magnitudes we analyzed 89 mutualistic networks involving plant pollinators or seed dispersers. Two static extinction procedures were implemented in which k-degree and k-risk were compared against other commonly used ranking indexes, as for example MusRank, explained in detail in Material and Methods. Results When extinctions take place in both guilds, k-risk is the best ranking index if the goal is to identify the key species to preserve the giant component. When species are removed only in the primary class and cascading extinctions are measured in the secondary class, the most effective ranking index to identify the key species to preserve the giant component is k-degree. However, MusRank index was more effective when the goal is to identify the key species to preserve the greatest species richness in the second class. Discussion The k-core decomposition offers a new topological view of the structure of mutualistic networks. The new k-radius, k-degree and k-risk magnitudes take advantage of its properties and provide new insight into the structure of mutualistic networks. The k-risk and k-degree ranking indexes are especially effective approaches to identify key species to preserve when conservation practitioners focus on the preservation of ecosystem functionality over species richness.
A demographic model for sex ratio evolution and the effects of sex‐biased offspring costs

Abstract The evolution of the primary sex ratio, the proportion of male births in an individual's offspring production strategy, is a frequency‐dependent process that selects against the more common sex. Because reproduction is shaped by the entire life cycle, sex ratio theory would benefit from explicitly two‐sex models that include some form of life cycle structure. We present a demographic approach to sex ratio evolution that combines adaptive dynamics with nonlinear matrix population models. We also determine the evolutionary and convergence stability of singular strategies using matrix calculus. These methods allow the incorporation of any population structure, including multiple sexes and stages, into evolutionary projections. Using this framework, we compare how four different interpretations of sex‐biased offspring costs affect sex ratio evolution. We find that demographic differences affect evolutionary outcomes and that, contrary to prior belief, sex‐biased mortality after parental investment can bias the primary sex ratio (but not the corresponding reproductive value ratio). These results differ qualitatively from the widely held conclusions of previous models that neglect demographic structure.
Review of evidence regarding trauma system effectiveness resulting from panel studies.

OBJECTIVE The objectives this study are to elucidate the advantages and disadvantages of the panel method for evaluating the quality of trauma care and to review the individual and collective evidence in support of regionalized trauma care derived from these studies. METHOD A review of the published literature was conducted and identified 10 panel studies that compared appropriateness of care and/or the preventability of deaths occurring either across hospitals in a trauma system versus non-trauma system, in a defined region before and after implementation of a trauma system, between trauma center and non-trauma center hospitals within a defined region, or across hospitals of varying levels of care presystem. RESULTS Panel studies vary widely in the approaches used to elicit judgments; low rates of inter-rater reliability have been reported. The strength of the evidence derived from panel studies in support of trauma system effectiveness must be reviewed in this context. CONCLUSION All panel studies are classified as providing weak, Class III evidence. Yet, collectively they provide some face validity in support of the hypothesis that treatment at a trauma versus non-trauma center may be associated with less inappropriate care and fewer preventable deaths among the seriously injured.
An Iterative Array Signal Segregation Algorithm: A method for interference cancelation and multipath mitigation in complex environments.

A frequency-domain array signal segregation using an iterative approach (ASSIA) is developed to estimate the directions of arrival (DoAs), magnitudes, and phases of the signals' spectral components in a multipath environment. This is accomplished by using a uniform circular antenna array whose elements are individually connected to the radiofrequency (RF) front end of a neoteric radio. This technique is utilized to spatially and spectrally separate the communication signals of interest from the strong interfering signals without a priori knowledge regarding their DoAs. Through an extensive comparison with the other techniques reported in the literature, it is shown that ASSIA can detect the DoAs and signal levels of wide dynamic range (DR) much more accurately than what can be done with the existing techniques, provided that the signals' angular spacing is larger than the array beamwidth. Array calibration to capture the fabrication errors is essential to achieve the high level of the DR of signals that ASSIA can handle. The performance of the algorithm in the presence of strong jammers in complex multipath environments with Rayleigh fading characteristics is examined using numerical simulations based on an accurate ray-tracing propagation model. A statistical analysis based on Monte Carlo simulations shows that in such an environment, an ASSIA radio with a 12-element uniform circular array can improve the signal-to-jammer ratio (SJR) from -20 to at least +2 dB (minimum of 22-dB improvement) in more than 70% of occasions.
Circadian Rhythm Profiles in Women with Night Eating Syndrome

Night eating syndrome (NES) is characterized by evening hyperphagia and frequent awakenings accompanied by food intake. Patients with NES display a delayed circadian pattern of food intake but retain a normal sleep-wake cycle. These characteristics initiated the current study, in which the phase and amplitude of behavioral and neuroendocrine circadian rhythms in patients with NES were evaluated. Fifteen women with NES (mean age ± SD, 40.8 ± 8.7 y) and 14 control subjects (38.6 ± 9.5 y) were studied in the laboratory for 3 nights, with food intake measured daily. Blood also was collected for 25 h (every 2 h from 0800 to 2000 h, and then hourly from 2100 to 0900 h) and assayed for glucose and 7 hormones (insulin, ghrelin, leptin, melatonin, cortisol, thyroid-stimulating hormone [TSH] and prolactin). Statistical analyses utilized linear mixed-effects cosinor analysis. Control subjects displayed normal phases and amplitudes for all circadian rhythms. In contrast, patients with NES showed a phase delay in the timing of meals, and delayed circadian rhythms for total caloric, fat, and carbohydrate intake. In addition, phase delays of 1.0 to 2.8 h were found in 2 food-regulatory rhythms—leptin and insulin—and in the circadian melatonin rhythm (with a trend for a delay in the circadian cortisol rhythm). In contrast, circulating levels of ghrelin, the primary hormone that stimulates food intake, were phase advanced by 5.2 h. The glucose rhythm showed an inverted circadian pattern. Patients with NES also showed reduced amplitudes in the circadian rhythms of food intake, cortisol, ghrelin, and insulin, but increased TSH amplitude. Thus, patients with NES demonstrated significant changes in the timing and amplitude of various behavioral and physiological circadian markers involved in appetite and neuroendocrine regulation. As such, NES may result from dissociations between central (suprachiasmatic nucleus) timing mechanisms and putative oscillators elsewhere in the central nervous system or periphery, such as the stomach or liver. Considering these results, chronobiologic treatments for NES such as bright light therapy may be useful. Indeed, bright light therapy has shown efficacy in reducing night eating in case studies and should be evaluated in controlled clinical trials.
Sex differences in genetic and environmental influences on DSM-III-R attention-deficit/hyperactivity disorder.

Approximately 5% of children are affected by attention-deficit/hyperactivity disorder (ADHD), and more boys are affected than girls. This study examined the magnitude of genetic and environmental influences on ADHD and several questions regarding sex differences in its prevalence and liability. The participants were 2,391 twin and sibling pairs from Australia, ages 3-18. ADHD symptoms in the general population were highly heritable (h2 = .85-.90), as were deviant ADHD scores in the selected population. The magnitude of familial influences was similar for boys and girls, although there were shared environmental influences on ADHD in girls but not boys and dominance genetic influences on ADHD in boys but not girls. Specific genetic and environmental influences were highly similar for boys and girls. Evidence supported the polygenic multiple threshold model rather than the constitutional variability model of sex differences in ADHD.
Comparison of Conjunctival and Nasal Provocation Test in Allergic Rhinitis to House Dust Mite

Background: Nasal allergen provocation tests (NPTs) are useful in confirming the diagnosis of allergic rhinitis, if data obtained by clinical history, skin tests and specific IgE determinations are not conclusive. Since NPTs are laborious, conjunctival provocation tests (CPTs) appear as an attractive alternative. The concordance of CPTs and NPTs with house dust mite allergen extract in sensitized and nonsensitized subjects should be evaluated. Methods: 50 otherwise healthy subjects with self-reported house dust mite allergy and positive skin prick tests and serum specific IgE to Dermatophagoides pteronyssinus and 45 sex- and age-matched healthy controls without allergic symptoms were included. For NPTs, 100 µl allergen extract [10,000 allergy units (AU/ml)] were applied to the less congested nasal cavity. A clinical symptom score and active anterior rhinomanometry were employed to assess the response. For CPTs, 50 µl low-concentrated D. pteronyssinus extract (1,000 AU/ml), and if negative, 50 µl normally concentrated extract (10,000 AU/ml) were applied to the lower conjunctival sac. The response was assessed employing clinical symptom scores. Results: NPTs and CPTs yielded concordant results in 90% of the subjects successfully tested (Cohen’s kappa = 0.78, p < 0.0001). The diagnostic efficacy of the CPT, with the NPT as the reference method, was 89%, whether or not conjunctival symptoms had been reported in addition to rhinitis symptoms. Both techniques were judged almost equally uncomfortable. Conclusion: CPTs are an acceptable alternative to NPTs in patients with allergic rhinitis to house dust mite, even if they have no conjunctival symptoms.
Closed-form capacity formula for multi-antenna cognitive radio networks with asymmetric fading

A cognitive radio network with a multiple-input single-output secondary link and a multi-antenna primary receiver is considered. The secondary transmitter steers its transmission into the direction of its intended destination in order to maximize the received signal-to-noise ratio. Under this beam-forming strategy, the power allocation is optimized to achieve the ergodic capacity under the constraint that the long-term interference, caused at the primary receiver, will not exceed a predefined threshold. Assuming line-of-sight communication (Rician fading) for the secondary link and Rayleigh fading for the secondary-to-primary link channel, we derive the exact closed-form expression for the ergodic capacity. Numerical results corroborate theoretical findings and illustrate the manifold impact of the system parameters into its performance.
Integrated Determination of Objective Criteria Weights in MCDM

In multiple criteria evaluation, criteria weights are of great importance. In practice, subjective criteria weights determined by specialists/experts are commonly used. The types of elements of a decision matrix also play an important role in the evaluation of alternatives. The objective weights help to estimate the structure of data. The entropy method is widely used for determining the weights (significances) of criteria. A new method of the criterion impact loss, CILOS, is used for determining a relative impact loss experienced by the criterion of an alternative, when another criterion is chosen to be the best. The authors of the paper have combined the best features of the entropy method and the CILOS approach to obtain a new method – Integrated Determination of Objective CRIteria Weights, or (IDOCRIW).
Increased cGMP promotes healthy expansion and browning of white adipose tissue

With more than half a billion individuals affected worldwide, obesity has reached pandemic proportions. Development of “brown‐like” or “brite” adipocytes within white adipose tissue (WAT) has potential antiobesity and insulin‐sensitizing effects. We investigated the role of cyclic GMP (cGMP) signaling, focusing on cGMP‐dependent protein kinase I (PKGI) in WAT. PKGI is expressed in murine WAT, primary adipocytes, and 3T3‐L1. Treatment of adipocytes with cGMP resulted in increased adipogenesis, with a 54% increase in expression of peroxisome proliferator‐activated receptor‐γ. Lentiviral overexpression of PKGI further increased adipogenesis, whereas loss of PKGI significantly reduced adipogenic differentiation. In addition to adipogenic effects, PKGI had an antihypertrophic and anti‐inflammatory effect via RhoA phosphorylation and reduction of proinflammatory adipokine expression. Moreover, PKGI induced a 4.3‐fold increase in abundance of UCP‐1 and the development of a brown‐like thermogenic program in primary adipocytes. Notably, treatment of C57BL/6 mice with phosphodiesterase inhibitor sildenafil (12 mg/kg/d) for 7 d caused 4.6‐fold increase in uncoupling protein‐1 expression and promoted establishment of a brown fat cell‐like phenotype (“browning”) of WAT in vivo. Taken together, PKGI is a key regulator of cell size, adipokine secretion and browning of white fat depots and thus could be a valuable target in developing novel treatments for obesity. —Mitschke, M. M. , Hoffmann, L. S. , Gnad, T. , Scholz, D. , Kruithoff, K. , Mayer, P., Haas, B. , Sassmann, A. , Alexander Pfeifer, A, Kilić, A. Increased cGMP promotes healthy expansion and browning of white adipose tissue. FASEB J. 27, 1621–1630 (2013). www.fasebj. org
Sexual abuse, sexual orientation, and obesity in women.

BACKGROUND Among adult women an association between childhood sexual abuse (CSA) and obesity has been observed. Research with lesbian women has consistently identified high rates of obesity as well as frequent reports of CSA, but associations between sexual abuse and obesity have not been fully explored. Our aim was to investigate the relationship between sexual abuse (SA) history and obesity among heterosexual (n = 392) and lesbian (n = 475) women (age 35-64) who participated in the Epidemiologic STudy of HEalth Risk in Women (ESTHER) Project in Pittsburgh, Pennsylvania. METHODS Obesity was defined as body mass index (BMI) > or =30. Covariates included self-reported SA, sexual orientation, demographic factors, and history of a depression or anxiety diagnosis. SA history was assessed by three factors: (1) SA experienced under the age of 18 by a family member or (2) by a nonfamily member and (3) forced, unwanted sexual experience(s) at age > or =18. Data were analyzed using chi-square tests and logistic regression models. RESULTS Multiple logistic regression analyses revealed that obesity was associated with African American race, lesbian sexual orientation, intrafamilial CSA, and history of mental health diagnosis. Protective factors were having a household income of at least $75,000 and having a bachelor's degree or higher. CONCLUSIONS Results suggest that lesbian women may be at greater risk of obesity than heterosexual women and that intrafamilial CSA--regardless of sexual orientation--may play a role in the development of obesity.
The US Legal System on Data Protection in the Field of Law Enforcement. Safeguards, Rights and Remedies for EU Citizens.

At the request of the LIBE Committee of the European Parliament, this study surveys the U.S. system of data protection in the field of federal law enforcement. Since the legal category of “data protection” does not formally exist in U.S. law, the study begins by setting out the substantive and procedural requirements of EU law that are canvassed in the context of information-gathering and surveillance by U.S. law enforcement agencies. The study then analyzes the data protection law governing federal agencies according to two criteria: sources and methods of surveillance and data collection. It first reviews the two principal sources of U.S. data protection law: the Fourth Amendment to the US Constitution and the Privacy Act of 1974. The study then considers the legally prescribed methods of data collection and surveillance, together with their associated data protection guarantees, in ordinary criminal investigations and national security investigations. Throughout, the study pays special attention to the rights afforded to EU citizens. The study calls attention to a number of discrepancies with respect to EU law, including: the relatively low legal threshold for engaging in bulk collection in national security investigations; the absence of significant legal restrictions on information sharing between intelligence and law enforcement agencies; and the two-track privacy scheme for U.S. and non-U.S. persons.
Expression of fibroblast growth factor-5 by bovine choroidal endothelial cells in vitro.

PURPOSE To demonstrate the expression of fibroblast growth factor-5 (FGF-5) by bovine choroidal microvascular endothelial (BCME) cells and to investigate its possible role as an autocrine mitogen in these cells. METHODS Expression of FGF-5 by BCME cells was studied by a combination of Northern and Western blot analyses. Total RNA was isolated from BCME cultures at passages 5 through 8 and analyzed by Northern blot analysis for the presence of FGF-5 transcripts, using a 1-kb human complemetary DNA. Slot-blot analysis was performed to determine possible cross-reactivity between this probe and acidic and basic FGFs of human and bovine species. A previously characterized antibody directed against the aminoterminus of the human FGF-5 sequence was used in Western blot analyses to identify immunoreactive proteins released by BCME cells into the medium. Finally, the mitogenic activity of human recombinant FGF-5 on a variety of cell types was evaluated, using a cellular proliferation assay. RESULTS Northern blot analysis provided evidence for the expression of two major FGF-5 transcripts at 4 kb and 3 kb and two minor transcripts at 2.2 kb and 1.7 kb. A single immunoreactive protein with a molecular weight of 34 kDa was identified by Western blot analysis of conditioned media. In cellular proliferation assays, human recombinant FGF-5 was not mitogenic in BCME cells but exhibited an approximate ED50 of 1.8 to 3.7 nM in BALB/c3T3 fibroblasts. This ED50 was within the range reported by the manufacturer, using a thymidine incorporation assay and a similar embryonic fibroblast cell line. Fibroblast growth factor-5 also stimulated proliferation of human retinal pigment epithelial cells. CONCLUSIONS Bovine choroidal microvascular endothelial cells exhibit expression in vitro of FGF-5 at the messenger RNA and protein levels. Perivascular and endothelial cell staining for FGF-5 seen previously in choroidal neovascular membranes may therefore arise from expression by choroidal endothelial cells. Because nonglycosylated recombinant FGF-5 does not appear to be a mitogen in BCME cells in vitro, it is reasonable to question its role as an autocrine mitogen in vivo. Fibroblast growth factor-5 may instead be serving paracrine roles in the stimulation of fibroblasts and retinal pigment epithelial cells during the formation of choroidal neovascular membranes. Studies with fully glycosylated recombinant FGF-5 will be required, however, to assess the biologic activity of this member of the FGF gene family.
Building Business-to-Consumer Competence in Chinese Fast-Growing Industries: A System Dynamics Model

Most existing econometric studies addressed the success factors of the Internet-based Business-to-Consumer (B2C) by analyzing one or two specific issues, while little has been done to offer a holistic view. Taking the System Dynamics (SD) perspective, this paper offers a qualitative model that illustrates and a formal model that simulates the dynamic process of building B2C in Chinese fast-growing industries. Preliminary results show that the performance of a traditional firm with B2C is not much higher than those without B2C. Order fulfillment quality, customer service quality, online store quality, product customization capability are suggested as the key leverage points for B2C performance improvement. Future research is also discussed.